%%% -*-BibTeX-*- %%% ==================================================================== %%% BibTeX-file{ %%% author = "Nelson H. F. Beebe", %%% version = "1.12", %%% date = "23 April 2025", %%% time = "15:13:32 MDT", %%% filename = "jcomputbiol.bib", %%% address = "University of Utah %%% Department of Mathematics, 110 LCB %%% 155 S 1400 E RM 233 %%% Salt Lake City, UT 84112-0090 %%% USA", %%% telephone = "+1 801 581 5254", %%% URL = "https://www.math.utah.edu/~beebe", %%% checksum = "28953 63337 236840 2618263", %%% email = "beebe at math.utah.edu, beebe at acm.org, %%% beebe at computer.org (Internet)", %%% codetable = "ISO/ASCII", %%% keywords = "bibliography; BibTeX; Journal of %%% Computational Biology", %%% license = "public domain", %%% supported = "yes", %%% docstring = "This is a COMPLETE bibliography of the %%% Journal of Computational Biology (CODEN %%% JCOBEM, ISSN 1066-5277 (print), 1557-8666 %%% (electronic)) which began with volume 1, %%% number 1, in January 1994. Volumes are %%% published annually, with 4 to 12 issues, and %%% issues are sometimes combined. The journal %%% is published by Mary Ann Liebert, Inc. %%% Publishers, New Rochelle, NY, USA. %%% %%% The publisher has World Wide Web sites for %%% the journal at %%% %%% http://home.liebertpub.com/cmb %%% https://www.liebertpub.com/loi/cmb/ %%% %%% At version 1.12, the COMPLETE year coverage %%% looked like this: %%% %%% 1994 ( 30) 2005 ( 83) 2016 ( 86) %%% 1995 ( 40) 2006 ( 113) 2017 ( 110) %%% 1996 ( 32) 2007 ( 87) 2018 ( 118) %%% 1997 ( 38) 2008 ( 88) 2019 ( 124) %%% 1998 ( 51) 2009 ( 118) 2020 ( 148) %%% 1999 ( 31) 2010 ( 114) 2021 ( 95) %%% 2000 ( 52) 2011 ( 136) 2022 ( 103) %%% 2001 ( 39) 2012 ( 97) 2023 ( 97) %%% 2002 ( 54) 2013 ( 79) 2024 ( 84) %%% 2003 ( 62) 2014 ( 72) 2025 ( 22) %%% 2004 ( 70) 2015 ( 90) %%% %%% Article: 2563 %%% %%% Total entries: 2563 %%% %%% Spelling has been verified with the UNIX %%% spell and GNU ispell programs using the %%% exception dictionary stored in the companion %%% file with extension .sok. %%% %%% BibTeX citation tags are uniformly chosen %%% as name:year:abbrev, where name is the %%% family name of the first author or editor, %%% year is a 4-digit number, and abbrev is a %%% 3-letter condensation of important title %%% words. Citation tags were automatically %%% generated by software developed for the %%% BibNet Project. %%% %%% In this bibliography, entries are sorted in %%% publication order within each journal, %%% using bibsort -byvolume. %%% %%% The checksum field above contains a CRC-16 %%% checksum as the first value, followed by the %%% equivalent of the standard UNIX wc (word %%% count) utility output of lines, words, and %%% characters. This is produced by Robert %%% Solovay's checksum utility.", %%% } %%% ==================================================================== %%% Provide a fallback of Polish ogonok accent to cedilla, and another %%% macro, if necessary %%% "\input url.sty" @Preamble{ "\ifx \stack \undefined \def \stack #1#2{\stackrel{\textstyle #1}{\textstyle #2}} \fi" # "\ifx \undefined \bioname \def \bioname #1{{{\em #1\/}}} \fi" # "\ifx \undefined \booktitle \def \booktitle #1{{{\em #1}}} \fi" # "\ifx \undefined \circled \def \circled #1{(#1)} \fi" # "\ifx \undefined \cprime \def \cprime {$\mathsurround=0pt '$} \fi" # "\ifx \undefined \Dbar \def \Dbar {\leavevmode\raise0.2ex\hbox{--}\kern-0.5emD} \fi" # "\ifx \undefined \k \let \k = \c \fi" # "\ifx \undefined \mathbb \def \mathbb #1{{\bf #1}} \fi" # "\ifx \undefined \mathcal \def \mathcal #1{{\cal #1}} \fi" # "\ifx \undefined \mathrm \def \mathrm #1{{\rm #1}} \fi" # "\ifx \undefined \pkg \def \pkg #1{{{\tt #1}}} \fi" # "\ifx \undefined \reg \def \reg {\circled{R}} \fi" # "\ifx \undefined \TM \def \TM {${}^{\sc TM}$} \fi" # "\ifx \undefined \url \def \url #1{{\tt #1}} \fi" } %%% ==================================================================== %%% Acknowledgement abbreviations: @String{ack-nhfb = "Nelson H. F. Beebe, University of Utah, Department of Mathematics, 110 LCB, 155 S 1400 E RM 233, Salt Lake City, UT 84112-0090, USA, Tel: +1 801 581 5254, e-mail: \path|beebe@math.utah.edu|, \path|beebe@acm.org|, \path|beebe@computer.org| (Internet), URL: \path|https://www.math.utah.edu/~beebe/|"} %%% ==================================================================== %%% Journal abbreviations: @String{j-J-COMPUT-BIOL = "Journal of Computational Biology"} %%% ==================================================================== %%% Bibliography entries, sorted in publication order, with %%% `bibsort -byvolume': @Article{Anonymous:1994:EWC, author = "Anonymous", title = "Editorial: Whither Computational Biology", journal = j-J-COMPUT-BIOL, volume = "1", number = "1", pages = "1--2", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:45:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Overton:1994:QSQ, author = "G. Christian Overton and Jeffrey S. Aaronson and Juergen Haas and Julie Adams", title = "{QGB}: a System for Querying Sequence Database Fields and Features", journal = j-J-COMPUT-BIOL, volume = "1", number = "1", pages = "3--14", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.3", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:45:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.3; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.3", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Forsten:1994:PAL, author = "Kimberly E. Forsten and Douglas A. Lauffenburger", title = "Probability of Autocrine Ligand Capture by Cell-Surface Receptors: Implications for Ligand Secretion Measurements", journal = j-J-COMPUT-BIOL, volume = "1", number = "1", pages = "15--23", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.15", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:45:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.15; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.15", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Leng:1994:PSS, author = "Bing Leng and Bruce G. Buchanan and Hugh B. Nicholas", title = "Protein Secondary Structure Prediction Using Two-Level Case-Based Reasoning", journal = j-J-COMPUT-BIOL, volume = "1", number = "1", pages = "25--38", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.25", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:45:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.25; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.25", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{States:1994:QCU, author = "David J. States and Warren Gish", title = "{QGB}: Combined Use of Sequence Similarity and Codon Bias for Coding Region Identification", journal = j-J-COMPUT-BIOL, volume = "1", number = "1", pages = "39--50", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.39", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:45:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.39; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.39", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Miller:1994:CAS, author = "Webb Miller and Mark Boguski and Balaji Raghavachari and Zheng Zhang and Ross C. Hardison", title = "Constructing Aligned Sequence Blocks", journal = j-J-COMPUT-BIOL, volume = "1", number = "1", pages = "51--64", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.51", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:45:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.51; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.51", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Keele:1994:CDM, author = "J. W. Keele and J. E. Wray and D. W. Behrens and G. A. Rohrer and S. L. F. Sunden and S. M. Kappes and M. D. Bishop and R. T. Stone and L. J. Alexander and C. W. Beattie", title = "A Conceptual Database Model for Genomic Research", journal = j-J-COMPUT-BIOL, volume = "1", number = "1", pages = "65--76", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.65", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:45:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.65; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.65", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Ferretti:1994:SBC, author = "V. Ferretti and B. F. Lang and D. Sankoff", title = "Skewed Base Compositions, Asymmetric Transition Matrices, and Phylogenetic Invariants", journal = j-J-COMPUT-BIOL, volume = "1", number = "1", pages = "77--92", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.77", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:45:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.77; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.77", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Goldstein:1994:APS, author = "Larry Goldstein and Michael S. Waterman", title = "Approximations to Profile Score Distributions", journal = j-J-COMPUT-BIOL, volume = "1", number = "2", pages = "93--104", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.93", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.93; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.93", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Dyer:1994:PUS, author = "Martin Dyer and Alan Frieze and Stephen Suen", title = "The Probability of Unique Solutions of Sequencing by Hybridization", journal = j-J-COMPUT-BIOL, volume = "1", number = "2", pages = "105--110", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.105", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", note = "See corrigendum \cite{Dyer:1996:CPU}.", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.105; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.105", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Rohrer:1994:SPE, author = "G. A. Rohrer and D. W. Behrens and J. W. Keele", title = "A Simplified Procedure for Entry of Raw Genotypic Data", journal = j-J-COMPUT-BIOL, volume = "1", number = "2", pages = "111--119", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.111", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.111; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.111", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Rustici:1994:TDS, author = "Mauro Rustici and Arthur M. Lesk", title = "Three-Dimensional Searching for Recurrent Structural Motifs in Data Bases of Protein Structures", journal = j-J-COMPUT-BIOL, volume = "1", number = "2", pages = "121--132", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.121", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.121; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.121", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Charleston:1994:ESL, author = "Michael A. Charleston and Michael D. Hendy and David Penny", title = "The Effects of Sequence Length, Tree Topology, and Number of Taxa on the Performance of Phylogenetic Methods", journal = j-J-COMPUT-BIOL, volume = "1", number = "2", pages = "133--151", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.133", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.133; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.133", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Steel:1994:RTW, author = "M. A. Steel and L. A. Sz{\'e}kely and M. D. Hendy", title = "Reconstructing Trees When Sequence Sites Evolve at Variable Rates", journal = j-J-COMPUT-BIOL, volume = "1", number = "2", pages = "153--163", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Fasman:1994:RGD, author = "Kenneth H. Fasman", title = "Restructuring the Genome Data Base: a Model for a Federation of Biological Databases", journal = j-J-COMPUT-BIOL, volume = "1", number = "2", pages = "165--171", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Robbins:1994:GIC, author = "Robert J. Robbins", title = "Genome Informatics I: Community Databases", journal = j-J-COMPUT-BIOL, volume = "1", number = "3", pages = "173--190", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Knuppel:1994:TRP, author = "R. Kn{\"u}ppel and P. Dietze and W. Lehnberg and K. Frech and E. Wingender", title = "{TRANSFAC} Retrieval Program: a Network Model Database of Eukaryotic Transcription Regulating Sequences and Proteins", journal = j-J-COMPUT-BIOL, volume = "1", number = "3", pages = "191--198", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.191", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.191; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.191", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Hide:1994:BED, author = "Winston Hide and John Burke and Daniel B. {Da Vison}", title = "Biological Evaluation of d$^2$, an Algorithm for High-Performance Sequence Comparison", journal = j-J-COMPUT-BIOL, volume = "1", number = "3", pages = "199--215", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.199", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.199; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.199", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Zhang:1994:CMA, author = "Zheng Zhang and Balaji Raghavachari and Ross C. Hardison and Webb Miller", title = "Chaining Multiple-Alignment Blocks", journal = j-J-COMPUT-BIOL, volume = "1", number = "3", pages = "217--226", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.217", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.217; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.217", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Wang:1994:SPR, author = "Chi Wang", title = "A Subgraph Problem from Restriction Maps of {DNA}", journal = j-J-COMPUT-BIOL, volume = "1", number = "3", pages = "227--234", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.227", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.227; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.227", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Zhang:1994:EEP, author = "Zheng Zhang", title = "An Exponential Example for a Partial Digest Mapping Algorithm", journal = j-J-COMPUT-BIOL, volume = "1", number = "3", pages = "235--239", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.235", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.235; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.235", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Martin:1994:ECD, author = "Daniela R. Martin", title = "Equivalence Classes for the Double-Digest Problem with Coincident Cut Sites", journal = j-J-COMPUT-BIOL, volume = "1", number = "3", pages = "241--253", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.241", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.241; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.241", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Gustfield:1994:MEL, author = "Dan Gustfield and David Shmoys and Jan Karel Lenstra and Tandy Warnow", title = "In Memoriam {Eugene L. Lawler}", journal = j-J-COMPUT-BIOL, volume = "1", number = "4", pages = "255--256", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.255", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.255", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Miller:1994:QCD, author = "Mark J. Miller and John I. Powell", title = "A Quantitative Comparison of {DNA} Sequence Assembly Programs", journal = j-J-COMPUT-BIOL, volume = "1", number = "4", pages = "257--269", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.257", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.257; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.257", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Chao:1994:RDL, author = "Kun-Mao Chao and Ross C. Hardison and Webb Miller", title = "Recent Developments in Linear-Space Alignment Methods: a Survey", journal = j-J-COMPUT-BIOL, volume = "1", number = "4", pages = "271--291", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.271", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.271; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.271", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Rioux:1994:PSE, author = "Pierre A. Rioux and William A. Gilbert and Timothy G. Littlejohn", title = "A Portable Search Engine and Browser for the Entrez Database", journal = j-J-COMPUT-BIOL, volume = "1", number = "4", pages = "293--295", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.293", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.293; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.293", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Taylor:1994:MBP, author = "William R. Taylor", title = "Motif-Biased Protein Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "1", number = "4", pages = "297--310", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.297", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.297; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.297", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Baldi:1994:HMM, author = "Pierre Baldi and Yves Chauvin", title = "Hidden {Markov} Models of the {G}-Protein-Coupled Receptor Family", journal = j-J-COMPUT-BIOL, volume = "1", number = "4", pages = "311--336", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.311", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.311; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.311", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Wang:1994:CMS, author = "Lusheng Wang and Tao Jiang", title = "On the Complexity of Multiple Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "1", number = "4", pages = "337--348", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.337", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.337; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.337", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Naor:1994:NOA, author = "Dalit Naor and Douglas L. Brutlag", title = "On Near-Optimal Alignments of Biological Sequences", journal = j-J-COMPUT-BIOL, volume = "1", number = "4", pages = "349--366", month = jan, year = "1994", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1994.1.349", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1994.1.349; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1994.1.349", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 June 2009", } @Article{Beaver:1995:CD, author = "Donald Beaver", title = "Computing with {DNA}", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "1--7", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.1; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Eddy:1995:MDH, author = "Sean R. Eddy and Graeme Mitchison and Richard Durbin", title = "Maximum Discrimination Hidden {Markov} Models of Sequence Consensus", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "9--23", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.9", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.9; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.9", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Sewell:1995:MCP, author = "Roger F. Sewell and Richard Durbin", title = "Method for Calculation of Probability of Matching a Bounded Regular Expression in a Random Data String", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "25--31", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.25", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.25; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.25", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Jain:1995:NSC, author = "Mudita Jain and Eugene W. Myers", title = "A Note on Scoring Clones Given a Probe Ordering", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "33--37", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.33", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.33; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.33", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Steel:1995:CCL, author = "M. A. Steel and Y. X. Fu", title = "Classifying and Counting Linear Phylogenetic Invariants for the Jukes--{Cantor} Model", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "39--47", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.39", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.39; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.39", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Weiss:1995:MPC, author = "Gunter Weiss and Arndt {Von Haeseler}", title = "Modeling the Polymerase Chain Reaction", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "49--61", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.49", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.49; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.49", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Sun:1995:PCR, author = "Fengzhu Sun", title = "The Polymerase Chain Reaction and Branching Processes", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "63--86", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.63", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.63; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.63", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Gelfand:1995:PFD, author = "M. S. Gelfand", title = "Prediction of Function in {DNA} Sequence Analysis", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "87--115", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.87", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.87; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.87", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Fickett:1995:OGH, author = "James W. Fickett", title = "{ORFs} and Genes: How Strong a Connection?", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "117--123", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.117", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.117; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.117", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Berger:1995:APS, author = "Bonnie Berger", title = "Algorithms for Protein Structural Motif Recognition", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "125--138", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Goldberg:1995:FSA, author = "Paul W. Goldberg and Martin C. Golumbic and Haim Kaplan and Ron Shamir", title = "Four Strikes Against Physical Mapping of {DNA}", journal = j-J-COMPUT-BIOL, volume = "2", number = "1", pages = "139--152", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.139", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.139; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.139", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Pevzner:1995:CMD, author = "Pavel A. Pevzner", title = "Combinatorial Methods for {DNA} Mapping and Sequencing", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "153--158", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Alizadeh:1995:PMC, author = "Farid Alizadeh and Richard M. Karp and Deborah K. Weisser and Geoffrey Zweig", title = "Physical Mapping of Chromosomes Using Unique Probes", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "159--184", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.159", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.159; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.159", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Gillett:1995:FCS, author = "Will Gillett and Jim Daues and Liz Hanks and Rob Capra", title = "Fragment Collapsing and Splitting While Assembling High-Resolution Restriction Maps", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "185--205", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Dyer:1995:OCL, author = "Martin Dyer and Alan Frieze and Stephen Suen", title = "Ordering Clone Libraries in Computational Biology", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "207--218", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.207", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.207; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.207", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Greenberg:1995:PMS, author = "David S. Greenberg and Sorin Istrail", title = "Physical Mapping by {STS} Hybridization: Algorithmic Strategies and the Challenge of Software Evaluation", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "219--273", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.219", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.219; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.219", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Myers:1995:TSA, author = "Eugene W. Myers", title = "Toward Simplifying and Accurately Formulating Fragment Assembly", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "275--290", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.275", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.275; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.275", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Idury:1995:NAD, author = "Ramana M. Idury and Michael S. Waterman", title = "A New Algorithm for {DNA} Sequence Assembly", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "291--306", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.291", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.291; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.291", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Armen:1995:SSS, author = "Chris Armen and Clifford Stein", title = "Short Superstrings and the Structure of Overlapping Strings", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "307--332", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.307", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.307; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.307", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Skiena:1995:RSS, author = "Steven S. Skiena and Gopalakrishnan Sundaram", title = "Reconstructing Strings from Substrings", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "333--353", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.333", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.333; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.333", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Milosavljevic:1995:DSR, author = "Aleksandar Milosavljevi{\'c}", title = "{DNA} Sequence Recognition by Hybridization to Short Oligomers", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "355--370", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.355", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.355; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.355", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Rubinov:1995:RSS, author = "A. R. Rubinov and M. S. Gelfand", title = "Reconstruction of a String from Substring Precedence Data", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "371--381", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.371", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.371; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.371", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Razgulyaev:1995:SPN, author = "Oleg Razgulyaev and Anatoly Rubinov and Mikhail Gelfand and Alexander Chetverin", title = "Sequencing Potential of Nested {Strand} Hybridization", journal = j-J-COMPUT-BIOL, volume = "2", number = "2", pages = "383--395", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.383", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.383; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.383", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Agarwala:1995:FAI, author = "Richa Agarwala and David Fern{\'a}ndez-Baca and Giora Slutzki", title = "Fast Algorithms for Inferring Evolutionary Trees", journal = j-J-COMPUT-BIOL, volume = "2", number = "3", pages = "397--407", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.397", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.397; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.397", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Sun:1995:ATG, author = "Jian Sun and Wen-Yuan Song and Li-Huang Zhu and Run-Sheng Chen", title = "Analysis of {tRNA} Gene Sequences by Neural Network", journal = j-J-COMPUT-BIOL, volume = "2", number = "3", pages = "409--416", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.409", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.409; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.409", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Schbath:1995:EMD, author = "Sophie Schbath and Bernard Prum and Elisabeth {De Turckheim}", title = "Exceptional Motifs in Different {Markov} Chain Models for a Statistical Analysis of {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "2", number = "3", pages = "417--437", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.417", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.417; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.417", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Charleston:1995:TCL, author = "M. A. Charleston", title = "Toward a Characterization of Landscapes of Combinatorial Optimization Problems, with Special Attention to the Phylogeny Problem", journal = j-J-COMPUT-BIOL, volume = "2", number = "3", pages = "439--450", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.439", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.439; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.439", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Worley:1995:INM, author = "K. C. Worley and K. Y. King and S. Chua and E. R. B. Mccabe and R. F. Smith", title = "Identification of New Members of a Carbohydrate Kinase-Encoding Gene Family", journal = j-J-COMPUT-BIOL, volume = "2", number = "3", pages = "451--458", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.451", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.451; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.451", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Gupta:1995:IPS, author = "Sandeep K. Gupta and John D. Kececioglu and Alejandro A. Sch{\"a}ffer", title = "Improving the Practical Space and Time Efficiency of the Shortest-Paths Approach to Sum-of-Pairs Multiple Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "2", number = "3", pages = "459--472", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.459", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.459; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.459", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Salzberg:1995:LPC, author = "Steven Salzberg", title = "Locating Protein Coding Regions in Human {DNA} Using a Decision Tree Algorithm", journal = j-J-COMPUT-BIOL, volume = "2", number = "3", pages = "473--485", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.473", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.473; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.473", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Baldi:1995:SMH, author = "Pierre Baldi", title = "Substitution Matrices and Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "2", number = "3", pages = "487--491", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.487", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.487; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.487", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Mirkin:1995:BCM, author = "Boris Mirkin and Ilya Muchnik and Temple F. Smith", title = "A Biologically Consistent Model for Comparing Molecular Phylogenies", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "493--507", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.493", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.493; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.493", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Wareham:1995:SPN, author = "H. Todd Wareham", title = "A Simplified Proof of the {NP}- and {MAX SNP}-Hardness of Multiple Sequence Tree Alignment", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "509--514", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.509", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.509; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.509", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Benham:1995:HTW, author = "Craig Benham and Sampath Kannan and Michael Paterson and Tandy Warnow", title = "{Hen}'s Teeth and {Whale}'s Feet: Generalized Characters and Their Compatibility", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "515--525", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.515", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.515; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.515", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Reva:1995:CLM, author = "Boris A. Reva and Dmitrii S. Rykunov and Arthur J. Olson and Alexei V. Finkelstein", title = "Constructing Lattice Models of Protein Chains with Side Groups", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "527--535", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.527", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.527; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.527", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Markowitz:1995:HMB, author = "Victor M. Markowitz", title = "Heterogeneous Molecular Biology Databases", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "537--538", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.537", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.537", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Letovsky:1995:BIM, author = "Stanley Letovsky", title = "Beyond the Information Maze", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "539--546", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.539", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.539; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.539", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Markowitz:1995:CHM, author = "Victor M. Markowitz and Otto Ritter", title = "Characterizing Heterogeneous Molecular Biology Database Systems", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "547--556", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.547", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.547; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.547", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Davidson:1995:CIB, author = "S. B. Davidson and C. Overton and P. Buneman", title = "Challenges in Integrating Biological Data Sources", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "557--572", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.557", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.557; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.557", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Karp:1995:SDI, author = "Peter D. Karp", title = "A Strategy for Database Interoperation", journal = j-J-COMPUT-BIOL, volume = "2", number = "4", pages = "573--586", month = jan, year = "1995", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1995.2.573", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1995.2.573; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1995.2.573", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Agarwal:1996:BED, author = "Pankaj Agarwal and David J. States", title = "A {Bayesian} Evolutionary Distance for Parametrically Aligned Sequences", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "1--17", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.1; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Hendy:1996:CFL, author = "Michael D. Hendy and David Penny", title = "Complete Families of Linear Invariants for Some Stochastic Models of Sequence Evolution, with and without the Molecular Clock Assumption", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "19--31", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.19", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.19; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.19", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Myers:1996:AMN, author = "Eugene W. Myers", title = "Approximate Matching of Network Expressions with Spacers", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "33--51", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.33", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.33; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.33", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Hart:1996:FPF, author = "William E. Hart and Sorin C. Istrail", title = "Fast Protein Folding in the Hydrophobic--Hydrophilic Model within Three-Eighths of Optimal", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "53--96", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.53", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.53; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.53", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Takahashi:1996:MSN, author = "Yoshikane Takahashi", title = "A Mathematical Solution to a Network Designing Problem", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "97--141", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.97", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.97; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.97", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Joshi:1996:PLI, author = "Rajani R. Joshi and K. Krishnanand", title = "Probabilistic Learning in Immune Network: Weighted Tree Matching Model", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "143--162", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.143; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Riis:1996:IPP, author = "S{\o}ren Kamaric Riis and Anders Krogh", title = "Improving Prediction of Protein Secondary Structure Using Structured Neural Networks and Multiple Sequence Alignments", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "163--183", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Tsang:1996:SFP, author = "Simon Tsang and Milton H. {Saier, Jr.}", title = "A Simple Flexible Program for the Computational Analysis of Amino Acyl Residue Distribution in Proteins: Application to the Distribution of Aromatic versus Aliphatic Hydrophobic Amino Acids in Transmembrane $ \alpha $-Helical Spanners of Integral Membrane Transport Proteins", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "185--190", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Karp:1996:IAM, author = "Peter D. Karp and Suzanne Paley", title = "Integrated Access to Metabolic and Genomic Data", journal = j-J-COMPUT-BIOL, volume = "3", number = "1", pages = "191--212", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.191", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.191; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.191", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Singh:1996:DTP, author = "Raj K. Singh and Alexander Tropsha and Iosif I. Vaisman", title = "{Delaunay} Tessellation of Proteins: Four Body Nearest-Neighbor Propensities of Amino Acid Residues", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "213--221", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.213", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.213; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.213", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Gelfand:1996:RGH, author = "M. S. Gelfand and L. I. Podolsky and T. V. Astakhova and M. A. Roytberg", title = "Recognition of Genes in Human {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "223--234", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.223", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.223; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.223", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Schierwater:1996:ENP, author = "Bernd Schierwater and Dirk Metzler and Katja Kr{\"u}ger and Bruno Streit", title = "The Effects of Nested Primer Binding Sites on the Reproducibility of {PCR}: Mathematical Modeling and Computer Simulation Studies", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "235--251", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.235", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.235; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.235", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Huynen:1996:BPP, author = "Martijn A. Huynen and Alan Perelson and Wayne A. Vieira and Peter F. Stadler", title = "Base Pairing Probabilities in a Complete {HIV-1} {RNA}", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "253--274", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.253", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.253; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.253", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Bryant:1996:HTB, author = "David Bryant", title = "Hunting for Trees in Binary Character Sets: Efficient Algorithms for Extraction, Enumeration, and Optimization", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "275--288", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.275", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.275; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.275", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Koch:1996:AFM, author = "Ina Koch and Thomas Lengauer and Egon Wanke", title = "An Algorithm for Finding Maximal Common Subtopologies in a Set of Protein Structures", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "289--306", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.289", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.289; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.289", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Kelly:1996:BAA, author = "Colleen Kelly and Gary A. Churchill", title = "Biases in Amino Acid Replacement Matrices and Alignment Scores Due to Rate Heterogeneity", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "307--318", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.307", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.307; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.307", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Nadkarni:1996:DWD, author = "Prakash Nadkarni and Kei-Hoi Cheung and Carmela Castiglione and Perry Miller and Kenneth Kidd", title = "{DNA} Workbench: a Database Package to Manage Regional Physical Mapping", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "319--329", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.319", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.319; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.319", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Dyer:1996:CPU, author = "Martin Dyer and Alan Frieze and Stephen Suen", title = "Corrigendum to {{\booktitle{Probability of Unique Solutions of Sequencing by Hybridization}}}", journal = j-J-COMPUT-BIOL, volume = "3", number = "2", pages = "331--331", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.331", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", note = "See \cite{Dyer:1994:PUS}.", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.331", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Xu:1996:IAC, author = "Ying Xu and Richard J. Mural and Edward C. Uberbacher", title = "An Iterative Algorithm for Correcting Sequencing Errors in {DNA} Coding Regions", journal = j-J-COMPUT-BIOL, volume = "3", number = "3", pages = "333--344", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.333", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.333; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.333", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Leung:1996:USD, author = "Ming-Ying Leung and Genevieve M. Marsh and Terence P. Speed", title = "Over- and Underrepresentation of Short {DNA} Words in Herpesvirus Genomes", journal = j-J-COMPUT-BIOL, volume = "3", number = "3", pages = "345--360", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.345", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.345; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.345", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Mamitsuka:1996:LMH, author = "Hiroshi Mamitsuka", title = "A Learning Method of Hidden {Markov} Models for Sequence Discrimination", journal = j-J-COMPUT-BIOL, volume = "3", number = "3", pages = "361--373", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.361", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.361; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.361", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Wu:1996:SBD, author = "Thomas D. Wu", title = "A Segment-Based Dynamic Programming Algorithm for Predicting Gene Structure", journal = j-J-COMPUT-BIOL, volume = "3", number = "3", pages = "375--394", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.375", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.375; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.375", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Knill:1996:IPE, author = "E. Knill and A. Schliep and D. C. Torney", title = "Interpretation of Pooling Experiments Using the {Markov} Chain {Monte Carlo} Method", journal = j-J-COMPUT-BIOL, volume = "3", number = "3", pages = "395--406", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.395", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.395; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.395", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Salamon:1996:DUC, author = "Hugh Salamon and Jorma Tarhio and Kjersti R{\o}nningen and Glenys Thomson", title = "On Distinguishing Unique Combinations in Biological Sequences", journal = j-J-COMPUT-BIOL, volume = "3", number = "3", pages = "407--423", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.407", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.407; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.407", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Arratia:1996:PPA, author = "Richard Arratia and Daniela Martin and Gesine Reinert and Michael S. Waterman", title = "{Poisson} Process Approximation for Sequence Repeats, and Sequencing by Hybridization", journal = j-J-COMPUT-BIOL, volume = "3", number = "3", pages = "425--463", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.425", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.425; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.425", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Robbins:1996:BEI, author = "Robert J. Robbins", title = "Bioinformatics: Essential Infrastructure for Global Biology$^1$", journal = j-J-COMPUT-BIOL, volume = "3", number = "3", pages = "465--478", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.465", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.465; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.465", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Griffiths:1996:AIS, author = "R. C. Griffiths and P. Marjoram", title = "Ancestral Inference from Samples of {DNA} Sequences with Recombination", journal = j-J-COMPUT-BIOL, volume = "3", number = "4", pages = "479--502", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.479", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.479; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.479", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Bhandarkar:1996:PCP, author = "Suchendra M. Bhandarkar and Sridhar Chirravuri and Jonathan Arnold", title = "Parallel Computing of Physical Maps --- a Comparative Study in {SIMD} and {MIMD} Parallelism", journal = j-J-COMPUT-BIOL, volume = "3", number = "4", pages = "503--528", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.503", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.503; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.503", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Joshi:1996:SOC, author = "Rajani R. Joshi", title = "A Self-Organizing Cognitive Network of Antibody Repertoire Development", journal = j-J-COMPUT-BIOL, volume = "3", number = "4", pages = "529--545", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.529", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.529; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.529", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Wu:1996:PCD, author = "Cathy H. Wu and Sheng Zhao and Hsi-Lien Chen", title = "A Protein Class Database Organized with {ProSite} Protein Groups and {PIR} Superfamilies", journal = j-J-COMPUT-BIOL, volume = "3", number = "4", pages = "547--561", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.547", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.547; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.547", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Myers:1996:PMA, author = "Gene Myers and Sanford Selznick and Zheng Zhang and Webb Miller", title = "Progressive Multiple Alignment with Constraints", journal = j-J-COMPUT-BIOL, volume = "3", number = "4", pages = "563--572", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.563", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.563; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.563", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Teitelman:1996:PCA, author = "Michael Teitelman and Frank H. Eeckman", title = "Principal Component Analysis and Large-Scale Correlations in Non-Coding Sequences of Human {DNA}", journal = j-J-COMPUT-BIOL, volume = "3", number = "4", pages = "573--576", month = jan, year = "1996", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1996.3.573", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1996.3.573; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1996.3.573", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Hart:1997:RPN, author = "William E. Hart and Sorin Istrail", title = "Robust Proofs of {NP-Hardness} for Protein Folding: General Lattices and Energy Potentials", journal = j-J-COMPUT-BIOL, volume = "4", number = "1", pages = "1--22", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.1; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Vingron:1997:TIM, author = "Martin Vingron and Arndt {Von Haeseler}", title = "Towards Integration of Multiple Alignment and Phylogenetic Tree Construction", journal = j-J-COMPUT-BIOL, volume = "4", number = "1", pages = "23--34", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.23", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.23; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.23", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Tanushev:1997:CLT, author = "Miroslav S. Tanushev and Richard Arratia", title = "Central Limit Theorem for Renewal Theory for Several Patterns", journal = j-J-COMPUT-BIOL, volume = "4", number = "1", pages = "35--44", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.35", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.35; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.35", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Bailey:1997:SDS, author = "Timothy L. Bailey and Michael Gribskov", title = "Score Distributions for Simultaneous Matching to Multiple Motifs", journal = j-J-COMPUT-BIOL, volume = "4", number = "1", pages = "45--59", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.45", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.45; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.45", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Schbath:1997:CPP, author = "Sophie Schbath", title = "Coverage Processes in Physical Mapping by Anchoring Random Clones", journal = j-J-COMPUT-BIOL, volume = "4", number = "1", pages = "61--82", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.61", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.61; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.61", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Ponomarenko:1997:GPP, author = "Michael P. Ponomarenko and Anna N. Kolchanova and Nikolay A. Kolchanov", title = "Generating Programs for Predicting the Activity of Functional Sites", journal = j-J-COMPUT-BIOL, volume = "4", number = "1", pages = "83--90", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.83", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.83; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.83", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Anantharaman:1997:GOM, author = "Thomas S. Anantharaman and Bud Mishra and David C. Schwartz", title = "Genomics via Optical Mapping {II}: Ordered Restriction Maps", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "91--118", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.91", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.91; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.91", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Dancik:1997:HFC, author = "Vlado Dan{\v{c}}{\'i}k and Sridhar Hannenhalli and S. Muthukrishnan", title = "Hardness of Flip-Cut Problems from Optical Mapping", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "119--125", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.119", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.119; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.119", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Henderson:1997:FGD, author = "John Henderson and Steven Salzberg and Kenneth H. Fasman", title = "Finding Genes in {DNA} with a Hidden {Markov} Model", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "127--141", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.127", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.127; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.127", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Kearney:1997:SPC, author = "Paul E. Kearney", title = "A Six-Point Condition for Ordinal Matrices", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "143--156", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.143; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Farach:1997:RCD, author = "Martin Farach", title = "Recognizing Circular Decomposable Metrics", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "157--162", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.157", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.157; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.157", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Hochbaum:1997:PCE, author = "Dorit S. Hochbaum and Anu Pathria", title = "Path Costs in Evolutionary Tree Reconstruction", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "163--175", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Zhang:1997:MMS, author = "Louxin Zhang", title = "On a {Mirkin--Muchnik--Smith} Conjecture for Comparing Molecular Phylogenies", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "177--187", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.177", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.177; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.177", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Schbath:1997:ESD, author = "Sophie Schbath", title = "An Efficient Statistic to Detect Over- and Under-represented Words in {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "189--192", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.189; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Dalgaard:1997:SMP, author = "Jacob Z. Dalgaard and Michael J. Moser and Richard Hughey and I. Saira Mian", title = "Statistical Modeling, Phylogenetic Analysis and Structure Prediction of a Protein Splicing Domain Common to Inteins and Hedgehog Proteins", journal = j-J-COMPUT-BIOL, volume = "4", number = "2", pages = "193--214", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.193", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.193; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.193", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Waterman:1997:PSR, author = "Michael S. Waterman and Sorin Istrail and Pavel A. Pevzner", title = "Preface: Special {RECOMB'97} Issues", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "215--215", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.215", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.215", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Smith:1997:CLP, author = "Temple F. Smith and Loredana {Lo Conte} and Jadwiga Bienkowska and Chrysanthe Gaitatzes and Robert G. {Rogers, Jr.} and Richard Lathrop", title = "Current Limitations to Protein Threading Approaches", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "217--225", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.217", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.217; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.217", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Dill:1997:PSE, author = "K. A. Dill and A. T. Phillips and J. B. Rosen", title = "Protein Structure and Energy Landscape Dependence on Sequence Using a Continuous Energy Function", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "227--239", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.227", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.227; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.227", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Hart:1997:LLS, author = "William E. Hart and Sorin Istrail", title = "Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86\% of Optimal", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "241--259", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.241", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.241; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.241", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Berger:1997:IMI, author = "Bonnie Berger and Mona Singh", title = "An Iterative Method for Improved Protein Structural Motif Recognition", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "261--273", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.261", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.261; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.261", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Agarwala:1997:LRP, author = "Richa Agarwala and Serafim Batzoglou and Vlado Dan{\v{c}}{\'i}k and Scott E. Decatur and Sridhar Hannenhalli and Martin Farach and S. Muthukrishnan and Steven Skiena", title = "Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the {HP} Model", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "275--296", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.275", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.275; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.275", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Sze:1997:VAG, author = "Sing-Hoi Sze and Pavel A. Pevzner", title = "{Las Vegas} Algorithms for Gene Recognition: Suboptimal and Error-Tolerant Spliced Alignment", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "297--309", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.297", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.297; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.297", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Reese:1997:ISS, author = "Martin G. Reese and Frank H. Eeckman and David Kulp and David Haussler", title = "Improved Splice Site Detection in {Genie}", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "311--323", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.311", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.311; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.311", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Xu:1997:AGI, author = "Ying Xu and Edward C. Uberbacher", title = "Automated Gene Identification in Large-Scale Genomic Sequences$^1$", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "325--338", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.325", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.325; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.325", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Zhang:1997:ADS, author = "Zheng Zhang and William R. Pearson and Webb Miller", title = "Aligning a {DNA} Sequence with a Protein Sequence", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "339--349", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.339", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.339; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.339", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Benson:1997:SAT, author = "Gary Benson", title = "Sequence Alignment with Tandem Duplication", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "351--367", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.351", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.351; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.351", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Anson:1997:RPR, author = "Eric L. Anson and Eugene W. Myers", title = "{ReAligner}: a Program for Refining {DNA} Sequence Multi-Alignments", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "369--383", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.369", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.369; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.369", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Shibuya:1997:NFA, author = "Tetsuo Shibuya and Hiroshi Imai", title = "New Flexible Approaches for Multiple Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "385--413", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.385", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.385; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.385", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Schwikowski:1997:DPH, author = "Benno Schwikowski and Martin Vingron", title = "The Deferred Path Heuristic for the Generalized Tree Alignment Problem", journal = j-J-COMPUT-BIOL, volume = "4", number = "3", pages = "415--431", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.415", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.415; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.415", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Christof:1997:BCA, author = "Thomas Christof and Michael J{\"u}nger and John Kececioglu and Petra Mutzel and Gerhard Reinelt", title = "A Branch-and-Cut Approach to Physical Mapping of Chromosomes by Unique End-Probes", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "433--447", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.433", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.433; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.433", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Jain:1997:ACI, author = "Mudita Jain and Eugene W. Myers", title = "Algorithms for Computing and Integrating Physical Maps Using Unique Probes", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "449--466", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.449", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.449; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.449", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Sun:1997:PSE, author = "Fengzhu Sun and Gary Benson and Norm Arnheim and Michael Waterman", title = "Pooling Strategies for Establishing Physical Genome Maps Using {FISH}", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "467--486", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.467", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.467; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.467", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Slonim:1997:BHG, author = "Donna Slonim and Leonid Kruglyak and Lincoln Stein and Eric Lander", title = "Building Human Genome Maps with Radiation Hybrids", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "487--504", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.487", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.487; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.487", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Heath:1997:MCM, author = "S. C. Heath", title = "{Markov} Chain {Monte Carlo} Methods for Radiation Hybrid Mapping", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "505--515", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.505", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.505; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.505", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Ben-Dor:1997:CRH, author = "Amir Ben-Dor and Benny Chor", title = "On Constructing Radiation Hybrid Maps", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "517--533", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.517", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.517; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.517", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Lin:1997:AHA, author = "Shili Lin and Terence P. Speed", title = "An Algorithm for Haplotype Analysis", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "535--546", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.535", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.535; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.535", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Cohen:1997:NTD, author = "Jaime Cohen and Martin Farach", title = "Numerical Taxonomy on Data: Experimental Results", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "547--558", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.547", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.547; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.547", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Sankoff:1997:CSI, author = "David Sankoff and Vincent Ferretti and Joseph H. Nadeau", title = "Conserved Segment Identification", journal = j-J-COMPUT-BIOL, volume = "4", number = "4", pages = "559--565", month = jan, year = "1997", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1997.4.559", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1997.4.559; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1997.4.559", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2009", } @Article{Kruglyak:1998:FML, author = "Leonid Kruglyak and Eric S. Lander", title = "Faster Multipoint Linkage Analysis Using {Fourier} Transforms", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "1--7", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.1; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Kosaraju:1998:AAG, author = "S. Rao Kosaraju and Alejandro A. Sch{\"a}ffer and Leslie G. Biesecker", title = "Approximation Algorithms for a Genetic Diagnostics Problem", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "9--26", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.9", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.9; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.9", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Berger:1998:PFH, author = "Bonnie Berger and Tom Leighton", title = "Protein Folding in the Hydrophobic--Hydrophilic ({{\em HP\/}}) Model is {NP}-Complete", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "27--40", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.27", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.27; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.27", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Escalier:1998:PMI, author = "Vincent Escalier and Jo{\'e}l Pothier and Henri Soldano and Alain Viari", title = "Pairwise and Multiple Identification of Three-Dimensional Common Substructures in Proteins", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "41--56", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.41", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.41; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.41", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Mian:1998:SMP, author = "I. Saira Mian and Michael J. Moser and William R. Holley and Aloke Chatterjee", title = "Statistical Modelling and Phylogenetic Analysis of a Deaminase Domain", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "57--72", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.57", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.57; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.57", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Bentil:1998:MSM, author = "Daniel E. Bentil", title = "Modelling and Simulation of Motility in Actomyosin Systems", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "73--86", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.73", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.73; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.73", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Benson:1998:DTM, author = "Gary Benson and Xiaoping Su", title = "On the Distribution of {$K$}-tuple Matches for Sequence Homology: a Constant Time Exact Calculation of the Variance", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "87--100", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.87", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.87; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.87", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Siegel:1998:EVT, author = "Andrew F. Siegel and Jared C. Roach and Ger {Van Den Engh}", title = "Expectation and Variance of True and False Fragment Matches in {DNA} Restriction Mapping", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "101--111", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.101; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.101", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Siegel:1998:ORF, author = "Andrew F. Siegel and Jared C. Roach and Charles Magness and Ed Thayer and Ger {Van Den Engh}", title = "Optimization of Restriction Fragment {DNA} Mapping", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "113--126", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Wang:1998:CAT, author = "Lusheng Wang and Dan Gusfield", title = "Constructing Additive Trees When the Error Is Small", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "127--133", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.127", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.127; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.127", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Eulenstein:1998:DBM, author = "O. Eulenstein and B. Mirkin and M. Vingron", title = "Duplication-Based Measures of Difference Between Gene and Species Trees", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "135--148", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.135", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.135; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.135", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{VonHaeseler:1998:EDA, author = "Arndt {Von Haeseler} and Michael Sch{\"o}niger", title = "Evolution of {DNA} or Amino Acid Sequences with Dependent Sites", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "149--163", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.149; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.149", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Kruglyak:1998:MSH, author = "Semyon Kruglyak", title = "Multistage Sequencing by Hybridization", journal = j-J-COMPUT-BIOL, volume = "5", number = "1", pages = "165--171", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Apostolico:1998:SAM, author = "Alberto Apostolico and Raffaele Giancarlo", title = "Sequence Alignment in Molecular Biology", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "173--196", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Zhang:1998:ALS, author = "Zheng Zhang and Piotr Berman and Webb Miller", title = "Alignments Without Low-Scoring Regions", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "197--210", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Bailey:1998:MSC, author = "Timothy L. Bailey and Michael Gribskov", title = "Methods and Statistics for Combining Motif Match Scores", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "211--221", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.211", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.211; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.211", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Reinert:1998:CPP, author = "Gesine Reinert and Sophie Schbath", title = "Compound {Poisson} and {Poisson} Process Approximations for Occurrences of Multiple Words in {Markov} Chains", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "223--253", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.223", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.223; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.223", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Smith:1998:SBA, author = "Lloyd M. Smith and Robert M. Corn and Anne E. Condon and Max G. Lagally and Anthony G. Frutos and Qinghua Liu and Andrew J. Thiel", title = "A Surface-Based Approach to {DNA} Computation", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "255--267", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.255", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.255; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.255", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Liu:1998:DCS, author = "Qinghua Liu and Anthony G. Frutos and Andrew J. Thiel and Robert M. Corn and Lloyd M. Smith", title = "{DNA} Computing on Surfaces: Encoding Information at the Single Base Level", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "269--278", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.269", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.269; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.269", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Brazma:1998:AAD, author = "Alvis Brazma and Inge Jonassen and Ingvar Eidhammer and David Gilbert", title = "Approaches to the Automatic Discovery of Patterns in Biosequences", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "279--305", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.279", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.279; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.279", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Laub:1998:FIE, author = "Michael T. Laub and Douglas W. Smith", title = "Finding Intron/Exon Splice Junctions Using {INFO}, {INterruption} Finder and Organizer", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "307--321", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.307", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.307; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.307", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Browning:1998:RIC, author = "Sharon Browning", title = "Relationship Information Contained in Gamete Identity by Descent Data", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "323--334", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.323", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.323; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.323", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Przytycka:1998:TRA, author = "Teresa M. Przytycka", title = "Transforming Rooted Agreement into Unrooted Agreement", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "335--349", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.335", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.335; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.335", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Benhabiles:1998:DAP, author = "Nora Benhabil{\`e}s and Xavier Gallet and Annick Thomas-Soumarmon and Robert Brasseur", title = "A Descriptive Analysis of Populations of Three-Dimensional Structures Calculated from Primary Sequences of Proteins by {OSIRIS}", journal = j-J-COMPUT-BIOL, volume = "5", number = "2", pages = "351--366", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.351", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.351; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.351", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Pevzner:1998:P, author = "Pavel A. Pevzner", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "367--367", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.367", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.367", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Badretdinov:1998:HHC, author = "Azat Ya Badretdinov and Alexei V. Finkelstein", title = "How Homologs Can Help to Predict Protein Folds Even Though They Cannot Be Predicted for Individual Sequences", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "369--376", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.369", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.369; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.369", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Ben-Dor:1998:CPQ, author = "Amir Ben-Dor and Benny Chor and Dan Graur and Ron Ophir and Dan Pelleg", title = "Constructing Phylogenies from Quartets: Elucidation of {Eutherian} Superordinal Relationships", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "377--390", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.377", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.377; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.377", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Bonet:1998:BMS, author = "Maria Bonet and Mike Steel and Tandy Warnow and Shibu Yooseph", title = "Better Methods for Solving Parsimony and Compatibility", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "391--407", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.391", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.391; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.391", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Chen:1998:HOM, author = "Cheng Che Chen and Jas Winder Pal Singh and Russ B. Altman", title = "Hierarchical Organization of Molecular Structure Computations", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "409--422", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.409", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.409; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.409", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Crescenzi:1998:CPF, author = "Pierluigi Crescenzi and Deborah Goldman and Christos Papadimitriou and Antonio Piccolboni and Mihalis Yannakakis", title = "On the Complexity of Protein Folding", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "423--465", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.423", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.423; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.423", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Gelfand:1998:ADC, author = "Israel Gelfand and Alexander Kister and Casimir Kulikowski and Ognyan Stoyanov", title = "Algorithmic Determination of Core Positions in the {$ V_L $} and {$ V_H $} Domains of Immunoglobulin Molecules", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "467--477", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.467", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.467; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.467", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Grundy:1998:HDF, author = "William Noble Grundy", title = "Homology Detection via Family Pairwise Search", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "479--491", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.479", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.479; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.479", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Holmes:1998:DPA, author = "Ian Holmes and Richard Durbin", title = "Dynamic Programming Alignment Accuracy", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "493--504", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.493", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.493; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.493", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Lee:1998:ERS, author = "Jae K. Lee and Vlado Dan{\v{c}}{\'\i}k and Michael S. Waterman", title = "Estimation for Restriction Sites Observed by Optical Mapping Using Reversible-Jump {Markov} Chain {Monte} {Carlo}", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "505--515", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.505", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.505; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.505", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Lenhof:1998:PAR, author = "Hans-Peter Lenhof and Knut Reinert and Martin Vingron", title = "A Polyhedral Approach to {RNA} Sequence Structure Alignment", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "517--530", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.517", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.517; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.517", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Reva:1998:OPS, author = "Boris A. Reva and D. S. Rykunov and Alexei V. Finkelstein and Jeffrey Skolnick", title = "Optimization of Protein Structure on Lattices Using a Self-Consistent Field Approach", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "531--538", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.531", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.531; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.531", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Sagot:1998:ISP, author = "Marie-France Sagot and Eugene W. Myers", title = "Identifying Satellites and Periodic Repetitions in Biological Sequences", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "539--553", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.539", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.539; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.539", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Sankoff:1998:MGR, author = "David Sankoff and Mathieu Blanchette", title = "Multiple Genome Rearrangement and Breakpoint Phylogeny", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "555--570", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.555", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.555; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.555", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Walker:1998:ACD, author = "Wynn L. Walker and David S. Goodsell and Elliot M. Landaw", title = "An Analysis of a Class of {DNA} Sequence Reading Molecules", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "571--583", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.571", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.571; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.571", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Wu:1998:RAM, author = "Thomas D. Wu and Scott C. Schmidler and Trevor Hastie and Douglas L. Brutlag", title = "Regression Analysis of Multiple Protein Structures", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "585--595", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.585", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.585; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.585", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Xu:1998:ECM, author = "Ying Xu and Dong Xu and Edward C. Uberbacher", title = "An Efficient Computational Method for Globally Optimal Threading1", journal = j-J-COMPUT-BIOL, volume = "5", number = "3", pages = "597--614", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.597", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.597; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.597", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Roweis:1998:SBM, author = "Sam Roweis and Erik Winfree and Richard Burgoyne and Nickolas V. Chelyapov and Myron F. Goodman and Paul W. K. Rothemund and Leonard M. Adleman", title = "A Sticker-Based Model for {DNA} Computation", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "615--629", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.615", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.615; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.615", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Sandak:1998:MBS, author = "Bilha Sandak and Ruth Nussinov and Haim J. Wolfson", title = "A Method for Biomolecular Structural Recognition and Docking Allowing Conformational Flexibility", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "631--654", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.631", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.631; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.631", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Wong:1998:TRB, author = "Wing Hung Wong and Yan Cui and Run Sheng Chen", title = "Torsional Relaxation for Biopolymers", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "655--665", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.655", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.655; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.655", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Salzberg:1998:DTS, author = "Steven Salzberg and Arthur L. Delcher and Kenneth H. Fasman and John Henderson", title = "A Decision Tree System for Finding Genes in {DNA}", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "667--680", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.667", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.667; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.667", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Guigo:1998:AGP, author = "Roderic Guig{\'o}", title = "Assembling Genes from Predicted Exons in Linear Time with Dynamic Programming", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "681--702", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.681", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.681; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.681", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Mallios:1998:ISD, author = "Ronna R. Mallios", title = "Iterative Stepwise Discriminant Analysis: a Meta-Algorithm for Detecting Quantitative Sequence Motifs", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "703--711", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.703", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.703; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.703", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Evans:1998:CCP, author = "Steven N. Evans and Xiaowen Zhou", title = "Constructing and Counting Phylogenetic Invariants", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "713--724", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.713", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.713; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.713", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Parida:1998:UFO, author = "Laxmi Parida", title = "A Uniform Framework for Ordered Restriction Map Problems", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "725--739", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.725", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.725; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.725", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Tran:1998:ECS, author = "Nicholas Tran", title = "An Easy Case of Sorting by Reversals", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "741--746", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.741", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.741; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.741", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Takai-Igarashi:1998:DCS, author = "Takako Takai-Igarashi and Yoko Nadaoka and Tsuguchika Kaminuma", title = "A Database for Cell Signaling Networks", journal = j-J-COMPUT-BIOL, volume = "5", number = "4", pages = "747--754", month = jan, year = "1998", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1998.5.747", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1998.5.747; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1998.5.747", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2009", } @Article{Berger:1999:SSC, author = "Bonnie Berger and Gunnar W. Hoest and James R. Paulson and Peter W. Shor", title = "On the Structure of the Scaffolding Core of Bacteriophage {T4}", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "1--12", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.1; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Nayak:1999:SCH, author = "Ashwin Nayak and Alistair Sinclair and Uri Zwick", title = "Spatial Codes and the Hardness of String Folding Problems", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "13--36", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.13", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.13; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.13", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Desper:1999:ITM, author = "Richard Desper and Feng Jiang and Olli-P. Kallioniemi and Holger Moch and Christos H. Papadimitriou and Alejandro A. Sch{\"a}ffer", title = "Inferring Tree Models for Oncogenesis from Comparative Genome Hybridization Data", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "37--51", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.37", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.37; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.37", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Adleman:1999:AMC, author = "Leonard M. Adleman and Paul W. K. Rothemund and Sam Roweis and Erik Winfree", title = "On Applying Molecular Computation to the {Data Encryption Standard}", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "53--63", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.53", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/cryptography1990.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.53; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.53", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Roweis:1999:RED, author = "Sam Roweis and Erik Winfree", title = "On the Reduction of Errors in {DNA} Computation", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "65--75", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.65", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.65; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.65", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Sun:1999:MDS, author = "Fengzhu Sun", title = "Modeling {DNA} Shuffling", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "77--90", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.77", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.77; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.77", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Mott:1999:ASG, author = "Richard Mott and Roger Tribe", title = "Approximate Statistics of Gapped Alignments", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "91--112", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.91", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.91; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.91", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Blazewicz:1999:DSP, author = "J. B{\l}a{\.z}ewicz and P. Formanowicz and M. Kasprzak and W. T. Markiewicz and J. W{\c{e}}glarz", title = "{DNA} Sequencing With Positive and Negative Errors", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "113--123", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Loewenstern:1999:SLE, author = "David Loewenstern and Peter N. Yianilos", title = "Significantly Lower Entropy Estimates for Natural {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "6", number = "1", pages = "125--142", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Istrail:1999:LSA, author = "S. Istrail and R. Schwartz and J. King", title = "Lattice Simulations of Aggregation Funnels for Protein Folding", journal = j-J-COMPUT-BIOL, volume = "6", number = "2", pages = "143--162", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.143; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Kim:1999:ASP, author = "Sun Kim and Alberto Maria Segre", title = "{AMASS}: a Structured Pattern Matching Approach to Shotgun Sequence Assembly", journal = j-J-COMPUT-BIOL, volume = "6", number = "2", pages = "163--186", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Fasulo:1999:AAM, author = "Dan Fasulo and Tao Jiang and Richard M. Karp and Reuben J. Settergren and Ed Thayer", title = "An Algorithmic Approach to Multiple Complete Digest Mapping", journal = j-J-COMPUT-BIOL, volume = "6", number = "2", pages = "187--207", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.187", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.187; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.187", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Wang:1999:NTD, author = "Jason T. L. Wang and Steve Rozen and Bruce A. Shapiro and Dennis Shasha and Zhiyuan Wang and Maisheng Yin", title = "New Techniques for {DNA} Sequence Classification", journal = j-J-COMPUT-BIOL, volume = "6", number = "2", pages = "209--218", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.209", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.209; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.209", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Wu:1999:MRS, author = "Thomas D. Wu and Craig G. Nevill-Manning and Douglas L. Brutlag", title = "Minimal-Risk Scoring Matrices for Sequence Analysis", journal = j-J-COMPUT-BIOL, volume = "6", number = "2", pages = "219--235", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.219", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.219; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.219", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Mayraz:1999:CPM, author = "Guy Mayraz and Ron Shamir", title = "Construction of Physical Maps from Oligonucleotide Fingerprints Data", journal = j-J-COMPUT-BIOL, volume = "6", number = "2", pages = "237--252", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.237", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.237; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.237", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Yu:1999:PSS, author = "Lihua Yu and Temple F. Smith", title = "Positional Statistical Significance in Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "6", number = "2", pages = "253--259", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.253", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.253; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.253", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Churchill:1999:BRH, author = "Gary A. Churchill and Betty Lazareva", title = "{Bayesian} Restoration of a Hidden {Markov} Chain with Applications to {DNA} Sequencing", journal = j-J-COMPUT-BIOL, volume = "6", number = "2", pages = "261--277", month = jan, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.1999.6.261", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.1999.6.261; https://www.liebertpub.com/doi/pdf/10.1089/cmb.1999.6.261", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2009", } @Article{Istrail:1999:SRI, author = "Sorin Istrail", title = "Special {RECOMB'99} Issue", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "279--279", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318265", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ben-Dor:1999:CGE, author = "Amir Ben-Dor and Ron Shamir and Zohar Yakhini", title = "Clustering Gene Expression Patterns", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "281--297", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318274", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bienkowska:1999:PTS, author = "Jadwiga R. Bie{\'n}kowska and Robert G. {Rogers, Jr.} and Temple F. Smith", title = "Performance of Threading Scoring Functions Designed Using New Optimization Method", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "299--311", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318283", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Chew:1999:FDC, author = "L. Paul Chew and Dan Huttenlocher and Klara Kedem and Jon Kleinberg", title = "Fast Detection of Common Geometric Substructure in Proteins", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "313--325", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318292", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Dancik:1999:NPS, author = "Vlado Dan{\v{c}}{\'\i}k and Theresa A. Addona and Karl R. Clauser and James E. Vath and Pavel A. Pevzner", title = "{{\em {De} Novo\/}} Peptide Sequencing via Tandem Mass Spectrometry", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "327--342", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318300", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Forst:1999:EMN, author = "Christian V. Forst and Klaus Schulten", title = "Evolution of Metabolisms: a New Method for the Comparison of Metabolic Pathways Using Genomics Information", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "343--360", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318319", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Frieze:1999:ORS, author = "Alan M. Frieze and Franco P. Preparata and Eli Upfal", title = "Optimal Reconstruction of a Sequence from its Probes", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "361--368", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318328", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Huson:1999:DCF, author = "Daniel H. Huson and Scott M. Nettles and Tandy J. Warnow", title = "Disk-Covering, a Fast-Converging Method for Phylogenetic Tree Reconstruction", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "369--386", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318337", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Kleinberg:1999:EAP, author = "Jon M. Kleinberg", title = "Efficient Algorithms for Protein Sequence Design and the Analysis of Certain Evolutionary Fitness Landscapes", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "387--404", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318346", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lathrop:1999:ALG, author = "Richard H. Lathrop", title = "An Anytime Local-to-Global Optimization Algorithm for Protein Threading in O(m$^2$ {\~n}$^2$ ) Space", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "405--418", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318355", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Pachter:1999:DBA, author = "Lior Pachter and Serafim Batzoglou and Valentin I. Spitkovsky and Eric Banks and Eric S. Lander and Daniel J. Kleitman and Bonnie Berger", title = "A Dictionary-Based Approach for Gene Annotation", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "419--430", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318364", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Sankoff:1999:PIG, author = "David Sankoff and Mathieu Blanchette", title = "Phylogenetic Invariants for Genome Rearrangements", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "431--445", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318373", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Willett:1999:DBA, author = "Peter Willett", title = "Dissimilarity-Based Algorithms for Selecting Structurally Diverse Sets of Compounds", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "447--457", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318382", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wooley:1999:TCB, author = "John C. Wooley", title = "Trends in Computational Biology: a Summary Based on a {RECOMB} Plenary Lecture, 1999", journal = j-J-COMPUT-BIOL, volume = "6", number = "3--4", pages = "459--474", month = oct, year = "1999", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652799318391", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Reinert:2000:PSP, author = "Gesine Reinert and Sophie Schbath and Michael S. Waterman", title = "Probabilistic and Statistical Properties of Words: An Overview", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "1--46", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081360", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Schbath:2000:ENC, author = "Sophie Schbath and Nathalie Bossard and Simon Tavar{\'e}", title = "The Effect of Nonhomogeneous Clone Length Distribution on the Progress of an {STS} Mapping Project", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "47--57", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081379", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bafna:2000:LRP, author = "Vineet Bafna and Sridhar Hannenhalli and Ken Rice and Lisa Vawter", title = "Ligand-Receptor Pairing Via Tree Comparison", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "59--70", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081388", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Apostolico:2000:EDU, author = "Alberto Apostolico and Mary Ellen Bock and Stefano Lonardi and Xuyan Xu", title = "Efficient Detection of Unusual Words", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "71--94", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081397", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Jaakkola:2000:DFD, author = "Tommi Jaakkola and Mark Diekhans and David Haussler", title = "A Discriminative Framework for Detecting Remote Protein Homologies", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "95--114", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081405", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Drasdo:2000:SLS, author = "Dirk Drasdo and Terence Hwa and Michael L{\"a}ssig", title = "Scaling Laws and Similarity Detection in Sequence Alignment with Gaps", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "115--141", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081414", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wang:2000:EMR, author = "Dai Wang and Cheng Zhao and Rong Cheng and Fengzhu Sun", title = "Estimation of the Mutation Rate During Error-prone Polymerase Chain Reaction", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "143--158", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081423", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{McGuire:2000:BMD, author = "Gr{\'a}inne McGuire and Frank Wright and Michael J. Prentice", title = "A {Bayesian} Model for Detecting Past Recombination Events in {DNA} Multiple Alignments", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "159--170", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081432", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Fekete:2000:PRB, author = "Martin Fekete and Ivo L. Hofacker and Peter F. Stadler", title = "Prediction of {RNA} Base Pairing Probabilities on Massively Parallel Computers", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "171--182", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081441", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Berezovsky:2000:HRA, author = "Igor N. Berezovsky and Natalia G. Esipova and Vladimir G. Tumanyan", title = "Hierarchy of Regions of Amino Acid Sequence with Respect to Their Role in the Protein Spatial Structure", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "183--192", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081450", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Schbath:2000:ODW, author = "Sophie Schbath", title = "An Overview on the Distribution of Word Counts in {Markov} Chains", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "193--201", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081469", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Zhang:2000:GAA, author = "Zheng Zhang and Scott Schwartz and Lukas Wagner and Webb Miller", title = "A Greedy Algorithm for Aligning {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "203--214", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081478", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ramensky:2000:DST, author = "V. E. Ramensky and V. Ju. Makeev and M. A. Roytberg and V. G. Tumanyan", title = "{DNA} Segmentation Through the {Bayesian} Approach", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "215--231", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081487", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Schmidler:2000:BSP, author = "Scott C. Schmidler and Jun S. Liu and Douglas L. Brutlag", title = "{Bayesian} Segmentation of Protein Secondary Structure", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "233--248", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081496", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Rodolphe:2000:TCM, author = "Fran{\c{c}}ois Rodolphe and Catherine Math{\'e}", title = "Translation Conditional Models for Protein Coding Sequences", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "249--260", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081504", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Gonnet:2000:EMM, author = "Gaston H. Gonnet and Chantal Korostensky and Steve Benner", title = "Evaluation Measures of Multiple Sequence Alignments", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "261--276", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081513", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Moulton:2000:MRS, author = "Vincent Moulton and Michael Zuker and Michael Steel and Robin Pointon and David Penny", title = "Metrics on {RNA} Secondary Structures", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "277--292", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081522", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Berman:2000:WSD, author = "Piotr Berman and Zheng Zhang and Yuri I. Wolf and Eugene V. Koonin and Webb Miller", title = "Winnowing Sequences from a Database Search", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "293--302", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081531", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Karp:2000:AOM, author = "Richard M. Karp and Ron Shamir", title = "Algorithms for Optical Mapping", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "303--316", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081540", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Thayer:2000:DPC, author = "Edward C. Thayer and Chris Bystroff and David Baker", title = "Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence", journal = j-J-COMPUT-BIOL, volume = "7", number = "1--2", pages = "317--327", month = feb, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050081559", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Shamir:2000:PSR, author = "Ron Shamir", title = "Preface: Special {RECOMB 2000} Issue", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "329--330", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050808", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Akutsu:2000:AIB, author = "Tatsuya Akutsu and Satoru Miyano and Satoru Kuhara", title = "Algorithms for Identifying {Boolean} Networks and Related Biological Networks Based on Matrix Multiplication and Fingerprint Function", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "331--343", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050817", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Marsan:2000:AES, author = "Laurent Marsan and Marie-France Sagot", title = "Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "345--362", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050826", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ohkubo:2000:PEF, author = "Y. Zenmei Ohkubo and Gordon M. Crippen", title = "Potential Energy Function for Continuous State Models of Globular Proteins", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "363--379", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050835", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Apostolico:2000:OAP, author = "Alberto Apostolico and Gill Bejerano", title = "Optimal Amnesic Probabilistic Automata or How to Learn and Classify Proteins in Linear Time and Space", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "381--393", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050844", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Heber:2000:CSP, author = "Steffen Heber and Jens Stoye and Marcus Frohme and J{\"o}rg Hoheisel and Martin Vingron", title = "Contig Selection in Physical Mapping", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "395--408", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050853", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lyngso:2000:RPP, author = "Rune B. Lyngs{\o} and Christian N. S. Pedersen", title = "{RNA} Pseudoknot Prediction in Energy-Based Models", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "409--427", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050862", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Chen:2000:NPD, author = "Kevin Chen and Dannie Durand and Martin Farach-Colton", title = "{NOTUNG}: a Program for Dating Gene Duplications and Optimizing Gene Family Trees", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "429--447", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050871", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Xu:2000:CMN, author = "Ying Xu and Dong Xu and Oakley H. Crawford and J. Ralph Einstein", title = "A Computational Method for {NMR-Constrained} Protein Threading", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "449--467", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050880", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Sorenson:2000:MSE, author = "Jon M. Sorenson and Teresa Head-Gordon", title = "Matching Simulation and Experiment: a New Simplified Model for Simulating Protein Folding", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "469--481", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050899", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Zien:2000:SIA, author = "Alexander Zien and Ralf Zimmer and Thomas Lengauer", title = "A Simple Iterative Approach to Parameter Optimization", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "483--501", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050907", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ben-Dor:2000:UDT, author = "Amir Ben-Dor and Richard Karp and Benno Schwikowski and Zohar Yakhini", title = "Universal {DNA} Tag Systems: a Combinatorial Design Scheme", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "503--519", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050916", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Sankoff:2000:EEE, author = "David Sankoff and David Bryant and M{\'e}lanie Deneault and B. Franz Lang and Gertraud Burger", title = "Early Eukaryote Evolution Based on Mitochondrial Gene Order Breakpoints", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "521--535", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050925", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bailey-Kellogg:2000:NJA, author = "Chris Bailey-Kellogg and Alik Widge and John J. Kelley and Marcelo J. Berardi and John H. Bushweller and Bruce Randall Donald", title = "The {NOESY} Jigsaw: Automated Protein Secondary Structure and Main-Chain Assignment from Sparse, Unassigned {NMR} Data", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "537--558", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050934", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ben-Dor:2000:TCG, author = "Amir Ben-Dor and Laurakay Bruhn and Nir Friedman and Iftach Nachman and Mich{\`e}l Schummer and Zohar Yakhini", title = "Tissue Classification with Gene Expression Profiles", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "559--583", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050943", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Hart:2000:SFA, author = "Reece K. Hart and Ajay K. Royyuru and Gustavo Stolovitzky and Andrea Califano", title = "Systematic and Fully Automated Identification of Protein Sequence Patterns", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "585--600", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050952", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Friedman:2000:UBN, author = "Nir Friedman and Michal Linial and Iftach Nachman and Dana Pe'er", title = "Using {Bayesian} Networks to Analyze Expression Data", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "601--620", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050961", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Preparata:2000:SHI, author = "Franco P. Preparata and Eli Upfal", title = "Sequencing-by-Hybridization at the Information-Theory Bound: an Optimal Algorithm", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "621--630", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050970", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Anonymous:2000:ATF, author = "Anonymous", title = "Abstracts from {TIGR's Fourth Annual Conference on Computational Genomics November 16--19, 2000 Baltimore, MD}", journal = j-J-COMPUT-BIOL, volume = "7", number = "3--4", pages = "631--651", month = aug, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652700750050989", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lermen:2000:PUA, author = "Martin Lermen and Knut Reinert", title = "The Practical Use of the {$ A* $} Algorithm for Exact Multiple Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "7", number = "5", pages = "655--671", month = oct, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701446134", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701446134; https://www.liebertpub.com/doi/pdf/10.1089/106652701446134", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Stoyanov:2000:GIC, author = "Ognyan Stoyanov and Alexander Kister and Israel Gelfand and Casimir Kulikowski and Cyrus Chothia", title = "Geometric Invariant Core for the {$ C_L $} and {$C$}$_{H 1}$ Domains of Immunoglobulin Molecules", journal = j-J-COMPUT-BIOL, volume = "7", number = "5", pages = "673--684", month = oct, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701446143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701446143; https://www.liebertpub.com/doi/pdf/10.1089/106652701446143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Eidhammer:2000:SCS, author = "Ingvar Eidhammer and Inge Jonassen and William R. Taylor", title = "Structure Comparison and Structure Patterns", journal = j-J-COMPUT-BIOL, volume = "7", number = "5", pages = "685--716", month = oct, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701446152", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701446152; https://www.liebertpub.com/doi/pdf/10.1089/106652701446152", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Cawley:2000:DST, author = "Simon E. Cawley and Terence P. Speed", title = "{DNA} Sequencing with Transposons", journal = j-J-COMPUT-BIOL, volume = "7", number = "5", pages = "717--729", month = oct, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701446161", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701446161; https://www.liebertpub.com/doi/pdf/10.1089/106652701446161", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Makarenkov:2000:CAT, author = "Vladimir Makarenkov and Bruno Leclerc", title = "Comparison of Additive Trees Using Circular Orders", journal = j-J-COMPUT-BIOL, volume = "7", number = "5", pages = "731--744", month = oct, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701446170", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701446170; https://www.liebertpub.com/doi/pdf/10.1089/106652701446170", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Karp:2000:ACD, author = "Richard M. Karp and Itsik Pe'er and Ron Shamir", title = "An Algorithm Combining Discrete and Continuous Methods for Optical Mapping", journal = j-J-COMPUT-BIOL, volume = "7", number = "5", pages = "745--760", month = oct, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701446189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701446189; https://www.liebertpub.com/doi/pdf/10.1089/106652701446189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Muller:2000:MAA, author = "Tobias M{\"u}ller and Martin Vingron", title = "Modeling Amino Acid Replacement", journal = j-J-COMPUT-BIOL, volume = "7", number = "6", pages = "761--776", month = dec, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050514918", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270050514918; https://www.liebertpub.com/doi/pdf/10.1089/10665270050514918", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Pevzner:2000:MTP, author = "Pavel A. Pevzner and Vlado Dan{\v{c}}{\'\i}k and Chris L. Tang", title = "Mutation-Tolerant Protein Identification by Mass Spectrometry", journal = j-J-COMPUT-BIOL, volume = "7", number = "6", pages = "777--787", month = dec, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050514927", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270050514927; https://www.liebertpub.com/doi/pdf/10.1089/10665270050514927", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Desper:2000:DBR, author = "Richard Desper and Feng Jiang and Olli-P. Kallioniemi and Holger Moch and Christos H. Papadimitriou and Alejandro A. Sch{\"a}ffer", title = "Distance-Based Reconstruction of Tree Models for Oncogenesis", journal = j-J-COMPUT-BIOL, volume = "7", number = "6", pages = "789--803", month = dec, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050514936", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270050514936; https://www.liebertpub.com/doi/pdf/10.1089/10665270050514936", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ideker:2000:TDE, author = "Trey Ideker and Vesteinn Thorsson and Andrew F. Siegel and Leroy E. Hood", title = "Testing for Differentially-Expressed Genes by Maximum-Likelihood Analysis of Microarray Data", journal = j-J-COMPUT-BIOL, volume = "7", number = "6", pages = "805--817", month = dec, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050514945", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270050514945; https://www.liebertpub.com/doi/pdf/10.1089/10665270050514945", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Kerr:2000:AVG, author = "M. Kathleen Kerr and Mitchell Martin and Gary A. Churchill", title = "Analysis of Variance for Gene Expression Microarray Data", journal = j-J-COMPUT-BIOL, volume = "7", number = "6", pages = "819--837", month = dec, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050514954", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270050514954; https://www.liebertpub.com/doi/pdf/10.1089/10665270050514954", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Faulhammer:2000:FEL, author = "Dirk Faulhammer and Richard J. Lipton and Laura F. Landweber", title = "Fidelity of Enzymatic Ligation for {DNA} Computing", journal = j-J-COMPUT-BIOL, volume = "7", number = "6", pages = "839--848", month = dec, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050514963", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270050514963; https://www.liebertpub.com/doi/pdf/10.1089/10665270050514963", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Mian:2000:RRA, author = "I. S. Mian and I. Dubchak", title = "Representing and Reasoning about Protein Families Using Generative and Discriminative Methods", journal = j-J-COMPUT-BIOL, volume = "7", number = "6", pages = "849--862", month = dec, year = "2000", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270050514972", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270050514972; https://www.liebertpub.com/doi/pdf/10.1089/10665270050514972", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Landau:2001:AAT, author = "Gad M. Landau and Jeanette P. Schmidt and Dina Sokol", title = "An Algorithm for Approximate Tandem Repeats", journal = j-J-COMPUT-BIOL, volume = "8", number = "1", pages = "1--18", month = feb, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300099038", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300099038; https://www.liebertpub.com/doi/pdf/10.1089/106652701300099038", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bailey-Kellogg:2001:RMD, author = "Chris Bailey-Kellogg and John J. Kelleyiii and Cliff Stein and Bruce Randall Donald", title = "Reducing Mass Degeneracy in {SAR} by {MS} by Stable Isotopic Labeling", journal = j-J-COMPUT-BIOL, volume = "8", number = "1", pages = "19--36", month = feb, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300099056", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300099056; https://www.liebertpub.com/doi/pdf/10.1089/106652701300099056", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Newton:2001:DVE, author = "M. A. Newton and C. M. Kendziorski and C. S. Richmond and F. R. Blattner and K. W. Tsui", title = "On Differential Variability of Expression Ratios: Improving Statistical Inference about Gene Expression Changes from Microarray Data", journal = j-J-COMPUT-BIOL, volume = "8", number = "1", pages = "37--52", month = feb, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300099074", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300099074; https://www.liebertpub.com/doi/pdf/10.1089/106652701300099074", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Liben-Nowell:2001:SSD, author = "David Liben-Nowell", title = "On the Structure of Syntenic Distance", journal = j-J-COMPUT-BIOL, volume = "8", number = "1", pages = "53--67", month = feb, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300099092", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300099092; https://www.liebertpub.com/doi/pdf/10.1089/106652701300099092", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wang:2001:PPN, author = "Lusheng Wang and Kaizhong Zhang and Louxin Zhang", title = "Perfect Phylogenetic Networks with Recombination", journal = j-J-COMPUT-BIOL, volume = "8", number = "1", pages = "69--78", month = feb, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300099119", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300099119; https://www.liebertpub.com/doi/pdf/10.1089/106652701300099119", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Charleston:2001:HHP, author = "Michael A. Charleston", title = "Hitch-Hiking: a Parallel Heuristic Search Strategy, Applied to the Phylogeny Problem", journal = j-J-COMPUT-BIOL, volume = "8", number = "1", pages = "79--91", month = feb, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300099137", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:46:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300099137; https://www.liebertpub.com/doi/pdf/10.1089/106652701300099137", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Leibowitz:2001:MGE, author = "Nathaniel Leibowitz and Ruth Nussinov and Haim J. Wolfson", title = "{MUSTA} --- a General, Efficient, Automated Method for Multiple Structure Alignment and Detection of Common Motifs: Application to Proteins", journal = j-J-COMPUT-BIOL, volume = "8", number = "2", pages = "93--121", month = apr, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300312896", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300312896; https://www.liebertpub.com/doi/pdf/10.1089/106652701300312896", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Gilbert:2001:ETC, author = "Peter B. Gilbert and Vladimir A. Novitsky and Monty A. Montano and Max Essex", title = "An Efficient Test for Comparing Sequence Diversity between Two Populations", journal = j-J-COMPUT-BIOL, volume = "8", number = "2", pages = "123--139", month = apr, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300312904", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300312904; https://www.liebertpub.com/doi/pdf/10.1089/106652701300312904", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Hubbell:2001:MSH, author = "Earl Hubbell", title = "Multiplex Sequencing by Hybridization", journal = j-J-COMPUT-BIOL, volume = "8", number = "2", pages = "141--149", month = apr, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300312913", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300312913; https://www.liebertpub.com/doi/pdf/10.1089/106652701300312913", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Elhai:2001:DBR, author = "Jeff Elhai", title = "Determination of Bias in the Relative Abundance of Oligonucleotides in {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "8", number = "2", pages = "151--175", month = apr, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300312922", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300312922; https://www.liebertpub.com/doi/pdf/10.1089/106652701300312922", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Dewey:2001:SAA, author = "T. Gregory Dewey", title = "A Sequence Alignment Algorithm with an Arbitrary Gap Penalty Function", journal = j-J-COMPUT-BIOL, volume = "8", number = "2", pages = "177--190", month = apr, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300312931", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300312931; https://www.liebertpub.com/doi/pdf/10.1089/106652701300312931", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Zhao:2001:RIU, author = "Hongyu Zhao and Feng Liang", title = "On Relationship Inference Using Gamete Identity by Descent Data", journal = j-J-COMPUT-BIOL, volume = "8", number = "2", pages = "191--200", month = apr, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701300312940", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701300312940; https://www.liebertpub.com/doi/pdf/10.1089/106652701300312940", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Marathe:2001:CDW, author = "Amit Marathe and Anne E. Condon and Robert M. Corn", title = "On Combinatorial {DNA} Word Design", journal = j-J-COMPUT-BIOL, volume = "8", number = "3", pages = "201--219", month = jun, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270152530818", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270152530818; https://www.liebertpub.com/doi/pdf/10.1089/10665270152530818", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Gu:2001:MMF, author = "Xun Gu", title = "Mathematical Modeling for Functional Divergence after Gene Duplication", journal = j-J-COMPUT-BIOL, volume = "8", number = "3", pages = "221--234", month = jun, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270152530827", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270152530827; https://www.liebertpub.com/doi/pdf/10.1089/10665270152530827", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Nicodeme:2001:FAM, author = "Pierre Nicod{\`e}me", title = "Fast Approximate Motif Statistics", journal = j-J-COMPUT-BIOL, volume = "8", number = "3", pages = "235--248", month = jun, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270152530836", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270152530836; https://www.liebertpub.com/doi/pdf/10.1089/10665270152530836", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Yu:2001:SSP, author = "Yi-Kuo Yu and Terence Hwa", title = "Statistical Significance of Probabilistic Sequence Alignment and Related Local Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "8", number = "3", pages = "249--282", month = jun, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270152530845", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270152530845; https://www.liebertpub.com/doi/pdf/10.1089/10665270152530845", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Horton:2001:TBB, author = "Paul Horton", title = "{Tsukuba BB}: a Branch and Bound Algorithm for Local Multiple Alignment of {DNA} and Protein Sequences", journal = j-J-COMPUT-BIOL, volume = "8", number = "3", pages = "283--303", month = jun, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270152530854", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270152530854; https://www.liebertpub.com/doi/pdf/10.1089/10665270152530854", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Gusfield:2001:IHS, author = "Dan Gusfield", title = "Inference of Haplotypes from Samples of Diploid Populations: Complexity and Algorithms", journal = j-J-COMPUT-BIOL, volume = "8", number = "3", pages = "305--323", month = jun, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270152530863", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270152530863; https://www.liebertpub.com/doi/pdf/10.1089/10665270152530863", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Chen:2001:DPA, author = "Ting Chen and Ming-Yang Kao and Matthew Tepel and John Rush and George M. Church", title = "A Dynamic Programming Approach to {De} {Novo} Peptide Sequencing via Tandem Mass Spectrometry", journal = j-J-COMPUT-BIOL, volume = "8", number = "3", pages = "325--337", month = jun, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270152530872", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270152530872; https://www.liebertpub.com/doi/pdf/10.1089/10665270152530872", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Searls:2001:JGL, author = "David B. Searls", title = "From {\em {Jabberwocky}\/} to Genome: {Lewis Carroll} and Computational Biology", journal = j-J-COMPUT-BIOL, volume = "8", number = "3", pages = "339--348", month = jun, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270152530881", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270152530881; https://www.liebertpub.com/doi/pdf/10.1089/10665270152530881", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Robin:2001:NCS, author = "St{\'e}phane Robin and Sophie Schbath", title = "Numerical Comparison of Several Approximations of the Word Count Distribution in Random Sequences", journal = j-J-COMPUT-BIOL, volume = "8", number = "4", pages = "349--359", month = sep, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701752236179", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701752236179; https://www.liebertpub.com/doi/pdf/10.1089/106652701752236179", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ben-Dor:2001:CPS, author = "A. Ben-Dor and I. Pe'er and R. Shamir and R. Sharan", title = "On the Complexity of Positional Sequencing by Hybridization", journal = j-J-COMPUT-BIOL, volume = "8", number = "4", pages = "361--371", month = sep, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701752236188", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701752236188; https://www.liebertpub.com/doi/pdf/10.1089/106652701752236188", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Mercier:2001:EDL, author = "S. Mercier and J. J. Daudin", title = "Exact Distribution for the Local Score of One i.i.d. Random Sequence", journal = j-J-COMPUT-BIOL, volume = "8", number = "4", pages = "373--380", month = sep, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701752236197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701752236197; https://www.liebertpub.com/doi/pdf/10.1089/106652701752236197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Devauchelle:2001:RMA, author = "C. Devauchelle and A. Grossmann and A. H{\'e}naut and M. Holschneider and M. Monnerot and J. L. Risler and B. Torr{\'e}sani", title = "Rate Matrices for Analyzing Large Families of Protein Sequences", journal = j-J-COMPUT-BIOL, volume = "8", number = "4", pages = "381--399", month = sep, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701752236205", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701752236205; https://www.liebertpub.com/doi/pdf/10.1089/106652701752236205", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Husmeier:2001:DRD, author = "Dirk Husmeier and Frank Wright", title = "Detection of Recombination in {DNA} Multiple Alignments with Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "8", number = "4", pages = "401--427", month = sep, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701752236214", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701752236214; https://www.liebertpub.com/doi/pdf/10.1089/106652701752236214", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wahde:2001:MGR, author = "Mattias Wahde and John Hertz", title = "Modeling Genetic Regulatory Dynamics in Neural Development", journal = j-J-COMPUT-BIOL, volume = "8", number = "4", pages = "429--442", month = sep, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701752236223", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701752236223; https://www.liebertpub.com/doi/pdf/10.1089/106652701752236223", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Goryachev:2001:UMD, author = "Andrew B. Goryachev and Pascale F. Macgregor and Aled M. Edwards", title = "Unfolding of Microarray Data", journal = j-J-COMPUT-BIOL, volume = "8", number = "4", pages = "443--461", month = sep, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701752236232", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701752236232; https://www.liebertpub.com/doi/pdf/10.1089/106652701752236232", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Kruglyak:2001:NES, author = "Semyon Kruglyak and Haixu Tang", title = "A New Estimator of Significance of Correlation in Time Series Data", journal = j-J-COMPUT-BIOL, volume = "8", number = "5", pages = "463--470", month = oct, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753216486", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753216486; https://www.liebertpub.com/doi/pdf/10.1089/106652701753216486", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lin:2001:AAS, author = "Kuang Lin and Alex C. W. May and William R. Taylor", title = "Amino Acid Substitution Matrices from an Artificial Neural Network Model", journal = j-J-COMPUT-BIOL, volume = "8", number = "5", pages = "471--481", month = oct, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753216495", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753216495; https://www.liebertpub.com/doi/pdf/10.1089/106652701753216495", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bader:2001:LTA, author = "David A. Bader and Bernard M. E. Moret and Mi Yan", title = "A Linear-Time Algorithm for Computing Inversion Distance between Signed Permutations with an Experimental Study", journal = j-J-COMPUT-BIOL, volume = "8", number = "5", pages = "483--491", month = oct, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753216503", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753216503; https://www.liebertpub.com/doi/pdf/10.1089/106652701753216503", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Muggleton:2001:GRU, author = "S. H. Muggleton and C. H. Bryant and A. Srinivasan and A. Whittaker and S. Topp and C. Rawlings", title = "Are Grammatical Representations Useful for Learning from Biological Sequence Data? --- a Case Study", journal = j-J-COMPUT-BIOL, volume = "8", number = "5", pages = "493--521", month = oct, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753216512", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753216512; https://www.liebertpub.com/doi/pdf/10.1089/106652701753216512", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Williams:2001:CGO, author = "Glenn A. Williams and Jonathan M. Dugan and Russ B. Altman", title = "Constrained Global Optimization for Estimating Molecular Structure from Atomic Distances", journal = j-J-COMPUT-BIOL, volume = "8", number = "5", pages = "523--547", month = oct, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753216521", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753216521; https://www.liebertpub.com/doi/pdf/10.1089/106652701753216521", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Storey:2001:AVL, author = "John D. Storey and David Siegmund", title = "Approximate {$P$}-Values for Local Sequence Alignments: Numerical Studies", journal = j-J-COMPUT-BIOL, volume = "8", number = "5", pages = "549--556", month = oct, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753216530", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753216530; https://www.liebertpub.com/doi/pdf/10.1089/106652701753216530", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Rocke:2001:MME, author = "David M. Rocke and Blythe Durbin", title = "A Model for Measurement Error for Gene Expression Arrays", journal = j-J-COMPUT-BIOL, volume = "8", number = "6", pages = "557--569", month = nov, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753307485", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753307485; https://www.liebertpub.com/doi/pdf/10.1089/106652701753307485", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Chen:2001:AIP, author = "Ting Chen and Jacob D. Jaffe and George M. Church", title = "Algorithms for Identifying Protein Cross-Links via Tandem Mass Spectrometry", journal = j-J-COMPUT-BIOL, volume = "8", number = "6", pages = "571--583", month = nov, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753307494", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753307494; https://www.liebertpub.com/doi/pdf/10.1089/106652701753307494", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Theilhaber:2001:BEF, author = "Joachim Theilhaber and Steven Bushnell and Amanda Jackson and Rainer Fuchs", title = "{Bayesian} Estimation of Fold-Changes in the Analysis of Gene Expression: The {PFOLD} Algorithm", journal = j-J-COMPUT-BIOL, volume = "8", number = "6", pages = "585--614", month = nov, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753307502", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753307502; https://www.liebertpub.com/doi/pdf/10.1089/106652701753307502", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Just:2001:CCM, author = "Winfried Just", title = "Computational Complexity of Multiple Sequence Alignment with {SP-Score}", journal = j-J-COMPUT-BIOL, volume = "8", number = "6", pages = "615--623", month = nov, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753307511", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753307511; https://www.liebertpub.com/doi/pdf/10.1089/106652701753307511", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wolfinger:2001:AGS, author = "Russell D. Wolfinger and Greg Gibson and Elizabeth D. Wolfinger and Lee Bennett and Hisham Hamadeh and Pierre Bushel and Cynthia Afshari and Richard S. Paules", title = "Assessing Gene Significance from {cDNA} Microarray Expression Data via Mixed Models", journal = j-J-COMPUT-BIOL, volume = "8", number = "6", pages = "625--637", month = nov, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753307520", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753307520; https://www.liebertpub.com/doi/pdf/10.1089/106652701753307520", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Baggerly:2001:IDE, author = "Keith A. Baggerly and Kevin R. Coombes and Kenneth R. Hess and David N. Stivers and Lynne V. Abruzzo and Wei Zhang", title = "Identifying Differentially Expressed Genes in {cDNA} Microarray Experiments", journal = j-J-COMPUT-BIOL, volume = "8", number = "6", pages = "639--659", month = nov, year = "2001", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652701753307539", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652701753307539; https://www.liebertpub.com/doi/pdf/10.1089/106652701753307539", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Sengupta:2002:QCM, author = "Rimli Sengupta and Martin Tompa", title = "Quality Control in Manufacturing Oligo Arrays: a Combinatorial Design Approach", journal = j-J-COMPUT-BIOL, volume = "9", number = "1", pages = "1--22", month = jan, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252833163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252833163; https://www.liebertpub.com/doi/pdf/10.1089/10665270252833163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Rajasekaran:2002:ECP, author = "S. Rajasekaran and X. Jin and J. L. Spouge", title = "The Efficient Computation of Position-Specific Match Scores with the Fast {Fourier} Transform", journal = j-J-COMPUT-BIOL, volume = "9", number = "1", pages = "23--33", month = jan, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252833172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252833172; https://www.liebertpub.com/doi/pdf/10.1089/10665270252833172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Sorenson:2002:PES, author = "Jon M. Sorenson and Teresa Head-Gordon", title = "Protein Engineering Study of Protein {L} by Simulation", journal = j-J-COMPUT-BIOL, volume = "9", number = "1", pages = "35--54", month = jan, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252833181", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252833181; https://www.liebertpub.com/doi/pdf/10.1089/10665270252833181", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Kooperberg:2002:IBC, author = "Charles Kooperberg and Thomas G. Fazzio and Jeffrey J. Delrow and Toshio Tsukiyama", title = "Improved Background Correction for Spotted {DNA} Microarrays", journal = j-J-COMPUT-BIOL, volume = "9", number = "1", pages = "55--66", month = jan, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252833190", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252833190; https://www.liebertpub.com/doi/pdf/10.1089/10665270252833190", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{deJong:2002:MSG, author = "Hidde de Jong", title = "Modeling and Simulation of Genetic Regulatory Systems: a Literature Review", journal = j-J-COMPUT-BIOL, volume = "9", number = "1", pages = "67--103", month = jan, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252833208", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252833208; https://www.liebertpub.com/doi/pdf/10.1089/10665270252833208", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Dougherty:2002:ICA, author = "Edward R. Dougherty and Junior Barrera and Marcel Brun and Seungchan Kim and Roberto M. Cesar and Yidong Chen and Michael Bittner and Jeffrey M. Trent", title = "Inference from Clustering with Application to Gene-Expression Microarrays", journal = j-J-COMPUT-BIOL, volume = "9", number = "1", pages = "105--126", month = jan, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252833217", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252833217; https://www.liebertpub.com/doi/pdf/10.1089/10665270252833217", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Kim:2002:SFS, author = "Seungchan Kim and Edward R. Dougherty and Junior Barrera and Yidong Chen and Michael L. Bittner and Jeffrey M. Trent", title = "Strong Feature Sets from Small Samples", journal = j-J-COMPUT-BIOL, volume = "9", number = "1", pages = "127--146", month = jan, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252833226", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252833226; https://www.liebertpub.com/doi/pdf/10.1089/10665270252833226", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lengauer:2002:PSR, author = "Thomas Lengauer", title = "Preface: Special {RECOMB 2001} Issue", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "147--148", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935386", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/10665270252935386", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Amato:2002:UMP, author = "Nancy M. Amato and Guang Song", title = "Using Motion Planning to Study Protein Folding Pathways", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "149--168", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935395", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935395; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935395", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Barash:2002:CSB, author = "Yoseph Barash and Nir Friedman", title = "Context-Specific {Bayesian} Clustering for Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "169--191", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935403", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935403; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935403", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bilu:2002:AFP, author = "Yonatan Bilu and Michal Linial", title = "The Advantage of Functional Prediction Based on Clustering of Yeast Genes and Its Correlation with Non-Sequence Based Classifications", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "193--210", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935412", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935412; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935412", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Blanchette:2002:APF, author = "Mathieu Blanchette and Benno Schwikowski and Martin Tompa", title = "Algorithms for Phylogenetic Footprinting", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "211--223", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935421", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935421; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935421", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Buhler:2002:FMU, author = "Jeremy Buhler and Martin Tompa", title = "Finding Motifs Using Random Projections", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "225--242", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935430", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935430; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935430", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bundschuh:2002:RSE, author = "Ralf Bundschuh", title = "Rapid Significance Estimation in Local Sequence Alignment with Gaps", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "243--260", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935449", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935449; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935449", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Cowen:2002:PBH, author = "Lenore Cowen and Phil Bradley and Matthew Menke and Jonathan King and Bonnie Berger", title = "Predicting the Beta-Helix Fold from Protein Sequence Data", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "261--276", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935458", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935458; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935458", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Csuros:2002:FRE, author = "Mikl{\'o}s Csur{\"o}s", title = "Fast Recovery of Evolutionary Trees with Thousands of Nodes", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "277--297", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935467", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935467; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935467", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Efrat:2002:GAA, author = "Alon Efrat and Frank Hoffmann and Klaus Kriegel and Christof Schultz and Carola Wenk", title = "Geometric Algorithms for the Analysis of {$2$D}-Electrophoresis Gels", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "299--315", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935476", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935476; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935476", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Filkov:2002:ATM, author = "Vladimir Filkov and Steven Skiena and Jizu Zhi", title = "Analysis Techniques for Microarray Time-Series Data", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "317--330", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935485", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935485; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935485", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Friedman:2002:SEA, author = "Nir Friedman and Matan Ninio and Itsik Pe'er and Tal Pupko", title = "A Structural {EM} Algorithm for Phylogenetic Inference", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "331--353", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935494", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935494; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935494", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Frieze:2002:OSH, author = "Alan M. Frieze and Bjarni V. Halld{\'o}rsson", title = "Optimal Sequencing by Hybridization in Rounds", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "355--369", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935502", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935502; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935502", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Jiang:2002:GED, author = "Tao Jiang and Guohui Lin and Bin Ma and Kaizhong Zhang", title = "A General Edit Distance between {RNA} Structures", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "371--388", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935511", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935511; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935511", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Pachter:2002:AGP, author = "Lior Pachter and Marina Alexandersson and Simon Cawley", title = "Applications of Generalized Pair Hidden {Markov} Models to Alignment and Gene Finding Problems", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "389--399", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935520", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935520; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935520", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Pavlidis:2002:LGF, author = "Paul Pavlidis and Jason Weston and Jinsong Cai and William Stafford Noble", title = "Learning Gene Functional Classifications from Multiple Data Types", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "401--411", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935539", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935539; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935539", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Shamir:2002:LSS, author = "Ron Shamir and Dekel Tsur", title = "Large Scale Sequencing by Hybridization", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "413--428", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935548", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935548; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935548", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Tang:2002:ZFG, author = "Mengxiang Tang and Michael Waterman and Shibu Yooseph", title = "Zinc Finger Gene Clusters and Tandem Gene Duplication", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "429--446", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935557", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935557; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935557", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Thijs:2002:GSM, author = "Gert Thijs and Kathleen Marchal and Magali Lescot and Stephane Rombauts and Bart {De Moor} and Pierre Rouz{\'e} and Yves Moreau", title = "A {Gibbs} Sampling Method to Detect Overrepresented Motifs in the Upstream Regions of Coexpressed Genes", journal = j-J-COMPUT-BIOL, volume = "9", number = "2", pages = "447--464", month = apr, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270252935566", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270252935566; https://www.liebertpub.com/doi/pdf/10.1089/10665270252935566", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Berloff:2002:SMC, author = "Natalia Berloff and Markus Perola and Kenneth Lange", title = "Spline Methods for the Comparison of Physical and Genetic Maps", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "465--475", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138565", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760138565; https://www.liebertpub.com/doi/pdf/10.1089/106652702760138565", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Shen:2002:SPA, author = "Shi-Yi Shen and Jun Yang and Adam Yao and Pei-Ing Hwang", title = "Super Pairwise Alignment {(SPA)}: an Efficient Approach to Global Alignment for Homologous Sequences", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "477--486", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138574", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760138574; https://www.liebertpub.com/doi/pdf/10.1089/106652702760138574", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Zhang:2002:AIC, author = "Jian Zhang", title = "Analysis of Information Content for Biological Sequences", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "487--503", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138583", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760138583; https://www.liebertpub.com/doi/pdf/10.1089/106652702760138583", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Radmacher:2002:PCP, author = "Michael D. Radmacher and Lisa M. McShane and Richard Simon", title = "A Paradigm for Class Prediction Using Gene Expression Profiles", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "505--511", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138592", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760138592; https://www.liebertpub.com/doi/pdf/10.1089/106652702760138592", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Clark:2002:CAG, author = "Terry Clark and Sanggyu Lee and L. Ridgway Scott and San Ming Wang", title = "Computational Analysis of Gene Identification with {SAGE}", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "513--526", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138600", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760138600; https://www.liebertpub.com/doi/pdf/10.1089/106652702760138600", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Sung:2002:CEP, author = "Myong-Hee Sung and Yingdong Zhao and Roland Martin and Richard Simon", title = "{T}-Cell Epitope Prediction with Combinatorial Peptide Libraries", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "527--539", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138619", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760138619; https://www.liebertpub.com/doi/pdf/10.1089/106652702760138619", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Nebel:2002:CPR, author = "Markus E. Nebel", title = "Combinatorial Properties of {RNA} Secondary Structures", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "541--573", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138628", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760138628; https://www.liebertpub.com/doi/pdf/10.1089/106652702760138628", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bailey:2002:EES, author = "Timothy L. Bailey and Michael Gribskov", title = "Estimating and Evaluating the Statistics of Gapped Local-Alignment Scores", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "575--593", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138637", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760138637; https://www.liebertpub.com/doi/pdf/10.1089/106652702760138637", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Anonymous:2002:Ca, author = "Anonymous", title = "Correction", journal = j-J-COMPUT-BIOL, volume = "9", number = "3", pages = "594--595", month = jun, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760138646", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/106652702760138646", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Althaus:2002:CAP, author = "Ernst Althaus and Oliver Kohlbacher and Hans-Peter Lenhof and Peter M{\"u}ller", title = "A Combinatorial Approach to Protein Docking with Flexible Side Chains", journal = j-J-COMPUT-BIOL, volume = "9", number = "4", pages = "597--612", month = aug, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760277336", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760277336; https://www.liebertpub.com/doi/pdf/10.1089/106652702760277336", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Yanikoglu:2002:MEC, author = "Berrin Yanikoglu and Burak Erman", title = "Minimum Energy Configurations of the $2$-Dimensional {HP-Model} of Proteins by Self-Organizing Networks", journal = j-J-COMPUT-BIOL, volume = "9", number = "4", pages = "613--620", month = aug, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760277345", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760277345; https://www.liebertpub.com/doi/pdf/10.1089/106652702760277345", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Horng:2002:RSD, author = "Jorng-Tzong Horng and Hsien-Da Huang and Ming-Hui Jin and Li-Cheng Wu and Shir-Ly Huang", title = "The Repetitive Sequence Database and Mining Putative Regulatory Elements in Gene Promoter Regions", journal = j-J-COMPUT-BIOL, volume = "9", number = "4", pages = "621--640", month = aug, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760277354", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760277354; https://www.liebertpub.com/doi/pdf/10.1089/106652702760277354", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Mercatanti:2002:MPA, author = "Alberto Mercatanti and Giuseppe Rainaldi and Laura Mariani and Roberto Marangoni and Lorenzo Citti", title = "A Method for Prediction of Accessible Sites on an {mRNA} Sequence for Target Selection of Hammerhead Ribozymes", journal = j-J-COMPUT-BIOL, volume = "9", number = "4", pages = "641--653", month = aug, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760277363", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760277363; https://www.liebertpub.com/doi/pdf/10.1089/106652702760277363", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Coombes:2002:IQS, author = "Kevin R. Coombes and W. Edward Highsmith and Tammy A. Krogmann and Keith A. Baggerly and David N. Stivers and Lynne V. Abruzzo", title = "Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density {cDNA} Membrane Arrays", journal = j-J-COMPUT-BIOL, volume = "9", number = "4", pages = "655--669", month = aug, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760277372", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760277372; https://www.liebertpub.com/doi/pdf/10.1089/106652702760277372", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Broet:2002:BHM, author = "Philippe Bro{\"e}t and Sylvia Richardson and Fran{\c{c}}ois Radvanyi", title = "{Bayesian} Hierarchical Model for Identifying Changes in Gene Expression from Microarray Experiments", journal = j-J-COMPUT-BIOL, volume = "9", number = "4", pages = "671--683", month = aug, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760277381", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702760277381; https://www.liebertpub.com/doi/pdf/10.1089/106652702760277381", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Anonymous:2002:Cb, author = "Anonymous", title = "Correction", journal = j-J-COMPUT-BIOL, volume = "9", number = "4", pages = "685--685", month = aug, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702760277390", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/106652702760277390", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Desper:2002:FAP, author = "Richard Desper and Olivier Gascuel", title = "Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle", journal = j-J-COMPUT-BIOL, volume = "9", number = "5", pages = "687--705", month = oct, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702761034136", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702761034136; https://www.liebertpub.com/doi/pdf/10.1089/106652702761034136", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Narasimhan:2002:MPS, author = "Giri Narasimhan and Changsong Bu and Yuan Gao and Xuning Wang and Ning Xu and Kalai Mathee", title = "Mining Protein Sequences for Motifs", journal = j-J-COMPUT-BIOL, volume = "9", number = "5", pages = "707--720", month = oct, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702761034145", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702761034145; https://www.liebertpub.com/doi/pdf/10.1089/106652702761034145", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Aspnes:2002:CTP, author = "James Aspnes and Julia Hartling and Ming-Yang Kao and Junhyong Kim and Gauri Shah", title = "A Combinatorial Toolbox for Protein Sequence Design and Landscape Analysis in the Grand Canonical Model", journal = j-J-COMPUT-BIOL, volume = "9", number = "5", pages = "721--741", month = oct, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702761034154", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702761034154; https://www.liebertpub.com/doi/pdf/10.1089/106652702761034154", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Meidanis:2002:LBR, author = "Jo{\~a}o Meidanis and Maria M. T. Walter and Zanoni Dias", title = "A Lower Bound on the Reversal and Transposition Diameter", journal = j-J-COMPUT-BIOL, volume = "9", number = "5", pages = "743--745", month = oct, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702761034163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702761034163; https://www.liebertpub.com/doi/pdf/10.1089/106652702761034163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Spang:2002:NAR, author = "Rainer Spang and Marc Rehmsmeier and Jens Stoye", title = "A Novel Approach to Remote Homology Detection: Jumping Alignments", journal = j-J-COMPUT-BIOL, volume = "9", number = "5", pages = "747--760", month = oct, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652702761034172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652702761034172; https://www.liebertpub.com/doi/pdf/10.1089/106652702761034172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Robin:2002:OPS, author = "S. Robin and J.-J. Daudin and H. Richard and M.-F. Sagot and S. Schbath", title = "Occurrence Probability of Structured Motifs in Random Sequences", journal = j-J-COMPUT-BIOL, volume = "9", number = "6", pages = "761--773", month = dec, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270260518254", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270260518254; https://www.liebertpub.com/doi/pdf/10.1089/10665270260518254", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Eskin:2002:USM, author = "Eleazar Eskin and William Stafford Noble and Yoram Singer", title = "Using Substitution Matrices to Estimate Probability Distributions for Biological Sequences", journal = j-J-COMPUT-BIOL, volume = "9", number = "6", pages = "775--791", month = dec, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270260518263", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270260518263; https://www.liebertpub.com/doi/pdf/10.1089/10665270260518263", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ljungberg:2002:EAQ, author = "Kajsa Ljungberg and Sverker Holmgren and {\"O}rjan Carlborg", title = "Efficient Algorithms for Quantitative Trait Loci Mapping Problems", journal = j-J-COMPUT-BIOL, volume = "9", number = "6", pages = "793--804", month = dec, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270260518272", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270260518272; https://www.liebertpub.com/doi/pdf/10.1089/10665270260518272", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{York:2002:BEN, author = "Thomas L. York and Richard Durrett and Rasmus Nielsen", title = "{Bayesian} Estimation of the Number of Inversions in the History of Two Chromosomes", journal = j-J-COMPUT-BIOL, volume = "9", number = "6", pages = "805--818", month = dec, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270260518281", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270260518281; https://www.liebertpub.com/doi/pdf/10.1089/10665270260518281", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Raje:2002:DFR, author = "D. V. Raje and H. J. Purohit and R. N. Singh", title = "Distinguishing Features of 16S {rDNA} Gene for Five Dominating Bacterial Genus Observed in Bioremediation", journal = j-J-COMPUT-BIOL, volume = "9", number = "6", pages = "819--829", month = dec, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270260518290", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270260518290; https://www.liebertpub.com/doi/pdf/10.1089/10665270260518290", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Piau:2002:MRS, author = "Didier Piau", title = "Mutation--Replication Statistics of Polymerase Chain Reactions", journal = j-J-COMPUT-BIOL, volume = "9", number = "6", pages = "831--847", month = dec, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270260518308", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270260518308; https://www.liebertpub.com/doi/pdf/10.1089/10665270260518308", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Doniger:2002:PCP, author = "Scott Doniger and Thomas Hofmann and Joanne Yeh", title = "Predicting {CNS} Permeability of Drug Molecules: Comparison of Neural Network and Support Vector Machine Algorithms", journal = j-J-COMPUT-BIOL, volume = "9", number = "6", pages = "849--864", month = dec, year = "2002", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270260518317", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/10665270260518317; https://www.liebertpub.com/doi/pdf/10.1089/10665270260518317", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lu:2003:SAN, author = "Bingwen Lu and Ting Chen", title = "A Suboptimal Algorithm for {{\em {De} Novo\/}} Peptide Sequencing via Tandem Mass Spectrometry", journal = j-J-COMPUT-BIOL, volume = "10", number = "1", pages = "1--12", month = feb, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703763255633", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703763255633; https://www.liebertpub.com/doi/pdf/10.1089/106652703763255633", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Schwartz:2003:RIH, author = "Russell Schwartz and Bjarni V. Halld{\'o}rsson and Vineet Bafna and Andrew G. Clark and Sorin Istrail", title = "Robustness of Inference of Haplotype Block Structure", journal = j-J-COMPUT-BIOL, volume = "10", number = "1", pages = "13--19", month = feb, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703763255642", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703763255642; https://www.liebertpub.com/doi/pdf/10.1089/106652703763255642", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Liu:2003:CCA, author = "Agatha H. Liu and Andrea Califano", title = "{CASTOR}: Clustering Algorithm for Sequence Taxonomical Organization and Relationships", journal = j-J-COMPUT-BIOL, volume = "10", number = "1", pages = "21--45", month = feb, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703763255651", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703763255651; https://www.liebertpub.com/doi/pdf/10.1089/106652703763255651", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Li:2003:IPS, author = "Xueliang Li and Zimao Li and Lusheng Wang", title = "The Inverse Problems for Some Topological Indices in Combinatorial Chemistry", journal = j-J-COMPUT-BIOL, volume = "10", number = "1", pages = "47--55", month = feb, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703763255660", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703763255660; https://www.liebertpub.com/doi/pdf/10.1089/106652703763255660", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Oliveira:2003:CMI, author = "Joseph S. Oliveira and Colin G. Bailey and Janet B. Jones-Oliveira and David A. Dixon and Dean W. Gull and Mary L. Chandler", title = "A Computational Model for the Identification of Biochemical Pathways in the {Krebs} Cycle", journal = j-J-COMPUT-BIOL, volume = "10", number = "1", pages = "57--82", month = feb, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703763255679", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703763255679; https://www.liebertpub.com/doi/pdf/10.1089/106652703763255679", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Chattopadhyay:2003:TCP, author = "Sujay Chattopadhyay and Jayprokas Chakrabarti", title = "Temporal Changes in Phosphoglycerate Kinase Coding Sequences: a Quantitative Measure", journal = j-J-COMPUT-BIOL, volume = "10", number = "1", pages = "83--93", month = feb, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703763255688", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703763255688; https://www.liebertpub.com/doi/pdf/10.1089/106652703763255688", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Aastrand:2003:CNO, author = "Magnus {\AA}strand", title = "Contrast Normalization of Oligonucleotide Arrays", journal = j-J-COMPUT-BIOL, volume = "10", number = "1", pages = "95--102", month = feb, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703763255697", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703763255697; https://www.liebertpub.com/doi/pdf/10.1089/106652703763255697", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Myers:2003:TDF, author = "Gene Myers and Richard Durbin", title = "A Table-Driven, Full-Sensitivity Similarity Search Algorithm", journal = j-J-COMPUT-BIOL, volume = "10", number = "2", pages = "103--117", month = apr, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703321825919", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703321825919; https://www.liebertpub.com/doi/pdf/10.1089/106652703321825919", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Mukherjee:2003:EDS, author = "Sayan Mukherjee and Pablo Tamayo and Simon Rogers and Ryan Rifkin and Anna Engle and Colin Campbell and Todd R. Golub and Jill P. Mesirov", title = "Estimating Dataset Size Requirements for Classifying {DNA} Microarray Data", journal = j-J-COMPUT-BIOL, volume = "10", number = "2", pages = "119--142", month = apr, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703321825928", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703321825928; https://www.liebertpub.com/doi/pdf/10.1089/106652703321825928", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lai:2003:MPM, author = "Yinglei Lai and Deepali Shinde and Norman Arnheim and Fengzhu Sun", title = "The Mutation Process of Microsatellites During the Polymerase Chain Reaction", journal = j-J-COMPUT-BIOL, volume = "10", number = "2", pages = "143--155", month = apr, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703321825937", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703321825937; https://www.liebertpub.com/doi/pdf/10.1089/106652703321825937", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Yang:2003:SMA, author = "Yaning Yang and Josephine Hoh and Clemens Broger and Martin Neeb and Joanne Edington and Klaus Lindpaintner and Jurg Ott", title = "Statistical Methods for Analyzing Microarray Feature Data with Replications", journal = j-J-COMPUT-BIOL, volume = "10", number = "2", pages = "157--169", month = apr, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703321825946", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703321825946; https://www.liebertpub.com/doi/pdf/10.1089/106652703321825946", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wan:2003:DSR, author = "Honghui Wan and Lugang Li and Scott Federhen and John C. Wootton", title = "Discovering Simple Regions in Biological Sequences Associated with Scoring Schemes", journal = j-J-COMPUT-BIOL, volume = "10", number = "2", pages = "171--185", month = apr, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703321825955", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703321825955; https://www.liebertpub.com/doi/pdf/10.1089/106652703321825955", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Eskin:2003:PFC, author = "Eleazar Eskin and William Stafford Noble and Yoram Singer", title = "Protein Family Classification Using Sparse {Markov} Transducers", journal = j-J-COMPUT-BIOL, volume = "10", number = "2", pages = "187--213", month = apr, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703321825964", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703321825964; https://www.liebertpub.com/doi/pdf/10.1089/106652703321825964", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Penchovsky:2003:DLD, author = "Robert Penchovsky and J{\"o}rg Ackermann", title = "{DNA} Library Design for Molecular Computation", journal = j-J-COMPUT-BIOL, volume = "10", number = "2", pages = "215--229", month = apr, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703321825973", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703321825973; https://www.liebertpub.com/doi/pdf/10.1089/106652703321825973", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Hwang:2003:ETP, author = "F. K. Hwang and Y. C. Liu", title = "Error-Tolerant Pooling Designs with Inhibitors", journal = j-J-COMPUT-BIOL, volume = "10", number = "2", pages = "231--236", month = apr, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703321825982", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703321825982; https://www.liebertpub.com/doi/pdf/10.1089/106652703321825982", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Myers:2003:SRI, author = "Eugene W. Myers", title = "Special {RECOMB 2002} Issue", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "237--237", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360687995", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Amato:2003:UMP, author = "Nancy M. Amato and Ken A. Dill and Guang Song", title = "Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "239--255", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Apaydin:2003:SRS, author = "Mehmet Serkan Apaydin and Douglas L. Brutlag and Carlos Guestrin and David Hsu and Jean-Claude Latombe and Chris Varma", title = "Stochastic Roadmap Simulation: an Efficient Representation and Algorithm for Analyzing Molecular Motion", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "257--281", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688011", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Apostolico:2003:MSL, author = "Alberto Apostolico and Mary Ellen Bock and Stefano Lonardi", title = "Monotony of Surprise and Large-Scale Quest for Unusual Words", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "283--311", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688020", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Arndt:2003:DSE, author = "Peter F. Arndt and Christopher B. Burge and Terence Hwa", title = "{DNA} Sequence Evolution with Neighbor-Dependent Mutation", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "313--322", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688039", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bafna:2003:HPP, author = "Vineet Bafna and Dan Gusfield and Giuseppe Lancia and Shibu Yooseph", title = "Haplotyping as Perfect Phylogeny: a Direct Approach", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "323--340", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688048", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Bar-Joseph:2003:CRT, author = "Ziv Bar-Joseph and Georg K. Gerber and David K. Gifford and Tommi S. Jaakkola and Itamar Simon", title = "Continuous Representations of Time-Series Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "341--356", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688057", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Berard:2003:CM, author = "S{\`e}verine B{\'e}rard and Eric Rivals", title = "Comparison of Minisatellites", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "357--372", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688066", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ben-Dor:2003:DLS, author = "Amir Ben-Dor and Benny Chor and Richard Karp and Zohar Yakhini", title = "Discovering Local Structure in Gene Expression Data: The Order-Preserving Submatrix Problem", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "373--384", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688075", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ben-Dor:2003:RSP, author = "Amir Ben-Dor and Richard M. Karp and Benno Schwikowski and Ron Shamir", title = "The Restriction Scaffold Problem", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "385--398", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Buhler:2003:PSI, author = "Jeremy Buhler", title = "Provably Sensitive Indexing Strategies for Biosequence Similarity Search", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "399--417", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688093", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Cohen:2003:NSA, author = "Barry Cohen and Steven Skiena", title = "Natural Selection and Algorithmic Design of {mRNA}", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "419--432", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Dror:2003:BET, author = "Ron O. Dror and Jonathan G. Murnick and Nicola J. Rinaldi and Voichita D. Marinescu and Ryan M. Rifkin and Richard A. Young", title = "{Bayesian} Estimation of Transcript Levels Using a General Model of Array Measurement Noise", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "433--452", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688110", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Durand:2003:TGC, author = "Dannie Durand and David Sankoff", title = "Tests for Gene Clustering", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "453--482", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Halperin:2003:HLT, author = "Eran Halperin and Shay Halperin and Tzvika Hartman and Ron Shamir", title = "Handling Long Targets and Errors in Sequencing by Hybridization", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "483--497", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688138", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Heath:2003:SHC, author = "Samuel A. Heath and Franco P. Preparata and Joel Young", title = "Sequencing by Hybridization by Cooperating Direct and Reverse Spectra", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "499--508", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688147", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lam:2003:PAS, author = "Fumei Lam and Marina Alexandersson and Lior Pachter", title = "Picking Alignments from ({Steiner}) Trees", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "509--520", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Langmead:2003:PIR, author = "Christopher James Langmead and Anthony K. Yan and C. Robertson McClung and Bruce Randall Donald", title = "Phase-Independent Rhythmic Analysis of Genome-Wide Expression Patterns", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "521--536", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Li:2003:SIM, author = "Jia Li and Webb Miller", title = "Significance of Interspecies Matches when Evolutionary Rate Varies", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "537--554", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688174", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Mumey:2003:NMM, author = "Brendan M. Mumey and Brian W. Bailey and Bonnie Kirkpatrick and Algirdas J. Jesaitis and Thomas Angel and Edward A. Dratz", title = "A New Method for Mapping Discontinuous Antibody Epitopes to Reveal Structural Features of Proteins", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "555--567", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688183", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ott:2003:SAA, author = "Jurg Ott and Josephine Hoh", title = "Set Association Analysis of {SNP} Case-Control and Microarray Data", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "569--574", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688192", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Siepel:2003:AES, author = "Adam C. Siepel", title = "An Algorithm to Enumerate Sorting Reversals for Signed Permutations", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "575--597", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688200", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Sinha:2003:DM, author = "Saurabh Sinha", title = "Discriminative Motifs", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "599--615", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688219", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Teodoro:2003:UPF, author = "Miguel L. Teodoro and George N. {Phillips, Jr.} and Lydia E. Kavraki", title = "Understanding Protein Flexibility through Dimensionality Reduction", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "617--634", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688228", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wildenberg:2003:DSV, author = "Andy Wildenberg and Steven Skiena and Pavel Sumazin", title = "Deconvolving Sequence Variation in Mixed {DNA} Populations", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "635--652", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688237", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Zien:2003:MHM, author = "Alexander Zien and Juliane Fluck and Ralf Zimmer and Thomas Lengauer", title = "Microarrays: How Many Do You Need?", journal = j-J-COMPUT-BIOL, volume = "10", number = "3--4", pages = "653--667", month = jun, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/10665270360688246", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Mossel:2003:IRA, author = "Elchanan Mossel", title = "On the Impossibility of Reconstructing Ancestral Data and Phylogenies", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "669--676", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539015", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539015; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539015", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Chung:2003:DMB, author = "Fan Chung and Linyuan Lu and T. Gregory Dewey and David J. Galas", title = "Duplication Models for Biological Networks", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "677--687", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539024", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539024; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539024", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Michailidis:2003:ARB, author = "George Michailidis and Kerby Shedden", title = "The Application of Rule-Based Methods to Class Prediction Problems in Genomics", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "689--698", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539033", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539033; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539033", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wang:2003:RTI, author = "Yonghong Wang and Hongyu Ou and Fengbiao Guo", title = "Recognition of Translation Initiation Sites of Eukaryotic Genes Based on an {EM} Algorithm", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "699--708", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539042", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539042; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539042", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lu:2003:TCO, author = "Wei-Fu Lu and Wen-Lian Hsu", title = "A Test for the Consecutive Ones Property on Noisy Data --- Application to Physical Mapping and Sequence Assembly", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "709--735", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539051", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539051; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539051", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Jonsson:2003:AML, author = "Henrik J{\"o}nsson and Bo S{\"o}derberg", title = "An Approximate Maximum Likelihood Approach, Applied to Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "737--749", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539060", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539060; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539060", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Faller:2003:NDM, author = "D. Faller and H. U. Voss and J. Timmer and U. Hobohm", title = "Normalization of {DNA-Microarray} Data by Nonlinear Correlation Maximization", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "751--762", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539079", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539079; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539079", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Piccolboni:2003:CFC, author = "Antonio Piccolboni and Dan Gusfield", title = "On the Complexity of Fundamental Computational Problems in Pedigree Analysis", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "763--773", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539088", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539088; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539088", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Heath:2003:SSS, author = "Lenwood S. Heath and John Paul C. Vergara", title = "Sorting by Short Swaps", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "775--789", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539097", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539097; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539097", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Pisanti:2003:PMP, author = "N. Pisanti and R. Marangoni and P. Ferragina and A. Frangioni and A. Savona and C. Pisanelli and F. Luccio", title = "{PaTre}: a Method for Paralogy Trees Construction", journal = j-J-COMPUT-BIOL, volume = "10", number = "5", pages = "791--802", month = oct, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322539105", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322539105; https://www.liebertpub.com/doi/pdf/10.1089/106652703322539105", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Zhang:2003:EPA, author = "Yu Zhang and Michael S. Waterman", title = "An {Eulerian} Path Approach to Global Multiple Alignment for {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "803--819", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756096; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756096", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Shatkay:2003:MBL, author = "Hagit Shatkay and Ronen Feldman", title = "Mining the Biomedical Literature in the Genomic Era: An Overview", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "821--855", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756104", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756104; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756104", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Liao:2003:CPS, author = "Li Liao and William Stafford Noble", title = "Combining Pairwise Sequence Similarity and Support Vector Machines for Detecting Remote Protein Evolutionary and Structural Relationships", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "857--868", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756113; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lunter:2003:EAS, author = "G. A. Lunter and I. Mikl{\'o}s and Y. S. Song and J. Hein", title = "An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "869--889", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756122", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756122; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756122", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Kerr:2003:LMM, author = "M. Kathleen Kerr", title = "Linear Models for Microarray Data Analysis: Hidden Similarities and Differences", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "891--901", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756131", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756131; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756131", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Navarro:2003:FSC, author = "Gonzalo Navarro and Mathieu Raffinot", title = "Fast and Simple Character Classes and Bounded Gaps Pattern Matching, with Applications to Protein Searching", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "903--923", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756140", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756140; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756140", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Lilien:2003:PDC, author = "Ryan H. Lilien and Hany Farid and Bruce R. Donald", title = "Probabilistic Disease Classification of Expression-Dependent Proteomic Data from Mass Spectrometry of Human Serum", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "925--946", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756159", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756159; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756159", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Deng:2003:PPF, author = "Minghua Deng and Kui Zhang and Shipra Mehta and Ting Chen and Fengzhu Sun", title = "Prediction of Protein Function Using Protein--Protein Interaction Data", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "947--960", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756168", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756168; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756168", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Segal:2003:RAM, author = "Mark R. Segal and Kam D. Dahlquist and Bruce R. Conklin", title = "Regression Approaches for Microarray Data Analysis", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "961--980", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756177", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756177; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756177", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Ieong:2003:PRS, author = "Samuel Ieong and Ming-Yang Kao and Tak-Wah Lam and Wing-Kin Sung and Siu-Ming Yiu", title = "Predicting {RNA} Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "981--995", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756186", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756186; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756186", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Veerassamy:2003:TPM, author = "Shalini Veerassamy and Andrew Smith and Elisabeth R. M. Tillier", title = "A Transition Probability Model for Amino Acid Substitutions from Blocks", journal = j-J-COMPUT-BIOL, volume = "10", number = "6", pages = "997--1010", month = dec, year = "2003", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652703322756195", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652703322756195; https://www.liebertpub.com/doi/pdf/10.1089/106652703322756195", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Huang:2004:DLS, author = "Haiyan Huang and Ming-Chih J. Kao and Xianghong Zhou and Jun S. Liu and Wing H. Wong", title = "Determination of Local Statistical Significance of Patterns in {Markov} Sequences with Application to Promoter Element Identification", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "1--14", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416858", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416858; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416858", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Apostolico:2004:IPM, author = "Alberto Apostolico and Laxmi Parida", title = "Incremental Paradigms of Motif Discovery", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "15--25", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416867", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416867; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416867", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Caprara:2004:OPS, author = "Alberto Caprara and Robert Carr and Sorin Istrail and Giuseppe Lancia and Brian Walenz", title = "1001 Optimal {PDB} Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "27--52", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416876", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416876; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416876", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wagner:2004:RPL, author = "Andreas Wagner", title = "Reconstructing Pathways in Large Genetic Networks from Genetic Perturbations", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "53--60", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416885", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416885; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416885", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Spiro:2004:LAM, author = "Peter A. Spiro and Natasa Macura", title = "A Local Alignment Metric for Accelerating Biosequence Database Search", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "61--82", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416894", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416894; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416894", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Shatsky:2004:FAF, author = "Maxim Shatsky and Ruth Nussinov and Haim J. Wolfson", title = "{FlexProt}: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "83--106", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416902", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416902; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416902", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Cheung:2004:URS, author = "Leo Wang-Kit Cheung", title = "Use of Runs Statistics for Pattern Recognition in Genomic {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "107--124", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416911", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416911; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416911", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Sung:2004:GCE, author = "Myong-Hee Sung and Richard Simon", title = "Genomewide Conserved Epitope Profiles of {HIV-1} Predicted by Biophysical Properties of {MHC} Binding Peptides", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "125--145", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416920", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416920; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416920", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Zhou:2004:GCB, author = "Xiaobo Zhou and Xiaodong Wang and Edward R. Dougherty and Daniel Russ and Edward Suh", title = "Gene Clustering Based on Clusterwide Mutual Information", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "147--161", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416939", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416939; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416939", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Adamiak:2004:AAN, author = "R. W. Adamiak and J. Blazewicz and P. Formanowicz and Z. Gdaniec and M. Kasprzak and M. Popenda and M. Szachniuk", title = "An Algorithm for an Automatic {NOE} Pathways Analysis of {$2$D} {NMR} Spectra of {RNA} Duplexes", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "163--179", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416948", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416948; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416948", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Wistrand:2004:TPP, author = "Markus Wistrand and Erik L. L. Sonnhammer", title = "Transition Priors for Protein Hidden {Markov} Models: An Empirical Study towards Maximum Discrimination", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "181--193", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416957", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416957; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416957", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Makarenkov:2004:PTR, author = "Vladimir Makarenkov and Pierre Legendre", title = "From a Phylogenetic Tree to a Reticulated Network", journal = j-J-COMPUT-BIOL, volume = "11", number = "1", pages = "195--212", month = jan, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/106652704773416966", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/106652704773416966; https://www.liebertpub.com/doi/pdf/10.1089/106652704773416966", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2004", } @Article{Miller:2004:SRI, author = "Webb Miller and Martin Vingron", title = "Special {RECOMB 2003} Issue", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "213--213", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410427", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Li:2004:EVD, author = "Wentian Li and Fengzhu Sun and Ivo Grosse", title = "Extreme Value Distribution Based Gene Selection Criteria for Discriminant Microarray Data Analysis Using Logistic Regression", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "215--226", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410445", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Krishnapuram:2004:JCF, author = "Balaji Krishnapuram and Lawrence Carin and Alexander J. Hartemink", title = "Joint Classifier and Feature Optimization for Comprehensive Cancer Diagnosis Using Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "227--242", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410463", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Yeang:2004:PNM, author = "Chen-Hsiang Yeang and Trey Ideker and Tommi Jaakkola", title = "Physical Network Models", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "243--262", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410382", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Fishelson:2004:OEG, author = "Maayan Fishelson and Dan Geiger", title = "Optimizing Exact Genetic Linkage Computations", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "263--275", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410409", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Langmead:2004:PTN, author = "Christopher James Langmead and Anthony Yan and Ryan Lilien and Lincong Wang and Bruce Randall Donald", title = "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated {NMR} Resonance Assignments", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "277--298", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410436", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Lotan:2004:APS, author = "Itay Lotan and Fabian Schwarzer", title = "Approximation of Protein Structure for Fast Similarity Measures", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "299--317", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410355", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Kellis:2004:MCG, author = "Manolis Kellis and Nick Patterson and Bruce Birren and Bonnie Berger and Eric S. Lander", title = "Methods in Comparative Genomics: Genome Correspondence, Gene Identification and Regulatory Motif Discovery", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "319--355", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410319", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Tanay:2004:MMI, author = "Amos Tanay and Ron Shamir", title = "Multilevel Modeling and Inference of Transcription Regulation", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "357--375", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410364", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Yeo:2004:MEM, author = "Gene Yeo and Christopher B. Burge", title = "Maximum Entropy Modeling of Short Sequence Motifs with Applications to {RNA} Splicing Signals", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "377--394", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410418", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Roskin:2004:SFD, author = "Krishna M. Roskin and Mark Diekhans and David Haussler", title = "Score Functions for Determining Regional Conservation in Two-Species Local Alignments", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "395--411", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410328", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Siepel:2004:CPH, author = "Adam Siepel and David Haussler", title = "Combining Phylogenetic and Hidden {Markov} Models in Biosequence Analysis", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "413--428", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410472", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Kahng:2004:SHD, author = "Andrew B. Kahng and Ion I. M{\u{a}}ndoiu and Pavel A. Pevzner and Sherief Reda and Alexander Z. Zelikovsky", title = "Scalable Heuristics for Design of {DNA} Probe Arrays", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "429--447", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410391", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Akutsu:2004:EEM, author = "Tatsuya Akutsu", title = "Efficient Extraction of Mapping Rules of Atoms from Enzymatic Reaction Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "449--462", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410337", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Deng:2004:IPM, author = "Minghua Deng and Ting Chen and Fengzhu Sun", title = "An Integrated Probabilistic Model for Functional Prediction of Proteins", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "463--475", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410346", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Ben-Dor:2004:TOM, author = "Amir Ben-Dor and Tzvika Hartman and Richard M. Karp and Benno Schwikowski and Roded Sharan and Zohar Yakhini", title = "Towards Optimally Multiplexed Applications of Universal Arrays", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "476--492", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410373", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Greenspan:2004:MBI, author = "Gideon Greenspan and Dan Geiger", title = "Model-Based Inference of Haplotype Block Variation", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "493--504", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410300", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Li:2004:HRS, author = "Lei M. Li and Jong Hyun Kim and Michael S. Waterman", title = "Haplotype Reconstruction from {SNP} Alignment", journal = j-J-COMPUT-BIOL, volume = "11", number = "2--3", pages = "505--516", month = mar, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/1066527041410454", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2004", } @Article{Benham:2004:ASI, author = "Craig J. Benham and Chengpeng Bi", title = "The Analysis of Stress-Induced Duplex Destabilization in Long Genomic {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "519--543", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.519", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.519; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.519", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Janes:2004:CSR, author = "Kevin A. Janes and Jason R. Kelly and Suzanne Gaudet and John G. Albeck and Peter K. Sorger and Douglas A. Lauffenburger", title = "Cue-Signal-Response Analysis of {TNF-Induced} Apoptosis by Partial Least Squares Regression of Dynamic Multivariate Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "544--561", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.544", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.544; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.544", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Wu:2004:MPM, author = "Rongling Wu and Chang-Xing Ma and George Casella", title = "A Mixed Polyploid Model for Linkage Analysis in Outcrossing Tetraploids Using a Pseudo-Test Backcross Design", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "562--580", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.562", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.562; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.562", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Helman:2004:BNC, author = "Paul Helman and Robert Veroff and Susan R. Atlas and Cheryl Willman", title = "A {Bayesian} Network Classification Methodology for Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "581--615", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.581", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.581; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.581", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Booth:2004:ESA, author = "Hilary S. Booth and John H. Maindonald and Susan R. Wilson and Jill E. Gready", title = "An Efficient {$Z$}-Score Algorithm for Assessing Sequence Alignments", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "616--625", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.616", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.616; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.616", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Levy:2004:CDD, author = "Dan Levy and Mariel Vazquez and Michael Cornforth and Bradford Loucas and Rainer K. Sachs and Javier Arsuaga", title = "Comparing {DNA} Damage-Processing Pathways by Computer Analysis of Chromosome Painting Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "626--641", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.626", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.626; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.626", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Ku:2004:CLL, author = "Jason Ku and Xiao-Jiang Feng and Herschel Rabitz", title = "Closed-Loop Learning Control of Bio-Networks", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "642--659", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.642", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.642; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.642", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Giurcarneanu:2004:FIG, author = "Ciprian Doru Giurc{\u{a}}rneanu and Ioan T{\u{a}}bu{\c{s}} and Jaakko Astola and Juha Ollila and Mauno Vihinen", title = "Fast Iterative Gene Clustering Based on Information Theoretic Criteria for Selecting the Cluster Structure", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "660--682", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.660", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.660; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.660", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Zhihua:2004:TQP, author = "Lin Zhihua and Wu Yuzhang and Zhu Bo and Ni Bing and Wang Li", title = "Toward the Quantitative Prediction of {T}-Cell Epitopes: {QSAR} Studies on Peptides Having Affinity with the Class {I} {MHC} Molecular {HLA-A*0201}", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "683--694", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.683", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.683; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.683", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Bergemann:2004:SDA, author = "T. L. Bergemann and R. J. Laws and F. Quiaoit and L. P. Zhao", title = "A Statistically Driven Approach for Image Segmentation and Signal Extraction in {cDNA} Microarrays", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "695--713", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.695", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.695; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.695", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Wang:2004:SSI, author = "Sue-Jane Wang and James J. Chen", title = "Sample Size for Identifying Differentially Expressed Genes in Microarray Experiments", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "714--726", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.714", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.714; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.714", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Galtier:2004:MMM, author = "N. Galtier and A. Jean-Marie", title = "{Markov}-Modulated {Markov} Chains and the Covarion Process of Molecular Evolution", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "727--733", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.727", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.727; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.727", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Roberts:2004:PSA, author = "Michael Roberts and Brian R. Hunt and James A. Yorke and Randall A. Bolanos and Arthur L. Delcher", title = "A Preprocessor for Shotgun Assembly of Large Genomes", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "734--752", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.734", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.734; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.734", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Preparata:2004:DSH, author = "Franco P. Preparata and John S. Oliver", title = "{DNA} Sequencing by Hybridization Using Semi-Degenerate Bases", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "753--765", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.753", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.753; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.753", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Berman:2004:FOG, author = "Piotr Berman and Paul Bertone and Bhaskar Dasgupta and Mark Gerstein and Ming-Yang Kao and Michael Snyder", title = "Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search", journal = j-J-COMPUT-BIOL, volume = "11", number = "4", pages = "766--785", month = aug, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.766", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.766; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.766", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Jia:2004:NSF, author = "Yuting Jia and T. Gregory Dewey and Ilya N. Shindyalov and Philip E. Bourne", title = "A New Scoring Function and Associated Statistical Significance for Structure Alignment by {CE}", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "787--799", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.787", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.787; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.787", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Shatkay:2004:TEA, author = "Hagit Shatkay and Jason Miller and Clark Mobarry and Michael Flanigan and Shibu Yooseph and Granger Sutton", title = "{ThurGood}: Evaluating Assembly-to-Assembly Mapping", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "800--811", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.800", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.800; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.800", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Oliveira:2004:HTA, author = "Joseph S. Oliveira and Janet B. Jones-Oliveira and David A. Dixon and Colin G. Bailey and Dean W. Gull", title = "Hyperdigraph-Theoretic Analysis of the {EGFR} Signaling Network: Initial Steps Leading to {GTP:Ras} Complex Formation", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "812--842", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.812", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.812; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.812", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Heger:2004:ADV, author = "Andreas Heger and Michael Lappe and Liisa Holm", title = "Accurate Detection of Very Sparse Sequence Motifs", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "843--857", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.843", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.843; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.843", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Bafna:2004:NEC, author = "Vineet Bafna and Dan Gusfield and Sridhar Hannenhalli and Shibu Yooseph", title = "A Note on Efficient Computation of Haplotypes via Perfect Phylogeny", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "858--866", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.858", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.858; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.858", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Bejerano:2004:EEV, author = "Gill Bejerano and Nir Friedman and Naftali Tishby", title = "Efficient Exact $p$-Value Computation for Small Sample, Sparse, and Surprising Categorical Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "867--886", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.867", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.867; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.867", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Figueroa:2004:CBF, author = "Andres Figueroa and James Borneman and Tao Jiang", title = "Clustering Binary Fingerprint Vectors with Missing Values for {DNA} Array Data Analysis", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "887--901", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.887", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.887; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.887", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Lotan:2004:ADS, author = "Itay Lotan and Fabian Schwarzer and Dan Halperin and Jean-Claude Latombe", title = "Algorithm and Data Structures for Efficient Energy Maintenance during {Monte Carlo} Simulation of Proteins", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "902--932", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.902", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.902; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.902", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Alkan:2004:RUC, author = "Can Alkan and Evan E. Eichler and Jeffrey A. Bailey and S. Cenk {\c{S}}ahinalp and Eray T{\"u}z{\"u}n", title = "The Role of Unequal Crossover in Alpha-Satellite {DNA} Evolution: a Computational Analysis", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "933--944", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.933", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.933; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.933", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Smith:2004:TQC, author = "Kaleigh Smith and Mike Hallett", title = "Towards Quality Control for {DNA} Microarrays", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "945--970", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.945", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.945; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.945", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Bay:2004:TAB, author = "S. D. Bay and L. Chrisman and A. Pohorille and J. Shrager", title = "Temporal Aggregation Bias and Inference of Causal Regulatory Networks", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "971--985", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.971", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.971; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.971", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Ye:2004:AMP, author = "Jieping Ye and Ravi Janardan", title = "Approximate Multiple Protein Structure Alignment Using the Sum-of-Pairs Distance", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "986--1000", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.986", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.986; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.986", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Csuros:2004:PGI, author = "Mikl{\'o}s Cs{\"u}r{\"o}s and Aleksandar Milosavljevic", title = "Pooled Genomic Indexing {(PGI)}: Analysis and Design of Experiments", journal = j-J-COMPUT-BIOL, volume = "11", number = "5", pages = "1001--1021", month = oct, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1001", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1001; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1001", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2004", } @Article{Nuel:2004:LSL, author = "G. Nuel", title = "{LD-SPatt}: Large Deviations Statistics for Patterns on {Markov} Chains", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1023--1033", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1023; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1023", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Gat-Viks:2004:MAH, author = "Irit Gat-Viks and Amos Tanay and Ron Shamir", title = "Modeling and Analysis of Heterogeneous Regulation in Biological Networks", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1034--1049", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1034", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1034; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1034", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Eres:2004:PPD, author = "Revital Eres and Gad M. Landau and Laxmi Parida", title = "Permutation Pattern Discovery in Biosequences", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1050--1060", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1050", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1050; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1050", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Comin:2004:PCM, author = "Matteo Comin and Concettina Guerra and Giuseppe Zanotti", title = "{PROuST}: a Comparison Method of Three-Dimensional Structures of Proteins Using Indexing Techniques", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1061--1072", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1061", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1061; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1061", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Bhattacharyya:2004:RSH, author = "C. Bhattacharyya and L. R. Grate and M. I. Jordan and L. {El Ghaoui} and I. S. Mian", title = "Robust Sparse Hyperplane Classifiers: Application to Uncertain Molecular Profiling Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1073--1089", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Chiappetta:2004:BSS, author = "P. Chiappetta and M. C. Roubaud and B. Torr{\'e}sani", title = "Blind Source Separation and the Analysis of Microarray Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1090--1109", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1090", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1090; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1090", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Bocker:2004:SCU, author = "Sebastian B{\"o}cker", title = "Sequencing from Compomers: Using Mass Spectrometry for {DNA} {\em de novo\/} Sequencing of 200+ nt", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1110--1134", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1110", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1110; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1110", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Dejori:2004:IIP, author = "Math{\"a}us Dejori and Martin Stetter", title = "Identifying Interventional and Pathogenic Mechanisms by Generative Inverse Modeling of Gene Expression Profiles", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1135--1148", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1135", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1135; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1135", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Palazoglu:2004:FDP, author = "Ahmet Palazoglu and Attila Gursoy and Yaman Arkun and Burak Erman", title = "Folding Dynamics of Proteins from Denatured to Native State: Principal Component Analysis", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1149--1168", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1149; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1149", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Barash:2004:SDS, author = "Danny Barash", title = "Spectral Decomposition for the Search and Analysis of {RNA} Secondary Structure", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1169--1174", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1169", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1169; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1169", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Ge:2004:EBS, author = "Nanxiang Ge and Charles B. Epstein", title = "An Empirical {Bayesian} Significance Test of {cDNA} Library Data", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1175--1188", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1175", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1175; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1175", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Conklin:2004:RHC, author = "Darrell Conklin", title = "Recognition of the Helical Cytokine Fold", journal = j-J-COMPUT-BIOL, volume = "11", number = "6", pages = "1189--1200", month = dec, year = "2004", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2004.11.1189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2004.11.1189; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2004.11.1189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2005", } @Article{Rodin:2005:MGE, author = "Andrei Rodin and Thomas H. {Mosley, Jr.} and Andrew G. Clark and Charles F. Sing and Eric Boerwinkle", title = "Mining Genetic Epidemiology Data with {Bayesian} Networks Application to {\em {APOE}\/} Gene Variation and Plasma Lipid Levels", journal = j-J-COMPUT-BIOL, volume = "12", number = "1", pages = "1--11", month = feb, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2005", } @Article{Yona:2005:URH, author = "Golan Yona and Klara Kedem", title = "The {URMS-RMS} Hybrid Algorithm for Fast and Sensitive Local Protein Structure Alignment", journal = j-J-COMPUT-BIOL, volume = "12", number = "1", pages = "12--32", month = feb, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.12", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.12; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.12", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2005", } @Article{Nedelec:2005:PAA, author = "Elodie N{\'e}d{\'e}lec and Thomas Moncion and Elisabeth Gassiat and Bruno Bossard and Guillemette Duchateau-Nguyen and Alain Denise and Michel Termier", title = "A Pairwise Alignment Algorithm Which Favors Clusters of Blocks", journal = j-J-COMPUT-BIOL, volume = "12", number = "1", pages = "33--47", month = feb, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.33", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.33; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.33", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2005", } @Article{Zwolak:2005:PEM, author = "Jason W. Zwolak and John J. Tyson and Layne T. Watson", title = "Parameter Estimation for a Mathematical Model of the Cell Cycle in Frog Eggs", journal = j-J-COMPUT-BIOL, volume = "12", number = "1", pages = "48--63", month = feb, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.48", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.48; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.48", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2005", } @Article{Blekas:2005:MBP, author = "Konstantinos Blekas and Dimitrios I. Fotiadis and Aristidis Likas", title = "Motif-Based Protein Sequence Classification Using Neural Networks", journal = j-J-COMPUT-BIOL, volume = "12", number = "1", pages = "64--82", month = feb, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.64", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.64; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.64", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2005", } @Article{Clote:2005:EAC, author = "P. Clote", title = "An Efficient Algorithm to Compute the Landscape of Locally Optimal {RNA} Secondary Structures with Respect to the {Nussinov--Jacobson} Energy Model", journal = j-J-COMPUT-BIOL, volume = "12", number = "1", pages = "83--101", month = feb, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.83", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.83; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.83", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2005", } @Article{Lin:2005:EAS, author = "Ying Chih Lin and Chin Lung Lu and Hwan-You Chang and Chuan Yi Tang", title = "An Efficient Algorithm for Sorting by Block-Interchanges and Its Application to the Evolution of Vibrio Species", journal = j-J-COMPUT-BIOL, volume = "12", number = "1", pages = "102--112", month = feb, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.102; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.102", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2005", } @Article{Pradines:2005:APL, author = "Jo{\"e}l R. Pradines and Victor Farutin and Steve Rowley and Vlado Dan{\v{c}}{\'\i}k", title = "Analyzing Protein Lists with Large Networks: Edge-Count Probabilities in Random Graphs with Given Expected Degrees", journal = j-J-COMPUT-BIOL, volume = "12", number = "2", pages = "113--128", month = mar, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2005", } @Article{Chen:2005:MRP, author = "Zhi-Zhong Chen and Guohui Lin and Romeo Rizzi and Jianjun Wen and Dong Xu and Ying Xu and Tao Jiang", title = "More Reliable Protein {NMR} Peak Assignment via Improved $2$-Interval Scheduling", journal = j-J-COMPUT-BIOL, volume = "12", number = "2", pages = "129--146", month = mar, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2005", } @Article{Song:2005:CMA, author = "Yun S. Song and Jotun Hein", title = "Constructing Minimal Ancestral Recombination Graphs", journal = j-J-COMPUT-BIOL, volume = "12", number = "2", pages = "147--169", month = mar, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.147", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.147; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.147", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2005", } @Article{Li:2005:EBP, author = "Lei M. Li and Henry Horng-Shing Lu", title = "Explore Biological Pathways from Noisy Array Data by Directed Acyclic {Boolean} Networks", journal = j-J-COMPUT-BIOL, volume = "12", number = "2", pages = "170--185", month = mar, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.170", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.170; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.170", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2005", } @Article{Hobolth:2005:AHM, author = "Asger Hobolth and Jens Ledet Jensen", title = "Applications of Hidden {Markov} Models for Characterization of Homologous {DNA} Sequences with a Common Gene", journal = j-J-COMPUT-BIOL, volume = "12", number = "2", pages = "186--203", month = mar, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.186", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.186; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.186", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2005", } @Article{Sturmfels:2005:TIPa, author = "Bernd Sturmfels and Seth Sullivant", title = "Toric Ideals of Phylogenetic Invariants", journal = j-J-COMPUT-BIOL, volume = "12", number = "2", pages = "204--228", month = mar, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.204", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.204; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.204", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2005", } @Article{Xing:2005:SMC, author = "Biao Xing and Mark J. van der Laan", title = "A Statistical Method for Constructing Transcriptional Regulatory Networks Using Gene Expression and Sequence Data", journal = j-J-COMPUT-BIOL, volume = "12", number = "2", pages = "229--246", month = mar, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.229", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.229; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.229", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2005", } @Article{Nov:2005:MAP, author = "Yuval Nov and Lawrence M. Wein", title = "Modeling and Analysis of Protein Design under Resource Constraints", journal = j-J-COMPUT-BIOL, volume = "12", number = "2", pages = "247--282", month = mar, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.247", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.247; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.247", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2005", } @Article{Wendl:2005:PAC, author = "Michael C. Wendl", title = "Probabilistic Assessment of Clone Overlaps in {DNA} Fingerprint Mapping via a Priori Models", journal = j-J-COMPUT-BIOL, volume = "12", number = "3", pages = "283--297", month = apr, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.283", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.283; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.283", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 April 2005", } @Article{Jia:2005:RPM, author = "Yuting Jia and T. Gregory Dewey", title = "A Random Polymer Model of the Statistical Significance of Structure Alignment", journal = j-J-COMPUT-BIOL, volume = "12", number = "3", pages = "298--313", month = apr, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.298", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.298; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.298", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 April 2005", } @Article{Hertzberg:2005:FMP, author = "Libi Hertzberg and Or Zuk and Gad Getz and Eytan Domany", title = "Finding Motifs in Promoter Regions", journal = j-J-COMPUT-BIOL, volume = "12", number = "3", pages = "314--330", month = apr, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.314", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.314; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.314", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 April 2005", } @Article{Leung:2005:NCP, author = "Ming-Ying Leung and Kwok Pui Choi and Aihua Xia and Louis H. Y. Chen", title = "Nonrandom Clusters of Palindromes in Herpesvirus Genomes", journal = j-J-COMPUT-BIOL, volume = "12", number = "3", pages = "331--354", month = apr, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.331", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.331; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.331", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 April 2005", } @Article{Wagner:2005:LRM, author = "Michael Wagner and Rafa{\l} Adamczak and Aleksey Porollo and Jaros{\l}aw Meller", title = "Linear Regression Models for Solvent Accessibility Prediction in Proteins", journal = j-J-COMPUT-BIOL, volume = "12", number = "3", pages = "355--369", month = apr, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.355", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.355; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.355", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 April 2005", } @Article{Li:2005:EHT, author = "Lang Li and Huidong Shi and Constantin Yiannoutsos and Tim Hui-Ming Huang and Kenneth P. Nephew", title = "Epigenetic Hypothesis Tests for Methylation and Acetylation in a Triple Microarray System", journal = j-J-COMPUT-BIOL, volume = "12", number = "3", pages = "370--390", month = apr, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.370", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.370; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.370", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 April 2005", } @Article{Zhang:2005:BNI, author = "Dabao Zhang and Martin T. Wells and Christine D. Smart and William E. Fry", title = "{Bayesian} Normalization and Identification for Differential Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "12", number = "4", pages = "391--406", month = may, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.391", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.391; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.391", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2005", } @Article{Lippert:2005:SEW, author = "Ross A. Lippert", title = "Space-Efficient Whole Genome Comparisons with {Burrows--Wheeler} Transforms", journal = j-J-COMPUT-BIOL, volume = "12", number = "4", pages = "407--415", month = may, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.407", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.407; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.407", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2005", } @Article{Keich:2005:SFA, author = "Uri Keich", title = "{sFFT}: a Faster Accurate Computation of the $p$-Value of the Entropy Score", journal = j-J-COMPUT-BIOL, volume = "12", number = "4", pages = "416--430", month = may, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.416", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.416; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.416", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2005", } @Article{Linhart:2005:DPD, author = "Chaim Linhart and Ron Shamir", title = "The Degenerate Primer Design Problem: Theory and Applications", journal = j-J-COMPUT-BIOL, volume = "12", number = "4", pages = "431--456", month = may, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.431", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.431; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.431", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2005", } @Article{Sturmfels:2005:TIPb, author = "Bernd Sturmfels and Seth Sullivant", title = "Toric Ideals of Phylogenetic Invariants", journal = j-J-COMPUT-BIOL, volume = "12", number = "4", pages = "457--481", month = may, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.457", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.457; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.457", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2005", } @Article{Pounds:2005:SDE, author = "Stan Pounds and Cheng Cheng", title = "Statistical Development and Evaluation of Microarray Gene Expression Data Filters", journal = j-J-COMPUT-BIOL, volume = "12", number = "4", pages = "482--495", month = may, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.482", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.482; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.482", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2005", } @Article{Dew:2005:TAM, author = "Ian M. Dew and Brian Walenz and Granger Sutton", title = "A Tool for Analyzing Mate Pairs in Assemblies {(TAMPA)}", journal = j-J-COMPUT-BIOL, volume = "12", number = "5", pages = "497--513", month = jun, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.497", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.497; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.497", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 June 2005", } @Article{Sharan:2005:MSG, author = "Roded Sharan and Jens Gramm and Zohar Yakhini and Amir Ben-Dor", title = "Multiplexing Schemes for Generic {SNP} Genotyping Assays", journal = j-J-COMPUT-BIOL, volume = "12", number = "5", pages = "514--533", month = jun, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.514", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.514; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.514", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 June 2005", } @Article{Berrar:2005:STA, author = "Daniel Berrar and Brian Sturgeon and Ian Bradbury and C. Stephen Downes and Werner Dubitzky", title = "Survival Trees for Analyzing Clinical Outcome in Lung Adenocarcinomas Based on Gene Expression Profiles: Identification of Neogenin and Diacylglycerol Kinase $ \alpha $ Expression as Critical Factors", journal = j-J-COMPUT-BIOL, volume = "12", number = "5", pages = "534--544", month = jun, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.534", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.534; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.534", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 June 2005", } @Article{Dehnert:2005:GPB, author = "Manuel Dehnert and Rainer Plaumann and Werner E. Helm and Marc-Th. H{\"u}tt", title = "Genome Phylogeny Based on Short-Range Correlations in {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "12", number = "5", pages = "545--553", month = jun, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.545", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.545; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.545", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 June 2005", } @Article{Schuemie:2005:WSD, author = "Martijn J. Schuemie and Jan A. Kors and Barend Mons", title = "Word Sense Disambiguation in the Biomedical Domain: An Overview", journal = j-J-COMPUT-BIOL, volume = "12", number = "5", pages = "554--565", month = jun, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.554", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.554; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.554", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 June 2005", } @Article{Gusfield:2005:PSR, author = "Dan Gusfield", title = "Preface: Special {RECOMB 2004} Issue", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "567--568", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.567", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.567", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Bailey-Kellogg:2005:RGA, author = "Chris Bailey-Kellogg and Sheetal Chainraj and Gopal Pandurangan", title = "A Random Graph Approach to {NMR} Sequential Assignment", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "569--583", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.569", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.569; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.569", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Beerenwinkel:2005:LME, author = "Niko Beerenwinkel and J{\"o}rg Rahnenf{\"u}hrer and Martin D{\"a}umer and Daniel Hoffmann and Rolf Kaiser and Joachim Selbig and Thomas Lengauer", title = "Learning Multiple Evolutionary Pathways from Cross-Sectional Data", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "584--598", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.584", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.584; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.584", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Chatterji:2005:LMO, author = "Sourav Chatterji and Lior Pachter", title = "Large Multiple Organism Gene Finding by Collapsed {Gibbs} Sampling", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "599--608", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.599", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.599; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.599", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Erdmann:2005:PSK, author = "Michael A. Erdmann", title = "Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "609--637", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.609", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.609; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.609", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{He:2005:ICG, author = "Xin He and Michael H. Goldwasser", title = "Identifying Conserved Gene Clusters in the Presence of Homology Families", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "638--656", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.638", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.638; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.638", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Huan:2005:CGR, author = "Jun Huan and Deepak Bandyopadhyay and Wei Wang and Jack Snoeyink and Jan Prins and Alexander Tropsha", title = "Comparing Graph Representations of Protein Structure for Mining Family-Specific Residue-Based Packing Motifs", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "657--671", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.657", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.657; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.657", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Ledent:2005:CHM, author = "Sabrina Ledent and St{\'e}phane Robin", title = "Checking Homogeneity of Motifs' Distribution in Heterogeneous Sequences", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "672--685", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.672", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.672; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.672", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Leung:2005:FMI, author = "Henry C. M. Leung and Francis Y. L. Chin and S. M. Yiu and Roni Rosenfeld and W. W. Tsang", title = "Finding Motifs with Insufficient Number of Strong Binding Sites", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "686--701", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.686", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.686; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.686", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Li:2005:CEK, author = "Haifeng Li and Tao Jiang", title = "A Class of Edit Kernels for {SVMs} to Predict Translation Initiation Sites in Eukaryotic {mRNAs}", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "702--718", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.702", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.702; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.702", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Li:2005:CMR, author = "Jing Li and Tao Jiang", title = "Computing the Minimum Recombinant Haplotype Configuration from Incomplete Genotype Data on a Pedigree by Integer Linear Programming", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "719--739", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.719", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.719; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.719", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Lilien:2005:NEB, author = "Ryan H. Lilien and Brian W. Stevens and Amy C. Anderson and Bruce R. Donald", title = "A Novel Ensemble-Based Scoring and Search Algorithm for Protein Redesign and Its Application to Modify the Substrate Specificity of the {Gramicidin} Synthetase {A} Phenylalanine Adenylation Enzyme", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "740--761", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.740", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.740; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.740", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Lippert:2005:FAG, author = "Ross A. Lippert and Xiaoyue Zhao and Liliana Florea and Clark Mobarry and Sorin Istrail", title = "Finding Anchors for Genomic Sequence Comparison", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "762--776", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.762", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.762; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.762", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Menke:2005:WPN, author = "Matthew Menke and Jonathan King and Bonnie Berger and Lenore Cowen", title = "Wrap-and-Pack: a New Paradigm for Beta Structural Motif Recognition with Application to Recognizing Beta Trefoils", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "777--795", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.777", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.777; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.777", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Nakhleh:2005:RRE, author = "Luay Nakhleh and Tandy Warnow and C. Randal Linder and Katherine {St.John}", title = "Reconstructing Reticulate Evolution in Species --- Theory and Practice", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "796--811", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.796", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.796; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.796", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Sankoff:2005:CBR, author = "David Sankoff and Phil Trinh", title = "Chromosomal Breakpoint Reuse in Genome Sequence Rearrangement", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "812--821", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.812", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.812; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.812", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Segal:2005:DMI, author = "Eran Segal and Roded Sharan", title = "A Discriminative Model for Identifying Spatial {\em cis\/}-Regulatory Modules", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "822--834", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.822", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.822; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.822", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Sharan:2005:IPC, author = "Roded Sharan and Trey Ideker and Brian Kelley and Ron Shamir and Richard M. Karp", title = "Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "835--846", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.835", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.835; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.835", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Sun:2005:DMS, author = "Yanni Sun and Jeremy Buhler", title = "Designing Multiple Simultaneous Seeds for {DNA} Similarity Search", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "847--861", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.847", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.847; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.847", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Tang:2005:UMP, author = "Xinyu Tang and Bonnie Kirkpatrick and Shawna Thomas and Guang Song and Nancy M. Amato", title = "Using Motion Planning to Study {RNA} Folding Kinetics", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "862--881", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.862", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.862; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.862", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Wu:2005:SMI, author = "Zhijin Wu and Rafael A. Irizarry", title = "Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "882--893", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.882", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.882; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.882", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Zhao:2005:FSD, author = "Xiaoyue Zhao and Haiyan Huang and Terence P. Speed", title = "Finding Short {DNA} Motifs Using Permuted {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "894--906", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.894", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.894; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.894", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Anonymous:2005:C, author = "Anonymous", title = "Correction", journal = j-J-COMPUT-BIOL, volume = "12", number = "6", pages = "907--907", month = jul, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.907", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:47:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.907", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2005", } @Article{Battle:2005:PDO, author = "Alexis Battle and Eran Segal and Daphne Koller", title = "Probabilistic Discovery of Overlapping Cellular Processes and Their Regulation", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "909--927", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.909", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.909; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.909", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Wexler:2005:FAT, author = "Ydo Wexler and Zohar Yakhini and Yechezkel Kashi and Dan Geiger", title = "Finding Approximate Tandem Repeats in Genomic Sequences", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "928--942", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.928", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.928; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.928", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Lippert:2005:SEC, author = "Ross A. Lippert and Clark M. Mobarry and Brian P. Walenz", title = "A Space-Efficient Construction of the {Burrows--Wheeler} Transform for Genomic Data", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "943--951", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.943", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.943; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.943", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Xie:2005:BMM, author = "Jun Xie and Nak-Kyeong Kim", title = "{Bayesian} Models and {Markov} Chain {Monte Carlo} Methods for Protein Motifs with the Secondary Characteristics", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "952--970", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.952", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.952; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.952", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Liu:2005:FCB, author = "Jian Liu and Ming Li", title = "Finding Cancer Biomarkers from Mass Spectrometry Data by Decision Lists", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "971--979", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.971", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.971; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.971", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Sharon:2005:CBV, author = "Itai Sharon and Aaron Birkland and Kuan Chang and Ran El-Yaniv and Golan Yona", title = "Correcting {BLAST} $e$-Values for Low-Complexity Segments", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "980--1003", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.980", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.980; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.980", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Tichy:2005:EPT, author = "Robert F. Tichy and Stephan Wagner", title = "Extremal Problems for Topological Indices in Combinatorial Chemistry", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "1004--1013", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1004", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1004; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1004", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Kaufman:2005:CPA, author = "Menachem Kaufman and David Bloch and Naomi Zurgil and Yana Shafran and Mordechai Deutsch", title = "A Cluster Pattern Algorithm for the Analysis of Multiparametric Cell Assays", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "1014--1028", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1014", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1014; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1014", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Zhu:2005:HTS, author = "Dongxiao Zhu and Alfred O. Hero and Zhaohui S. Qin and Anand Swaroop", title = "High Throughput Screening of Co-Expressed Gene Pairs with Controlled False Discovery Rate {(FDR)} and Minimum Acceptable Strength {(MAS)}", journal = j-J-COMPUT-BIOL, volume = "12", number = "7", pages = "1029--1045", month = sep, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1029", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1029; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1029", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2005", } @Article{Zhao:2005:CAQ, author = "Sheng Zhao and Russell D. Fernald", title = "Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction", journal = j-J-COMPUT-BIOL, volume = "12", number = "8", pages = "1047--1064", month = oct, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1047", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1047; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1047", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 October 2005", } @Article{Morgante:2005:SMS, author = "Michele Morgante and Alberto Policriti and Nicola Vitacolonna and Andrea Zuccolo", title = "Structured Motifs Search", journal = j-J-COMPUT-BIOL, volume = "12", number = "8", pages = "1065--1082", month = oct, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1065", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1065; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1065", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 October 2005", } @Article{Hoberman:2005:SAS, author = "Rose Hoberman and David Sankoff and Dannie Durand", title = "The Statistical Analysis of Spatially Clustered Genes under the Maximum Gap Criterion", journal = j-J-COMPUT-BIOL, volume = "12", number = "8", pages = "1083--1102", month = oct, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1083", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1083; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1083", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 October 2005", } @Article{Yang:2005:GCU, author = "Albert C.-C. Yang and Ary L. Goldberger and C.-K. Peng", title = "Genomic Classification Using an Information-Based Similarity Index: Application to the {SARS} Coronavirus", journal = j-J-COMPUT-BIOL, volume = "12", number = "8", pages = "1103--1116", month = oct, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 October 2005", } @Article{Rajasekaran:2005:EAP, author = "S. Rajasekaran and S. Balla and C.-H. Huang", title = "Exact Algorithms for Planted Motif Problems", journal = j-J-COMPUT-BIOL, volume = "12", number = "8", pages = "1117--1128", month = oct, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1117", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1117; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1117", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 October 2005", } @Article{DYachkov:2005:CPD, author = "A. D'Yachkov and Frank Hwang and Antony Macula and Pavel Vilenkin and Chih-Wen Weng", title = "A Construction of Pooling Designs with Some Happy Surprises", journal = j-J-COMPUT-BIOL, volume = "12", number = "8", pages = "1129--1136", month = oct, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 October 2005", } @Article{Preparata:2005:QPS, author = "Franco P. Preparata and Louxin Zhang and Kwok Pui Choi", title = "Quick, Practical Selection of Effective Seeds for Homology Search", journal = j-J-COMPUT-BIOL, volume = "12", number = "9", pages = "1137--1152", month = nov, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1137", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1137; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1137", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 November 2005", } @Article{Yin:2005:FCC, author = "Changchuan Yin and Stephen S.-T. Yau", title = "A {Fourier} Characteristic of Coding Sequences: Origins and a Non-{Fourier} Approximation", journal = j-J-COMPUT-BIOL, volume = "12", number = "9", pages = "1153--1165", month = nov, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 November 2005", } @Article{Christensen:2005:PLA, author = "Ole F. Christensen and Asger Hobolth and Jens L. Jensen", title = "Pseudo-Likelihood Analysis of Codon Substitution Models with Neighbor-Dependent Rates", journal = j-J-COMPUT-BIOL, volume = "12", number = "9", pages = "1166--1182", month = nov, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1166", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1166; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1166", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 November 2005", } @Article{Rosenberg:2005:ASI, author = "Noah A. Rosenberg", title = "Algorithms for Selecting Informative Marker Panels for Population Assignment", journal = j-J-COMPUT-BIOL, volume = "12", number = "9", pages = "1183--1201", month = nov, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1183", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1183; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1183", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 November 2005", } @Article{Yang:2005:EED, author = "Chu-Wen Yang and Chin-Fu Hsiao and Chen-Kung Chou", title = "Evaluation of Experimental Designs for Two-Color {cDNA} Microarrays", journal = j-J-COMPUT-BIOL, volume = "12", number = "9", pages = "1202--1220", month = nov, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1202", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1202; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1202", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 November 2005", } @Article{Aung:2005:APS, author = "Zeyar Aung and Kian-Lee Tan", title = "Automatic {$3$D} Protein Structure Classification without Structural Alignment", journal = j-J-COMPUT-BIOL, volume = "12", number = "9", pages = "1221--1241", month = nov, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1221", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1221; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1221", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 November 2005", } @Article{Kimmel:2005:BFH, author = "Gad Kimmel and Ron Shamir", title = "A Block-Free Hidden {Markov} Model for Genotypes and Its Application to Disease Association", journal = j-J-COMPUT-BIOL, volume = "12", number = "10", pages = "1243--1260", month = dec, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1243; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1243", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 December 2005", } @Article{Huang:2005:AAH, author = "Yao-Ting Huang and Kun-Mao Chao and Ting Chen", title = "An Approximation Algorithm for Haplotype Inference by Maximum Parsimony", journal = j-J-COMPUT-BIOL, volume = "12", number = "10", pages = "1261--1274", month = dec, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1261", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1261; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1261", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 December 2005", } @Article{Dunlavy:2005:HHO, author = "Daniel M. Dunlavy and Dianne P. O'leary and Dmitri Klimov and D. Thirumalai", title = "{HOPE}: a Homotopy Optimization Method for Protein Structure Prediction", journal = j-J-COMPUT-BIOL, volume = "12", number = "10", pages = "1275--1288", month = dec, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1275", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1275; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1275", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 December 2005", } @Article{Landau:2005:GPA, author = "Gad M. Landau and Laxmi Parida and Oren Weimann", title = "Gene Proximity Analysis across Whole Genomes via {PQ} Trees$^1$", journal = j-J-COMPUT-BIOL, volume = "12", number = "10", pages = "1289--1306", month = dec, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1289", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1289; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1289", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 December 2005", } @Article{Liebermeister:2005:PPC, author = "Wolfram Liebermeister", title = "Predicting Physiological Concentrations of Metabolites from Their Molecular Structure", journal = j-J-COMPUT-BIOL, volume = "12", number = "10", pages = "1307--1315", month = dec, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1307", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1307; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1307", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 December 2005", } @Article{Tosatto:2005:VFF, author = "Silvio C. E. Tosatto", title = "The {Victor/FRST} Function for Model Quality Estimation", journal = j-J-COMPUT-BIOL, volume = "12", number = "10", pages = "1316--1327", month = dec, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1316", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1316; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1316", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 December 2005", } @Article{Gupta:2005:SAI, author = "Arvind Gupta and J{\'a}n Ma{\v{n}}uch and Ladislav Stacho", title = "Structure-Approximating Inverse Protein Folding Problem in the {$2$D} {HP} Model", journal = j-J-COMPUT-BIOL, volume = "12", number = "10", pages = "1328--1345", month = dec, year = "2005", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2005.12.1328", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2005.12.1328; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2005.12.1328", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 December 2005", } @Article{West:2006:VPS, author = "Joseph West and John Healy and Michael Wigler and William Casey and Bud Mishra", title = "Validation of \bioname{S. Pombe} Sequence Assembly by Microarray Hybridization", journal = j-J-COMPUT-BIOL, volume = "13", number = "1", pages = "1--20", month = jan, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 February 2006", } @Article{Chiang:2006:GTC, author = "David Chiang and Aravind K. Joshi and Ken A. Dill", title = "A Grammatical Theory for the Conformational Changes of Simple Helix Bundles", journal = j-J-COMPUT-BIOL, volume = "13", number = "1", pages = "21--42", month = jan, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.21", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.21; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.21", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 February 2006", } @Article{Vesterstrom:2006:FSS, author = "Jakob Vesterstr{\o}m and William R. Taylor", title = "Flexible Secondary Structure Based Protein Structure Comparison Applied to the Detection of Circular Permutation", journal = j-J-COMPUT-BIOL, volume = "13", number = "1", pages = "43--63", month = jan, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.43", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.43; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.43", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 February 2006", } @Article{Havilio:2006:SDB, author = "Moshe Havilio", title = "Signal Deconvolution Based Expression-Detection and Background Adjustment for Microarray Data", journal = j-J-COMPUT-BIOL, volume = "13", number = "1", pages = "63--80", month = jan, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.63", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.63; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.63", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 February 2006", } @Article{Gambin:2006:ACD, author = "Anna Gambin and Jerzy Tiuryn and Jerzy Tyszkiewicz", title = "Alignment with Context Dependent Scoring Function", journal = j-J-COMPUT-BIOL, volume = "13", number = "1", pages = "81--101", month = jan, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.81", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.81; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.81", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 February 2006", } @Article{Bhasin:2006:RCH, author = "Manoj Bhasin and Ellis L. Reinherz and Pedro A. Reche", title = "Recognition and Classification of Histones Using Support Vector Machine", journal = j-J-COMPUT-BIOL, volume = "13", number = "1", pages = "102--112", month = jan, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.102; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.102", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 February 2006", } @Article{Hohm:2006:MEM, author = "Tim Hohm and Philipp Limbourg and Daniel Hoffmann", title = "A Multiobjective Evolutionary Method for the Design of Peptidic Mimotopes", journal = j-J-COMPUT-BIOL, volume = "13", number = "1", pages = "113--125", month = jan, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 February 2006", } @Article{Yeh:2006:PMP, author = "Joanne I. Yeh and Lisong Mao", title = "Prediction of Membrane Proteins in \bioname{Mycobacterium tuberculosis} Using a Support Vector Machine Algorithm", journal = j-J-COMPUT-BIOL, volume = "13", number = "1", pages = "126--129", month = jan, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.126", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.126; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.126", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 February 2006", } @Article{Miyano:2006:PSR, author = "Satoru Miyano", title = "Preface: Special {RECOMB 2005} Issue", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "131--132", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.131", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.131", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Scott:2006:EAD, author = "Jacob Scott and Trey Ideker and Richard M. Karp and Roded Sharan", title = "Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "133--144", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.133", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.133; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.133", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Jaimovich:2006:TIP, author = "Ariel Jaimovich and Gal Elidan and Hanah Margalit and Nir Friedman", title = "Towards an Integrated Protein--Protein Interaction Network: a Relational {Markov} Network Approach", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "145--164", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.145", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.145; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.145", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Gat-Viks:2006:PMI, author = "Irit Gat-Viks and Amos Tanay and Daniela Raijman and Ron Shamir", title = "A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "165--181", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Koyuturk:2006:PAP, author = "Mehmet Koyut{\"u}rk and Yohan Kim and Umut Topkara and Shankar Subramaniam and Wojciech Szpankowski and Ananth Grama", title = "Pairwise Alignment of Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "182--199", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.182", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.182; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.182", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Frey:2006:GGM, author = "Brendan J. Frey and Quaid D. Morris and Timothy R. Hughes", title = "{GenRate}: a Generative Model that Reveals Novel Transcripts in Genome-Tiling Microarray Data", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "200--214", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.200", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.200; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.200", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Lipson:2006:ECI, author = "Doron Lipson and Yonatan Aumann and Amir Ben-Dor and Nathan Linial and Zohar Yakhini", title = "Efficient Calculation of Interval Scores for {DNA} Copy Number Data Analysis", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "215--228", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.215", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.215; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.215", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Wu:2006:RET, author = "Kun-Pin Wu and Jia-Ming Chang and Jun-Bo Chen and Chi-Fon Chang and Wen-Jin Wu and Tai-Huang Huang and Ting-Yi Sung and Wen-Lian Hsu", title = "{RIBRA} --- An Error-Tolerant Algorithm for the {NMR} Backbone Assignment Problem", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "229--244", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.229", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.229; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.229", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Zilberstein:2006:HTA, author = "Chaya Ben-Zaken Zilberstein and Michal Ziv-Ukelson and Ron Y. Pinter and Zohar Yakhini", title = "A High-Throughput Approach for Associating {MicroRNAs} with Their Activity Conditions", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "245--266", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.245", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.245; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.245", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Alkan:2006:RRI, author = "Can Alkan and Emre Karako{\c{c}} and Joseph H. Nadeau and S. Cenk Sahinalp and Kaizhong Zhang", title = "{RNA--RNA} Interaction Prediction and Antisense {RNA} Target Search", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "267--282", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.267", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.267; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.267", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Bafna:2006:CFU, author = "Vineet Bafna and Haixu Tang and Shaojie Zhang", title = "Consensus Folding of Unaligned {RNA} Sequences Revisited", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "283--295", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.283", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.283; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.283", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Rasmussen:2006:EGF, author = "Kim R. Rasmussen and Jens Stoye and Eugene W. Myers", title = "Efficient $q$-Gram Filters for Finding All $ \epsilon $-Matches over a Given Length", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "296--308", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.296", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.296; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.296", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Sze:2006:PTS, author = "Sing-Hoi Sze and Yue Lu and Qingwu Yang", title = "A Polynomial Time Solvable Formulation of Multiple Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "309--319", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.309", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.309; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.309", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Durand:2006:HMM, author = "Dannie Durand and Bjarni V. Halld{\'o}rsson and Benjamin Vernot", title = "A Hybrid Micro--Macroevolutionary Approach to Gene Tree Reconstruction", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "320--335", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.320", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.320; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.320", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Ulitsky:2006:ACS, author = "Igor Ulitsky and David Burstein and Tamir Tuller and Benny Chor", title = "The Average Common Substring Approach to Phylogenomic Reconstruction", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "336--350", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.336", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.336; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.336", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Przytycka:2006:GTI, author = "Teresa Przytycka and George Davis and Nan Song and Dannie Durand", title = "Graph Theoretical Insights into Evolution of Multidomain Proteins", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "351--363", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.351", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.351; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.351", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Bern:2006:NAP, author = "Marshall Bern and David Goldberg", title = "{{\em {De} Novo\/}} Analysis of Peptide Tandem Mass Spectra by Spectral Graph Partitioning", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "364--378", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.364", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.364; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.364", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Gross:2006:UMA, author = "Samuel S. Gross and Michael R. Brent", title = "Using Multiple Alignments to Improve Gene Prediction", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "379--393", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.379", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.379; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.379", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Liu:2006:PFR, author = "Yan Liu and Jaime Carbonell and Peter Weigele and Vanathi Gopalakrishnan", title = "Protein Fold Recognition Using Segmentation Conditional Random Fields {(SCRFs)}", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "394--406", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.394", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.394; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.394", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Shatsky:2006:MCP, author = "Maxim Shatsky and Alexandra Shulman-Peleg and Ruth Nussinov and Haim J. Wolfson", title = "The Multiple Common Point Set Problem and Its Application to Molecule Binding Pattern Detection", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "407--428", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.407", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.407; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.407", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Chia:2006:PAS, author = "Nicholas Chia and Ralf Bundschuh", title = "A Practical Approach to Significance Assessment in Alignment with Gaps", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "429--441", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.429", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.429; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.429", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Valouev:2006:AOM, author = "Anton Valouev and Lei Li and Yu-Chi Liu and David C. Schwartz and Yi Yang and Yu Zhang and Michael S. Waterman", title = "Alignment of Optical Maps", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "442--462", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.442", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.442; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.442", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Yeang:2006:MCF, author = "Chen-Hsiang Yeang and Tommi Jaakkola", title = "Modeling the Combinatorial Functions of Multiple Transcription Factors", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "463--480", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.463", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.463; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.463", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Halperin:2006:HEH, author = "Eran Halperin and Elad Hazan", title = "{HAPLOFREQ} --- Estimating Haplotype Frequencies Efficiently", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "481--500", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.481", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.481; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.481", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Bafna:2006:IAR, author = "Vineet Bafna and Vikas Bansal", title = "Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "501--521", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.501", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.501; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.501", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Ding:2006:LTA, author = "Zhihong Ding and Vladimir Filkov and Dan Gusfield", title = "A Linear-Time Algorithm for the Perfect Phylogeny Haplotyping {(PPH)} Problem", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "522--553", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.522", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.522; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.522", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Mazowita:2006:SRM, author = "Matthew Mazowita and Lani Haque and David Sankoff", title = "Stability of Rearrangement Measures in the Comparison of Genome Sequences", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "554--566", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.554", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.554; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.554", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Bergeron:2006:ST, author = "Anne Bergeron and Julia Mixtacki and Jens Stoye", title = "On Sorting by Translocations", journal = j-J-COMPUT-BIOL, volume = "13", number = "2", pages = "567--578", month = mar, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.567", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.567; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.567", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2006", } @Article{Keles:2006:MTM, author = "S{\"u}nd{\"u}z Kele{\c{s}} and Mark J. {Van Der Laan} and Sandrine Dudoit and Simon E. Cawley", title = "Multiple Testing Methods For {ChIP--Chip} High Density Oligonucleotide Array Data", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "579--613", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.579", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.579; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.579", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Potra:2006:PIA, author = "Florian A. Potra and Xing Liu and Fran{\c{c}}oise Seillier-Moiseiwitsch and Anindya Roy and Yaming Hang and Mark R. Marten and Babu Raman and Carol Whisnant", title = "Protein Image Alignment via Piecewise Affine Transformations", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "614--630", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.614", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.614; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.614", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Pollastri:2006:MDR, author = "Gianluca Pollastri and Alessandro Vullo and Paolo Frasconi and Pierre Baldi", title = "Modular {DAG--RNN} Architectures for Assembling Coarse Protein Structures", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "631--650", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.631", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.631; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.631", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Nicolas:2006:RJM, author = "Pierre Nicolas and Anne-Sophie Tocquet and Vincent Miele and Florence Muri", title = "A Reversible Jump {Markov} Chain {Monte Carlo} Algorithm for Bacterial Promoter Motifs Discovery", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "651--667", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.651", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.651; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.651", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Konagurthu:2006:OSP, author = "Arun S. Konagurthu and Peter J. Stuckey", title = "Optimal Sum-of-Pairs Multiple Sequence Alignment Using Incremental {Carrillo} and {Lipman} Bounds", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "668--685", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.668", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.668; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.668", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Carlson:2006:BBS, author = "Jonathan M. Carlson and Arijit Chakravarty and Robert H. Gross", title = "{BEAM}: a Beam Search Algorithm for the Identification of {{\em Cis\/}}-Regulatory Elements in Groups of Genes", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "686--701", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.686", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.686; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.686", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Jansson:2006:LGS, author = "Jesper Jansson and Ngo Trung Hieu and Wing-Kin Sung", title = "Local Gapped Subforest Alignment and Its Application in Finding {RNA} Structural Motifs", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "702--718", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.702", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.702; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.702", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Ferre:2006:FMP, author = "S{\'e}bastien Ferr{\'e} and Ross D. King", title = "Finding Motifs in Protein Secondary Structure for Use in Function Prediction", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "719--731", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.719", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.719; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.719", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Mandoiu:2006:EAA, author = "Ion I. M{\u{a}}ndoiu and Drago{\c{s}} Trinc{\u{a}}", title = "Exact and Approximation Algorithms for {DNA} Tag Set Design", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "732--744", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.732", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.732; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.732", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Reddy:2006:SBB, author = "Chandan K. Reddy and Hsiao-Dong Chiang", title = "A Stability Boundary Based Method for Finding Saddle Points on Potential Energy Surfaces", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "745--766", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.745", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.745; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.745", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Ayers:2006:RAH, author = "Kristin L. Ayers and Chiara Sabatti and Kenneth Lange", title = "Reconstructing Ancestral Haplotypes with a Dictionary Model", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "767--785", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.767", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.767; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.767", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Huang:2006:LPW, author = "Shuguang Huang and Yongming Qu", title = "The Loss in Power When the Test of Differential Expression Is Performed under a Wrong Scale", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "786--797", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.786", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.786; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.786", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Raghavan:2006:MGF, author = "N. Raghavan and D. Amaratunga and J. Cabrera and A. Nie and J. Qin and M. McMillian", title = "On Methods for Gene Function Scoring as a Means of Facilitating the Interpretation of Microarray Results", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "798--809", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.798", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.798; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.798", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Khanin:2006:HSF, author = "Raya Khanin and Ernst Wit", title = "How Scale-Free Are Biological Networks", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "810--818", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.810", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.810; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.810", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Chor:2006:MLM, author = "Benny Chor and Amit Khetan and Sagi Snir", title = "Maximum Likelihood Molecular Clock Comb: Analytic Solutions", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "819--837", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.819", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.819; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.819", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Golightly:2006:BSI, author = "Andrew Golightly and Darren J. Wilkinson", title = "{Bayesian} Sequential Inference for Stochastic Kinetic Biochemical Network Models", journal = j-J-COMPUT-BIOL, volume = "13", number = "3", pages = "838--851", month = apr, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.838", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.838; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.838", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2006", } @Article{Hjelm:2006:NPN, author = "Marcus Hjelm and Mattias H{\"o}glund and Jens Lagergren", title = "New Probabilistic Network Models and Algorithms for Oncogenesis", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "853--865", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.853", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.853; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.853", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{DYachkov:2006:NGI, author = "Arkadii G. D'Yachkov and Anthony J. Macula and Wendy K. Pogozelski and Thomas E. Renz and Vyacheslav V. Rykov and David C. Torney", title = "New $t$-Gap Insertion-Deletion-Like Metrics for {DNA} Hybridization Thermodynamic Modeling", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "866--881", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.866", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.866; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.866", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Metzler:2006:RVG, author = "Dirk Metzler", title = "Robust {$E$}-Values for Gapped Local Alignments", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "882--896", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.882", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.882; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.882", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Vijayasatya:2006:OAP, author = "Ravi Vijayasatya and Amar Mukherjee", title = "An Optimal Algorithm for Perfect Phylogeny Haplotyping", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "897--928", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.897", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.897; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.897", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Gunewardena:2006:EPT, author = "Sumedha Gunewardena and Peter Jeavons and Zhaolei Zhang", title = "Enhancing the Prediction of Transcription Factor Binding Sites by Incorporating Structural Properties and Nucleotide Covariations", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "929--945", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.929", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.929; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.929", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Turutina:2006:IAA, author = "Vera P. Turutina and Andrew A. Laskin and Nikolay A. Kudryashov and Konstantin G. Skryabin and Eugene V. Korotkov", title = "Identification of Amino Acid Latent Periodicity within 94 Protein Families", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "946--964", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.946", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.946; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.946", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Cameron:2006:DFA, author = "Michael Cameron and Hugh E. Williams and Adam Cannane", title = "A Deterministic Finite Automaton for Faster Protein Hit Detection in {BLAST}", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "965--978", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.965", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.965; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.965", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Colannino:2006:LTA, author = "Justin Colannino and Mirela Damian and Ferran Hurtado and John Iacono and Henk Meijer and Suneeta Ramaswami and Godfried Toussaint", title = "An {$ O(n \log n) $}-Time Algorithm for the Restriction Scaffold Assignment Problem", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "979--989", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.979", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.979; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.979", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Du:2006:NCT, author = "Ding-Zhu Du and F. K. Hwang and Weili Wu and Taieb Znati", title = "New Construction for Transversal Design", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "990--995", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.990", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.990; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.990", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Chudin:2006:MTV, author = "E. Chudin and S. Kruglyak and S. C. Baker and S. Oeser and D. Barker and T. K. McDaniel", title = "A Model of Technical Variation of Microarray Signals", journal = j-J-COMPUT-BIOL, volume = "13", number = "4", pages = "996--1003", month = may, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.996", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.996; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.996", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2006", } @Article{Sankoff:2006:DGD, author = "David Sankoff and Lani Haque", title = "The Distribution of Genomic Distance between Random Genomes", journal = j-J-COMPUT-BIOL, volume = "13", number = "5", pages = "1005--1012", month = jun, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1005", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1005; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1005", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2006", } @Article{Kent:2006:CSE, author = "Carmel Kent and Gad M. Landau and Michal Ziv-Ukelson", title = "On the Complexity of Sparse Exon Assembly", journal = j-J-COMPUT-BIOL, volume = "13", number = "5", pages = "1013--1027", month = jun, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1013", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1013; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1013", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2006", } @Article{Morgulis:2006:FSD, author = "Aleksandr Morgulis and E. Michael Gertz and Alejandro A. Sch{\"a}ffer and Richa Agarwala", title = "A Fast and Symmetric {DUST} Implementation to Mask Low-Complexity {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "13", number = "5", pages = "1028--1040", month = jun, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1028", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1028; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1028", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2006", } @Article{Maximova:2006:NAN, author = "Tatiana Maximova and Chen Keasar", title = "A Novel Algorithm for Non-Bonded-List Updating in Molecular Simulations", journal = j-J-COMPUT-BIOL, volume = "13", number = "5", pages = "1041--1048", month = jun, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1041", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1041; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1041", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2006", } @Article{Goutsias:2006:STR, author = "John Goutsias and Seungchan Kim", title = "Stochastic Transcriptional Regulatory Systems with Time Delays: a Mean-Field Approximation", journal = j-J-COMPUT-BIOL, volume = "13", number = "5", pages = "1049--1076", month = jun, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1049", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1049; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1049", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2006", } @Article{Chiang:2006:GRM, author = "David Chiang and Aravind K. Joshi and David B. Searls", title = "Grammatical Representations of Macromolecular Structure", journal = j-J-COMPUT-BIOL, volume = "13", number = "5", pages = "1077--1100", month = jun, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1077", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1077; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1077", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2006", } @Article{Allman:2006:ITT, author = "Elizabeth S. Allman and John A. Rhodes", title = "The Identifiability of Tree Topology for Phylogenetic Models, Including Covarion and Mixture Models", journal = j-J-COMPUT-BIOL, volume = "13", number = "5", pages = "1101--1113", month = jun, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1101; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1101", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2006", } @Article{Beattie:2006:BSP, author = "Bradley J. Beattie and Peter N. Robinson", title = "Binary State Pattern Clustering: a Digital Paradigm for Class and Biomarker Discovery in Gene Microarray Studies of Cancer", journal = j-J-COMPUT-BIOL, volume = "13", number = "5", pages = "1114--1130", month = jun, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1114", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1114; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1114", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2006", } @Article{Presson:2006:MMD, author = "Angela P. Presson and Eric Sobel and Kenneth Lange and Jeanette C. Papp", title = "Merging Microsatellite Data", journal = j-J-COMPUT-BIOL, volume = "13", number = "6", pages = "1131--1147", month = jul, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1131", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1131; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1131", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2006", } @Article{Wu:2006:CED, author = "Jing Wu and David Haussler", title = "Coding Exon Detection Using Comparative Sequences", journal = j-J-COMPUT-BIOL, volume = "13", number = "6", pages = "1148--1164", month = jul, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1148", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1148; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1148", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2006", } @Article{Horesh:2006:DAC, author = "Yair Horesh and Ramit Mehr and Ron Unger", title = "Designing an {$ A* $} Algorithm for Calculating Edit Distance between Rooted-Unordered Trees", journal = j-J-COMPUT-BIOL, volume = "13", number = "6", pages = "1165--1176", month = jul, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2006", } @Article{Wendl:2006:GCT, author = "Michael C. Wendl", title = "A General Coverage Theory for Shotgun {DNA} Sequencing", journal = j-J-COMPUT-BIOL, volume = "13", number = "6", pages = "1177--1196", month = jul, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1177", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1177; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1177", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2006", } @Article{Rodland:2006:PRS, author = "Einar Andreas R{\o}dland", title = "Pseudoknots in {RNA} Secondary Structures: Representation, Enumeration, and Prevalence", journal = j-J-COMPUT-BIOL, volume = "13", number = "6", pages = "1197--1213", month = jul, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2006", } @Article{Christodoulakis:2006:CRR, author = "M. Christodoulakis and C. Iliopoulos and L. Mouchard and K. Perdikuri and A. Tsakalidis and K. Tsichlas", title = "Computation of Repetitions and Regularities of Biologically Weighted Sequences", journal = j-J-COMPUT-BIOL, volume = "13", number = "6", pages = "1214--1231", month = jul, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1214", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1214; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1214", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2006", } @Article{Sitharam:2006:MVS, author = "Meera Sitharam and Mavis Agbandje-Mckenna", title = "Modeling Virus Self-Assembly Pathways: Avoiding Dynamics Using Geometric Constraint Decomposition", journal = j-J-COMPUT-BIOL, volume = "13", number = "6", pages = "1232--1265", month = jul, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1232", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1232; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1232", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2006", } @Article{Wang:2006:PTA, author = "Lincong Wang and Ramgopal R. Mettu and Bruce Randall Donald", title = "A Polynomial-Time Algorithm for {{\em {De} Novo\/}} Protein Backbone Structure Determination from Nuclear Magnetic Resonance Data", journal = j-J-COMPUT-BIOL, volume = "13", number = "7", pages = "1267--1288", month = sep, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1267", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1267; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1267", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2006", } @Article{Haimovich:2006:WAD, author = "Adrian D. Haimovich and Bruce Byrne and Ramakrishna Ramaswamy and William J. Welsh", title = "Wavelet Analysis of {DNA} Walks", journal = j-J-COMPUT-BIOL, volume = "13", number = "7", pages = "1289--1298", month = sep, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1289", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1289; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1289", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2006", } @Article{Koyuturk:2006:DCI, author = "Mehmet Koyut{\"u}rk and Yohan Kim and Shankar Subramaniam and Wojciech Szpankowski and Ananth Grama", title = "Detecting Conserved Interaction Patterns in Biological Networks", journal = j-J-COMPUT-BIOL, volume = "13", number = "7", pages = "1299--1322", month = sep, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1299", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1299; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1299", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2006", } @Article{Elias:2006:SIM, author = "Isaac Elias", title = "Settling the Intractability of Multiple Alignment", journal = j-J-COMPUT-BIOL, volume = "13", number = "7", pages = "1323--1339", month = sep, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1323", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1323; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1323", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2006", } @Article{Bergeron:2006:SSP, author = "Anne Bergeron and Jens Stoye", title = "On the Similarity of Sets of Permutations and Its Applications to Genome Comparison", journal = j-J-COMPUT-BIOL, volume = "13", number = "7", pages = "1340--1354", month = sep, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1340", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1340; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1340", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2006", } @Article{Xu:2006:OMS, author = "Jinbo Xu and Daniel Brown and Ming Li and Bin Ma", title = "Optimizing Multiple Spaced Seeds for Homology Search", journal = j-J-COMPUT-BIOL, volume = "13", number = "7", pages = "1355--1368", month = sep, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1355", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1355; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1355", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2006", } @Article{Keith:2006:SEG, author = "Jonathan M. Keith", title = "Segmenting Eukaryotic Genomes with the Generalized {Gibbs} Sampler", journal = j-J-COMPUT-BIOL, volume = "13", number = "7", pages = "1369--1383", month = sep, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1369", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1369; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1369", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2006", } @Article{Potra:2006:AFT, author = "Florian A. Potra and Xing Liu", title = "Aligning Families of Two-Dimensional Gels by a Combined Multiresolution Forward-Inverse Transformation Approach", journal = j-J-COMPUT-BIOL, volume = "13", number = "7", pages = "1384--1395", month = sep, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1384", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1384; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1384", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2006", } @Article{Swidan:2006:RAP, author = "Firas Swidan and Michal Ziv-Ukelson and Ron Y. Pinter", title = "On the Repeat-Annotated Phylogenetic Tree Reconstruction Problem", journal = j-J-COMPUT-BIOL, volume = "13", number = "8", pages = "1397--1418", month = oct, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1397", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1397; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1397", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2006", } @Article{Bonet:2006:ASD, author = "Maria Luisa Bonet and Katherine {St.John} and Ruchi Mahindru and Nina Amenta", title = "Approximating Subtree Distances Between Phylogenies", journal = j-J-COMPUT-BIOL, volume = "13", number = "8", pages = "1419--1434", month = oct, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1419", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1419; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1419", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2006", } @Article{Just:2006:RED, author = "Winfried Just", title = "Reverse Engineering Discrete Dynamical Systems from Data Sets with Random Input Vectors", journal = j-J-COMPUT-BIOL, volume = "13", number = "8", pages = "1435--1456", month = oct, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1435", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1435; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1435", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2006", } @Article{Richardson:2006:FSE, author = "Joel E. Richardson", title = "{\tt fjoin}: Simple and Efficient Computation of Feature Overlaps", journal = j-J-COMPUT-BIOL, volume = "13", number = "8", pages = "1457--1464", month = oct, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1457", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1457; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1457", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2006", } @Article{Didier:2006:LDS, author = "Gilles Didier and Ivan Laprevotte and Maude Pupin and Alain H{\'e}naut", title = "Local Decoding of Sequences and Alignment-Free Comparison", journal = j-J-COMPUT-BIOL, volume = "13", number = "8", pages = "1465--1476", month = oct, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1465", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1465; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1465", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2006", } @Article{Menconi:2006:CBA, author = "Giulia Menconi and Roberto Marangoni", title = "A Compression-Based Approach for Coding Sequences Identification. {I}. {Application} to Prokaryotic Genomes", journal = j-J-COMPUT-BIOL, volume = "13", number = "8", pages = "1477--1488", month = oct, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1477", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1477; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1477", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2006", } @Article{Mooney:2006:PSM, author = "Catherine Mooney and Alessandro Vullo and Gianluca Pollastri", title = "Protein Structural Motif Prediction in Multidimensional $ \phi $--$ \psi $ Space Leads to Improved Secondary Structure Prediction", journal = j-J-COMPUT-BIOL, volume = "13", number = "8", pages = "1489--1502", month = oct, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1489", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1489; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1489", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2006", } @Article{Emmert-Streib:2006:ACK, author = "Frank Emmert-Streib", title = "Algorithmic Computation of Knot Polynomials of Secondary Structure Elements of Proteins", journal = j-J-COMPUT-BIOL, volume = "13", number = "8", pages = "1503--1512", month = oct, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1503", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1503; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1503", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2006", } @Article{Moerkerke:2006:SSD, author = "B. Moerkerke and E. Goetghebeur", title = "Selecting ``Significant'' Differentially Expressed Genes from the Combined Perspective of the Null and the Alternative", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1513--1531", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1513", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1513; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1513", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Chen:2006:DEA, author = "Peter C. Y. Chen", title = "A Discrete-Event Approach to Transcription Control with Dynamic Event-Controllability", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1532--1545", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1532", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1532; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1532", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Ruths:2006:HGS, author = "Derek A. Ruths and Luay Nakhleh and M. Sriram Iyengar and Shrikanth A. G. Reddy and Prahlad T. Ram", title = "Hypothesis Generation in Signaling Networks", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1546--1557", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1546", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1546; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1546", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Jaklic:2006:CCB, author = "Ga{\v{s}}per Jakli{\v{c}} and Toma{\v{z}} Pisanski and Milan Randi{\'c}", title = "Characterization of Complex Biological Systems by Matrix Invariants", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1558--1564", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1558", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1558; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1558", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Chen:2006:FRT, author = "Yu Chen and Gordon M. Crippen", title = "Fold Recognition via a Tree", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1565--1573", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1565", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1565; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1565", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Bruno:2006:TPD, author = "William J. Bruno and John E. Pearson", title = "Transformations that Preserve Detailed Balance in {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1574--1578", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1574", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1574; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1574", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Han:2006:PDRa, author = "Pengfei Han and Xiuzhen Zhang and Raymond S. Norton and Zhi-Ping Feng", title = "Predicting Disordered Regions in Proteins Based on Decision Trees of Reduced Amino Acid Composition", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1579--1590", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1579", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1579; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1579", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Mertens:2006:MSP, author = "Bart J. A. Mertens and M. E. {De Noo} and R. A. E. M. Tollenaar and A. M. Deelder", title = "Mass Spectrometry Proteomic Diagnosis: Enacting the Double Cross-Validatory Paradigm", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1591--1605", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1591", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1591; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1591", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Liu:2006:GWT, author = "Zhenqiu Liu and Shili Lin and Ming Tan", title = "Genome-Wide Tagging {SNPs} with Entropy-Based {Monte Carlo} Method", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1606--1614", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1606", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1606; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1606", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Kim:2006:PMAa, author = "Nak-Kyeong Kim and Jun Xie", title = "Protein Multiple Alignment Incorporating Primary and Secondary Structure Information", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1615--1629", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1615", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1615; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1615", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Ribeiro:2006:GMS, author = "Andre Ribeiro and Rui Zhu and Stuart A. Kauffman", title = "A General Modeling Strategy for Gene Regulatory Networks with Stochastic Dynamics", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1630--1639", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1630", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1630; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1630", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Clote:2006:CSS, author = "P. Clote", title = "Combinatorics of Saturated Secondary Structures of {RNA}", journal = j-J-COMPUT-BIOL, volume = "13", number = "9", pages = "1640--1657", month = nov, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1640", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1640; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1640", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2006", } @Article{Alon:2006:MNG, author = "Noga Alon and Vera Asodi and Charles Cantor and Simon Kasif and John Rachlin", title = "Multi-Node Graphs: a Framework for Multiplexed Biological Assays", journal = j-J-COMPUT-BIOL, volume = "13", number = "10", pages = "1659--1672", month = dec, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1659", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1659; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1659", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2007", } @Article{Wang:2006:EIA, author = "Lu-yong Wang and Dorin Comaniciu and Daniel Fasulo", title = "Exploiting Interactions among Polymorphisms Contributing to Complex Disease Traits with Boosted Generative Modeling", journal = j-J-COMPUT-BIOL, volume = "13", number = "10", pages = "1673--1684", month = dec, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1673", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1673; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1673", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2007", } @Article{Parida:2006:UPS, author = "Laxmi Parida", title = "Using {PQ} Structures for Genomic Rearrangement Phylogeny", journal = j-J-COMPUT-BIOL, volume = "13", number = "10", pages = "1685--1700", month = dec, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1685", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1685; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1685", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2007", } @Article{Lartillot:2006:CGS, author = "Nicolas Lartillot", title = "Conjugate {Gibbs} Sampling for {Bayesian} Phylogenetic Models", journal = j-J-COMPUT-BIOL, volume = "13", number = "10", pages = "1701--1722", month = dec, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1701", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1701; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1701", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2007", } @Article{Han:2006:PDRb, author = "Pengfei Han and Xiuzhen Zhang and Raymond S. Norton and Zhi-Ping Feng", title = "Predicting Disordered Regions in Proteins Based on Decision Trees of Reduced Amino Acid Composition", journal = j-J-COMPUT-BIOL, volume = "13", number = "10", pages = "1723--1734", month = dec, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1723", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1723; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1723", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2007", } @Article{Kim:2006:PMAb, author = "Nak-Kyeong Kim and Jun Xie", title = "Protein Multiple Alignment Incorporating Primary and Secondary Structure Information", journal = j-J-COMPUT-BIOL, volume = "13", number = "10", pages = "1735--1748", month = dec, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1735", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1735; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1735", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2007", } @Article{Roy:2006:HSM, author = "Sushmita Roy and Terran Lane and Chris Allen and Anthony D. Aragon and Margaret Werner-Washburne", title = "A Hidden-State {Markov} Model for Cell Population Deconvolution", journal = j-J-COMPUT-BIOL, volume = "13", number = "10", pages = "1749--1774", month = dec, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1749", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1749; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1749", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2007", } @Article{Hung:2006:CUC, author = "Chun-Min Hung and Yueh-Min Huang and Ming-Shi Chang", title = "{CSAM}: Using Clustering-Hashing-Signal Anchoring Method to Explore Human Novel Genes", journal = j-J-COMPUT-BIOL, volume = "13", number = "10", pages = "1775--1789", month = dec, year = "2006", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.13.1775", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.13.1775; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.13.1775", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2007", } @Article{Gronau:2007:NJA, author = "Ilan Gronau and Shlomo Moran", title = "Neighbor Joining Algorithms for Inferring Phylogenies via {LCA} Distances", journal = j-J-COMPUT-BIOL, volume = "14", number = "1", pages = "1--15", month = jan, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0115; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0115", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2007", } @Article{Rastegari:2007:PNA, author = "Baharak Rastegari and Anne Condon", title = "Parsing Nucleic Acid Pseudoknotted Secondary Structure: Algorithm and Applications", journal = j-J-COMPUT-BIOL, volume = "14", number = "1", pages = "16--32", month = jan, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0108; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0108", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2007", } @Article{Siebert:2007:DPA, author = "Sven Siebert and Rolf Backofen", title = "A Dynamic Programming Approach for Finding Common Patterns in {RNAs}", journal = j-J-COMPUT-BIOL, volume = "14", number = "1", pages = "33--44", month = jan, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0089", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0089; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0089", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2007", } @Article{Parida:2007:GPP, author = "Laxmi Parida", title = "Gapped Permutation Pattern Discovery for Gene Order Comparisons", journal = j-J-COMPUT-BIOL, volume = "14", number = "1", pages = "45--55", month = jan, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2007", } @Article{Yang:2007:PMG, author = "Qingwu Yang and Sing-Hoi Sze", title = "Path Matching and Graph Matching in Biological Networks", journal = j-J-COMPUT-BIOL, volume = "14", number = "1", pages = "56--67", month = jan, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0076", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0076; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0076", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2007", } @Article{Lees:2007:GMA, author = "Karen Lees and Stephen Roberts and Pari Skamnioti and Sarah Gurr", title = "Gene Microarray Analysis Using Angular Distribution Decomposition", journal = j-J-COMPUT-BIOL, volume = "14", number = "1", pages = "68--83", month = jan, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0098", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0098; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0098", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2007", } @Article{Bishop:2007:GTA, author = "Morgan Bishop and Anthony J. Macula and Kayla Nimmo and Lauren Wood and Wendy K. Pogozelski and Thomas E. Renz", title = "Group Testing to Annihilate Pairs Applied to {DNA} Cross-Hybridization Elimination Using {SYBR Green I}", journal = j-J-COMPUT-BIOL, volume = "14", number = "1", pages = "84--96", month = jan, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0114", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0114; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0114", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2007", } @Article{Saha:2007:VEP, author = "Nilanjan Saha and Layne T. Watson and Karen Kafadar and Naren Ramakrishnan and Alexey Onufriev and Shrinivasrao Mane and Cecilia Vasquez-Robinet", title = "Validation and Estimation of Parameters for a General Probabilistic Model of the {PCR} Process", journal = j-J-COMPUT-BIOL, volume = "14", number = "1", pages = "97--112", month = jan, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0123", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0123; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0123", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2007", } @Article{Zhou:2007:DSS, author = "Leming Zhou and Liliana Florea", title = "Designing Sensitive and Specific Spaced Seeds for Cross-Species {mRNA-to-Genome} Alignment", journal = j-J-COMPUT-BIOL, volume = "14", number = "2", pages = "113--130", month = mar, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0130", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0130; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0130", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2007", } @Article{Agarwal:2007:FMS, author = "Pankaj K. Agarwal and Nabil H. Mustafa and Yusu Wang", title = "Fast Molecular Shape Matching Using Contact Maps", journal = j-J-COMPUT-BIOL, volume = "14", number = "2", pages = "131--143", month = mar, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0004", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0004; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0004", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2007", } @Article{Levy:2007:ICA, author = "Dan Levy and Christopher Reeder and Bradford Loucas and Lynn Hlatky and Allen Chen and Michael Cornforth and Rainer Sachs", title = "Interpreting Chromosome Aberration Spectra", journal = j-J-COMPUT-BIOL, volume = "14", number = "2", pages = "144--155", month = mar, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0127", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0127; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0127", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2007", } @Article{Stefankovic:2007:PMM, author = "Daniel {\v{S}}tefankovi{\v{c}} and Eric Vigoda", title = "Phylogeny of Mixture Models: Robustness of Maximum Likelihood and Non-Identifiable Distributions", journal = j-J-COMPUT-BIOL, volume = "14", number = "2", pages = "156--189", month = mar, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0126", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0126; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0126", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2007", } @Article{Waldispuhl:2007:CPF, author = "J. Waldisp{\"u}hl and P. Clote", title = "Computing the Partition Function and Sampling for Saturated Secondary Structures of {RNA}, with Respect to the {Turner} Energy Model", journal = j-J-COMPUT-BIOL, volume = "14", number = "2", pages = "190--215", month = mar, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0012", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0012; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0012", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2007", } @Article{Elias:2007:RAG, author = "Isaac Elias and Tamir Tuller", title = "Reconstruction of Ancestral Genomic Sequences Using Likelihood", journal = j-J-COMPUT-BIOL, volume = "14", number = "2", pages = "216--237", month = mar, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0101; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0101", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2007", } @Article{Kong:2007:GCF, author = "Yong Kong", title = "Generalized Correlation Functions and Their Applications in Selection of Optimal Multiple Spaced Seeds for Homology Search", journal = j-J-COMPUT-BIOL, volume = "14", number = "2", pages = "238--254", month = mar, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2007", } @Article{Li:2007:QMS, author = "Haifeng Li and Anton Valouev and David C. Schwartz and Michael S. Waterman and Lei M. Li", title = "A Quantile Method for Sizing Optical Maps", journal = j-J-COMPUT-BIOL, volume = "14", number = "3", pages = "255--266", month = apr, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0006", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0006; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0006", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2007", } @Article{Xing:2007:BHI, author = "Eric P. Xing and Michael I. Jordan and Roded Sharan", title = "{Bayesian} Haplotype Inference via the {Dirichlet} Process", journal = j-J-COMPUT-BIOL, volume = "14", number = "3", pages = "267--284", month = apr, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0102; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0102", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2007", } @Article{Bock:2007:DSR, author = "Mary Ellen Bock and Claudio Garutti and Concettina Guerra", title = "Discovery of Similar Regions on Protein Surfaces", journal = j-J-COMPUT-BIOL, volume = "14", number = "3", pages = "285--299", month = apr, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0145", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0145; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0145", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2007", } @Article{Parida:2007:DTM, author = "Laxmi Parida", title = "Discovering Topological Motifs Using a Compact Notation", journal = j-J-COMPUT-BIOL, volume = "14", number = "3", pages = "300--323", month = apr, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0142", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0142; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0142", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2007", } @Article{Kaminski:2007:PGM, author = "Naftali Kaminski and Ziv Bar-Joseph", title = "A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies", journal = j-J-COMPUT-BIOL, volume = "14", number = "3", pages = "324--338", month = apr, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0001", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0001; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0001", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2007", } @Article{Rempala:2007:VMM, author = "Grzegorz A. Rempala and Kenneth S. Ramos and Ted Kalbfleisch and Ivo Teneng", title = "Validation of a Mathematical Model of Gene Transcription in Aggregated Cellular Systems: Application to {L1} Retrotransposition", journal = j-J-COMPUT-BIOL, volume = "14", number = "3", pages = "339--349", month = apr, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2007", } @Article{Lubomirski:2007:CAA, author = "Mariusz Lubomirski and Michael R. D'Andrea and Stanley M. Belkowski and Javier Cabrera and James M. Dixon and Dhammika Amaratunga", title = "A Consolidated Approach to Analyzing Data from High-Throughput Protein Microarrays with an Application to Immune Response Profiling in Humans", journal = j-J-COMPUT-BIOL, volume = "14", number = "3", pages = "350--359", month = apr, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0116", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0116; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0116", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2007", } @Article{Rosenberg:2007:CCH, author = "Noah A. Rosenberg", title = "Counting Coalescent Histories", journal = j-J-COMPUT-BIOL, volume = "14", number = "3", pages = "360--377", month = apr, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0109", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0109; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0109", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2007", } @Article{Angibaud:2007:PBF, author = "S{\'e}bastien Angibaud and Guillaume Fertin and Irena Rusu and St{\'e}phane Vialette", title = "A Pseudo-{Boolean} Framework for Computing Rearrangement Distances between Genomes with Duplicates", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "379--393", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A001", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A001; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A001", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Blin:2007:GML, author = "Guillaume Blin and Eric Blais and Danny Hermelin and Pierre Guillon and Mathieu Blanchette and Nadia El-Mabrouk", title = "Gene Maps Linearization Using Genomic Rearrangement Distances", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "394--407", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A002; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A002", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Ozery-Flato:2007:SRT, author = "Michal Ozery-Flato and Ron Shamir", title = "Sorting by Reciprocal Translocations via Reversals Theory", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "408--422", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A003", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A003; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A003", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Xu:2007:PCB, author = "Wei Xu and Chunfang Zheng and David Sankoff", title = "Paths and Cycles in Breakpoint Graph of Random Multichromosomal Genomes", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "423--435", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A004", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A004; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A004", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Adam:2007:CIS, author = "Zaky Adam and Monique Turmel and Claude Lemieux and David Sankoff", title = "Common Intervals and Symmetric Difference in a Model-Free Phylogenomics, with an Application to Streptophyte Evolution", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "436--445", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A005", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A005; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A005", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Diallo:2007:EHA, author = "Abdoulaye Banire Diallo and Vladimir Makarenkov and Mathieu Blanchette", title = "Exact and Heuristic Algorithms for the Indel Maximum Likelihood Problem", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "446--461", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A006", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A006; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A006", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Lajoie:2007:DIH, author = "Mathieu Lajoie and Denis Bertrand and Nadia El-Mabrouk and Olivier Gascuel", title = "Duplication and Inversion History of a Tandemly Repeated Genes Family", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "462--478", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A007", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A007; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A007", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Wojtowicz:2007:EGF, author = "Damian W{\'o}jtowicz and Jerzy Tiuryn", title = "Evolution of Gene Families Based on Gene Duplication, Loss, Accumulated Change, and Innovation", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "479--495", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Song:2007:DAC, author = "N. Song and R. D. Sedgewick and D. Durand", title = "Domain Architecture Comparison for Multidomain Homology Identification", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "496--516", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A009", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A009; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A009", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Than:2007:CFH, author = "Cuong Than and Derek Ruths and Hideki Innan and Luay Nakhleh", title = "Confounding Factors in {HGT} Detection: Statistical Error, Coalescent Effects, and Multiple Solutions", journal = j-J-COMPUT-BIOL, volume = "14", number = "4", pages = "517--535", month = may, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.A010", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.A010; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.A010", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2007", } @Article{Apostolico:2007:Pa, author = "Alberto Apostolico", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "537--538", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.00P1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.00P1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Przytycka:2007:SCC, author = "Teresa Przytycka", title = "Stability of Characters and Construction of Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "539--549", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R001", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R001; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R001", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Huang:2007:BIM, author = "Jim C. Huang and Quaid D. Morris and Brendan J. Frey", title = "{Bayesian} Inference of {MicroRNA} Targets from Sequence and Expression Data", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "550--563", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R002; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R002", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Xu:2007:PAP, author = "Jinbo Xu and Feng Jiao and Bonnie Berger", title = "A Parameterized Algorithm for Protein Structure Alignment", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "564--577", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R003", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R003; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R003", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Chiang:2007:USR, author = "Tsung-Han Chiang and Mehmet Serkan Apaydin and Douglas L. Brutlag and David Hsu and Jean-Claude Latombe", title = "Using Stochastic Roadmap Simulation to Predict Experimental Quantities in Protein Folding Kinetics: Folding Rates and Phi-Values", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "578--593", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R004", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R004; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R004", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Cameron:2007:CSR, author = "Michael Cameron and Yaniv Bernstein and Hugh E. Williams", title = "Clustered Sequence Representation for Fast Homology Search", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "594--614", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R005", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R005; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R005", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Bader:2007:SWR, author = "Martin Bader and Enno Ohlebusch", title = "Sorting by Weighted Reversals, Transpositions, and Inverted Transpositions", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "615--636", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R006", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R006; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R006", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Xie:2007:RBE, author = "Wei Xie and Nikolaos V. Sahinidis", title = "A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "637--654", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R007", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R007; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R007", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Messer:2007:ELR, author = "Philipp W. Messer and Ralf Bundschuh and Martin Vingron and Peter F. Arndt", title = "Effects of Long-Range Correlations in {DNA} on Sequence Alignment Score Statistics", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "655--668", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Scheid:2007:CUC, author = "Stefanie Scheid and Rainer Spang", title = "Compensating for Unknown Confounders in Microarray Data Analysis Using Filtered Permutations", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "669--681", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R009", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R009; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R009", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Andersson:2007:MYS, author = "Samuel A. Andersson and Jens Lagergren", title = "{Motif Yggdrasil}: Sampling Sequence Motifs from a Tree Mixture Model", journal = j-J-COMPUT-BIOL, volume = "14", number = "5", pages = "682--697", month = jun, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R010", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R010; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R010", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2007", } @Article{Apostolico:2007:Pb, author = "Alberto Apostolico", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "699--700", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.00P2", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.00P2", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Angelov:2007:EEP, author = "Stanislav Angelov and Boulos Harb and Sampath Kannan and Sanjeev Khanna and Junhyong Kim", title = "Efficient Enumeration of Phylogenetically Informative Substrings", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "701--723", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R011", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R011; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R011", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Pattengale:2007:ECR, author = "Nicholas D. Pattengale and Eric J. Gottlieb and Bernard M. E. Moret", title = "Efficiently Computing the {Robinson--Foulds} Metric", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "724--735", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R012", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R012; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R012", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Heckerman:2007:LIA, author = "David Heckerman and Carl Kadie and Jennifer Listgarten", title = "Leveraging Information Across {HLA} Alleles/Supertypes Improves Epitope Prediction", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "736--746", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R013", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R013; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R013", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Koyuturk:2007:ASC, author = "Mehmet Koyut{\"u}rk and Wojciech Szpankowski and Ananth Grama", title = "Assessing Significance of Connectivity and Conservation in Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "747--764", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R014", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R014; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R014", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Chennubhotla:2007:MMH, author = "Chakra Chennubhotla and Ivet Bahar", title = "{Markov} Methods for Hierarchical Coarse-Graining of Large Protein Dynamics", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "765--776", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R015", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R015; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R015", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Ye:2007:HMM, author = "Xiaoduan Ye and Alan M. Friedman and Chris Bailey-Kellogg", title = "Hypergraph Model of Multi-Residue Interactions in Proteins: Sequentially-Constrained Partitioning Algorithms for Optimization of Site-Directed Protein Recombination", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "777--790", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R016", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R016; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R016", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Chen:2007:MPP, author = "Brian Y. Chen and Viacheslav Y. Fofanov and Drew H. Bryant and Bradley D. Dodson and David M. Kristensen and Andreas M. Lisewski and Marek Kimmel and Olivier Lichtarge and Lydia E. Kavraki", title = "The {MASH} Pipeline for Protein Function Prediction and an Algorithm for the Geometric Refinement of {$3$D} Motifs", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "791--816", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R017", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R017; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R017", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Chor:2007:BNC, author = "Benny Chor and Tamir Tuller", title = "Biological Networks: Comparison, Conservation, and Evolution via Relative Description Length", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "817--838", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R018", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R018; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R018", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Thomas:2007:SPM, author = "Shawna Thomas and Xinyu Tang and Lydia Tapia and Nancy M. Amato", title = "Simulating Protein Motions with Rigidity Analysis", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "839--855", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R019", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R019; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R019", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Wexler:2007:SAM, author = "Ydo Wexler and Chaya Zilberstein and Michal Ziv-Ukelson", title = "A Study of Accessible Motifs and {RNA} Folding Complexity", journal = j-J-COMPUT-BIOL, volume = "14", number = "6", pages = "856--872", month = jul, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.R020", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.R020; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.R020", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2007", } @Article{Domanic:2007:NAD, author = "Nevzat Onur Domani{\c{c}} and Franco P. Preparata", title = "A Novel Approach to the Detection of Genomic Approximate Tandem Repeats in the {Levenshtein} Metric", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "873--891", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0018", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0018; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0018", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Narayanan:2007:CPI, author = "Manikandan Narayanan and Richard M. Karp", title = "Comparing Protein Interaction Networks via a Graph Match-and-Split Algorithm", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "892--907", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0025", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0025; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0025", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Veksler-Lublinsky:2007:SBF, author = "Isana Veksler-Lublinsky and Michal Ziv-Ukelson and Danny Barash and Klara Kedem", title = "A Structure-Based Flexible Search Method for Motifs in {RNA}", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "908--926", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0061", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0061; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0061", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Albert:2007:NMS, author = "R{\'e}ka Albert and Bhaskar DasGupta and Riccardo Dondi and Sema Kachalo and Eduardo Sontag and Alexander Zelikovsky and Kelly Westbrooks", title = "A Novel Method for Signal Transduction Network Inference from Indirect Experimental Evidence", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "927--949", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0015", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0015; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0015", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Zhang:2007:NCC, author = "Liqing Zhang and Layne T. Watson", title = "Note on the Computation of Critical Effective Population Sizes", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "950--960", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0007", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0007; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0007", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Emmert-Streib:2007:CFS, author = "Frank Emmert-Streib", title = "The Chronic Fatigue Syndrome: a Comparative Pathway Analysis", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "961--972", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0041", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0041; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0041", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Andrecut:2007:PAG, author = "M. Andrecut and S. A. Kauffman", title = "A Physical Analogy of the Genetic Toggle Switch", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "973--983", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0038", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0038; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0038", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Zeiser:2007:MHO, author = "Stefan Zeiser and Johannes M{\"u}ller and Volkmar Liebscher", title = "Modeling the {Hes1} Oscillator", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "984--1000", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0029", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0029; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0029", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Christodoulakis:2007:EAC, author = "Manolis Christodoulakis and G. Brian Golding and Costas S. Iliopoulos and Yoan Jos{\'e} Pinz{\'o}n Ardila and William F. Smyth", title = "Efficient Algorithms for Counting and Reporting Segregating Sites in Genomic Sequences", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "1001--1010", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0136", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0136; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0136", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Shi:2007:QMB, author = "Yi Y. Shi and Gerald A. Miller and Oleg Denisenko and Hong Qian and Karol Bomsztyk", title = "Quantitative Model for Binary Measurements of Protein-Protein Interactions", journal = j-J-COMPUT-BIOL, volume = "14", number = "7", pages = "1011--1023", month = sep, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0024", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0024; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0024", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2007", } @Article{Wu:2007:HPI, author = "Xue Wu and Chau-Wen Tseng and Nathan Edwards", title = "{HMMatch}: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "14", number = "8", pages = "1025--1043", month = oct, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0071", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0071; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0071", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2007", } @Article{Frenkel:2007:ENF, author = "Zakharia M. Frenkel and Edward N. Trifonov", title = "Evolutionary Networks in the Formatted Protein Sequence Space", journal = j-J-COMPUT-BIOL, volume = "14", number = "8", pages = "1044--1057", month = oct, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0066", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0066; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0066", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2007", } @Article{Sterner:2007:PAC, author = "Beckett Sterner and Rohit Singh and Bonnie Berger", title = "Predicting and Annotating Catalytic Residues: An Information Theoretic Approach", journal = j-J-COMPUT-BIOL, volume = "14", number = "8", pages = "1058--1073", month = oct, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0042", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0042; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0042", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2007", } @Article{Backofen:2007:LGR, author = "Rolf Backofen and Shihyen Chen and Danny Hermelin and Gad M. Landau and Mikhail A. Roytberg and Oren Weimann and Kaizhong Zhang", title = "Locality and Gaps in {RNA} Comparison", journal = j-J-COMPUT-BIOL, volume = "14", number = "8", pages = "1074--1087", month = oct, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0062", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0062; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0062", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2007", } @Article{Bishop:2007:FEG, author = "Morgan A. Bishop and Arkadii G. D'Yachkov and Anthony J. Macula and Thomas E. Renz and Vyacheslav V. Rykov", title = "Free Energy Gap and Statistical Thermodynamic Fidelity of {DNA} Codes", journal = j-J-COMPUT-BIOL, volume = "14", number = "8", pages = "1088--1104", month = oct, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0083", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0083; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0083", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2007", } @Article{Deforche:2007:ERC, author = "Koen Deforche and Ricardo Camacho and Kristel {Van Laethem} and Beth Shapiro and Yves Moreau and Andrew Rambaut and Anne-Mieke Vandamme and Philippe Lemey", title = "Estimating the Relative Contribution of {dNTP} Pool Imbalance and {APOBEC3G\slash 3F} Editing to {HIV} Evolution {{\em In Vivo\/}}", journal = j-J-COMPUT-BIOL, volume = "14", number = "8", pages = "1105--1114", month = oct, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2007", } @Article{Stojmirovic:2007:IFI, author = "Aleksandar Stojmirovi{\'c} and Yi-Kuo Yu", title = "Information Flow in Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "14", number = "8", pages = "1115--1143", month = oct, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0069", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0069; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0069", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2007", } @Article{Parida:2007:SSL, author = "Laxmi Parida", title = "Statistical Significance of Large Gene Clusters", journal = j-J-COMPUT-BIOL, volume = "14", number = "9", pages = "1145--1159", month = nov, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:50 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0064; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0064", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2007", } @Article{Fu:2007:MHT, author = "Zheng Fu and Xin Chen and Vladimir Vacic and Peng Nan and Yang Zhong and Tao Jiang", title = "{MSOAR}: a High-Throughput Ortholog Assignment System Based on Genome Rearrangement", journal = j-J-COMPUT-BIOL, volume = "14", number = "9", pages = "1160--1175", month = nov, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0048", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:50 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0048; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0048", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2007", } @Article{Martin:2007:IVR, author = "Francis L. Martin and Matthew J. German and Ernst Wit and Thomas Fearn and Narasimhan Ragavan and Hubert M. Pollock", title = "Identifying Variables Responsible for Clustering in Discriminant Analysis of Data from Infrared Microspectroscopy of a Biological Sample", journal = j-J-COMPUT-BIOL, volume = "14", number = "9", pages = "1176--1184", month = nov, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0057", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:50 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0057; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0057", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2007", } @Article{Fuss:2007:DSF, author = "Hendrik Fu{\ss} and Werner Dubitzky and C. Stephen Downes and Mary Jo Kurth", title = "Deactivation of {Src} Family Kinases: Hypothesis Testing Using a {Monte Carlo} Sensitivity Analysis of Systems-Level Properties", journal = j-J-COMPUT-BIOL, volume = "14", number = "9", pages = "1185--1200", month = nov, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0095", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:50 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0095; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0095", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2007", } @Article{Shibuya:2007:ESR, author = "Tetsuo Shibuya", title = "Efficient Substructure {RMSD} Query Algorithms", journal = j-J-COMPUT-BIOL, volume = "14", number = "9", pages = "1201--1207", month = nov, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0079", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:50 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0079; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0079", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2007", } @Article{Cheng:2007:ECD, author = "Yongxi Cheng and Ding-Zhu Du", title = "Efficient Constructions of Disjunct Matrices with Applications to {DNA} Library Screening", journal = j-J-COMPUT-BIOL, volume = "14", number = "9", pages = "1208--1216", month = nov, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0052", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:50 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0052; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0052", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2007", } @Article{Tresch:2007:DDI, author = "Achim Tresch and T. Beissbarth and H. S{\"u}ltmann and R. Kuner and A. Poustka and A. Buness", title = "Discrimination of Direct and Indirect Interactions in a Network of Regulatory Effects", journal = j-J-COMPUT-BIOL, volume = "14", number = "9", pages = "1217--1228", month = nov, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0085", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:50 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0085; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0085", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2007", } @Article{Havukkala:2007:RIP, author = "Ilkka Havukkala and Stijn Vanderlooy", title = "On the Reliable Identification of Plant Sequences Containing a Polyadenylation Site", journal = j-J-COMPUT-BIOL, volume = "14", number = "9", pages = "1229--1245", month = nov, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0058", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:50 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0058; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0058", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2007", } @Article{Gusfield:2007:DTP, author = "Dan Gusfield and Vikas Bansal and Vineet Bafna and Yun S. Song", title = "A Decomposition Theory for Phylogenetic Networks and Incompatible Characters", journal = j-J-COMPUT-BIOL, volume = "14", number = "10", pages = "1247--1272", month = dec, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0137", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0137; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0137", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2007", } @Article{Song:2007:ADR, author = "Yun S. Song and Zhihong Ding and Dan Gusfield and Charles H. Langley and Yufeng Wu", title = "Algorithms to Distinguish the Role of Gene-Conversion from Single-Crossover Recombination in the Derivation of {SNP} Sequences in Populations", journal = j-J-COMPUT-BIOL, volume = "14", number = "10", pages = "1273--1286", month = dec, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0096; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0096", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2007", } @Article{Schmidler:2007:SES, author = "Scott C. Schmidler and Joseph E. Lucas and Terrence G. Oas", title = "Statistical Estimation of Statistical Mechanical Models: Helix-Coil Theory and Peptide Helicity Prediction", journal = j-J-COMPUT-BIOL, volume = "14", number = "10", pages = "1287--1310", month = dec, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2007", } @Article{Zhu:2007:BHM, author = "Dongxiao Zhu and Alfred O. {Hero III}", title = "{Bayesian} Hierarchical Model for Large-Scale Covariance Matrix Estimation", journal = j-J-COMPUT-BIOL, volume = "14", number = "10", pages = "1311--1326", month = dec, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2007", } @Article{Hirsch:2007:OSS, author = "Michael Hirsch and Stephen Swift and Xiohui Liu", title = "Optimal Search Space for Clustering Gene Expression Data via Consensus", journal = j-J-COMPUT-BIOL, volume = "14", number = "10", pages = "1327--1341", month = dec, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2007", } @Article{Zhu:2007:PLS, author = "Binhai Zhu", title = "Protein Local Structure Alignment Under the Discrete {Fr{\'e}chet} Distance", journal = j-J-COMPUT-BIOL, volume = "14", number = "10", pages = "1343--1351", month = dec, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0156; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0156", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2007", } @Article{Aastrand:2007:ICM, author = "Magnus {\AA}strand and Petter Mostad and Mats Rudemo", title = "Improved Covariance Matrix Estimators for Weighted Analysis of Microarray Data", journal = j-J-COMPUT-BIOL, volume = "14", number = "10", pages = "1353--1367", month = dec, year = "2007", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2007", } @Article{Picard:2008:AEN, author = "F. Picard and J.-J. Daudin and M. Koskas and S. Schbath and S. Robin", title = "Assessing the Exceptionality of Network Motifs", journal = j-J-COMPUT-BIOL, volume = "15", number = "1", pages = "1--20", month = jan, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0137", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0137; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0137", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 February 2008", } @Article{Andrecut:2008:SRG, author = "M. Andrecut and S. A. Kauffman", title = "On the Sparse Reconstruction of Gene Networks", journal = j-J-COMPUT-BIOL, volume = "15", number = "1", pages = "21--30", month = jan, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 February 2008", } @Article{Lorenz:2008:ARS, author = "W. A. Lorenz and Y. Ponty and P. Clote", title = "Asymptotics of {RNA} Shapes", journal = j-J-COMPUT-BIOL, volume = "15", number = "1", pages = "31--63", month = jan, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2006.0153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2006.0153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2006.0153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 February 2008", } @Article{Swanson:2008:IMQ, author = "Rosemarie Swanson and Ioannis Kagiampakis and Jerry W. Tsai", title = "An Information Measure of the Quality of Protein Secondary Structure Prediction", journal = j-J-COMPUT-BIOL, volume = "15", number = "1", pages = "65--79", month = jan, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0199", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0199; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0199", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 January 2008", } @Article{Brinza:2008:DVM, author = "Dumitru Brinza and Alexander Zelikovsky", title = "Design and Validation of Methods Searching for Risk Factors in Genotype Case-Control Studies", journal = j-J-COMPUT-BIOL, volume = "15", number = "1", pages = "81--90", month = jan, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0081", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0081; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0081", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 January 2008", } @Article{Snir:2008:SQP, author = "Sagi Snir and Tandy Warnow and Satish Rao", title = "Short Quartet Puzzling: a New Quartet-Based Phylogeny Reconstruction Algorithm", journal = j-J-COMPUT-BIOL, volume = "15", number = "1", pages = "91--103", month = jan, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 January 2008", } @Article{Bidot:2008:MMC, author = "C. Bidot and F. Gruy and C.-S. Haudin and F. {El Hentati} and B. Guy and C. Lambert", title = "Mathematical Modeling of {T}-Cell Activation Kinetic", journal = j-J-COMPUT-BIOL, volume = "15", number = "1", pages = "105--128", month = jan, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2008", } @Article{Huang:2008:SAA, author = "Xiaoqiu Huang", title = "Sequence Alignment with an Appropriate Substitution Matrix", journal = j-J-COMPUT-BIOL, volume = "15", number = "2", pages = "129--138", month = mar, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0155", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0155; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0155", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 March 2008", } @Article{Jabbari:2008:NER, author = "Hosna Jabbari and Anne Condon and Shelly Zhao", title = "Novel and Efficient {RNA} Secondary Structure Prediction Using Hierarchical Folding", journal = j-J-COMPUT-BIOL, volume = "15", number = "2", pages = "139--163", month = mar, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0198", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0198; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0198", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 March 2008", } @Article{Anandakrishnan:2008:ABC, author = "Ramu Anandakrishnan and Alexey Onufriev", title = "Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules", journal = j-J-COMPUT-BIOL, volume = "15", number = "2", pages = "165--184", month = mar, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0144", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0144; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0144", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 March 2008", } @Article{Gebert:2008:IGG, author = "Jutta Gebert and Susanne Motameny and Ulrich Faigle and Christian V. Forst and Rainer Schrader", title = "Identifying Genes of Gene Regulatory Networks Using Formal Concept Analysis", journal = j-J-COMPUT-BIOL, volume = "15", number = "2", pages = "185--194", month = mar, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0107", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0107; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0107", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 March 2008", } @Article{Cheng:2008:NCO, author = "Yongxi Cheng and Ding-Zhu Du", title = "New Constructions of One- and Two-Stage Pooling Designs", journal = j-J-COMPUT-BIOL, volume = "15", number = "2", pages = "195--205", month = mar, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0195", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0195; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0195", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 March 2008", } @Article{Santafe:2008:IPS, author = "Guzm{\'a}n Santaf{\'e} and Jose A. Lozano and Pedro Larra{\~n}aga", title = "Inference of Population Structure Using Genetic Markers and a {Bayesian} Model Averaging Approach for Clustering", journal = j-J-COMPUT-BIOL, volume = "15", number = "2", pages = "207--220", month = mar, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0051", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0051; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0051", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 March 2008", } @Article{Stolte:2008:MCE, author = "Thomas Stolte and Volker H{\"o}sel and Johannes M{\"u}ller and Michael Speicher", title = "Modeling Clonal Expansion from {M-FISH} Experiments", journal = j-J-COMPUT-BIOL, volume = "15", number = "2", pages = "221--230", month = mar, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0076", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0076; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0076", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 March 2008", } @Article{Nicola:2008:NMA, author = "George Nicola and Colin A. Smith and Ruben Abagyan", title = "New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome", journal = j-J-COMPUT-BIOL, volume = "15", number = "3", pages = "231--240", month = apr, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0178", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0178; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0178", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2008", } @Article{Li:2008:PSS, author = "Jing Li", title = "Prioritize and Select {SNPs} for Association Studies with Multi-Stage Designs", journal = j-J-COMPUT-BIOL, volume = "15", number = "3", pages = "241--257", month = apr, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0090", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0090; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0090", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 March 2008", } @Article{Haus:2008:CKS, author = "Utz-Uwe Haus and Steffen Klamt and Tamon Stephen", title = "Computing Knock-Out Strategies in Metabolic Networks", journal = j-J-COMPUT-BIOL, volume = "15", number = "3", pages = "259--268", month = apr, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0229", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0229; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0229", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2008", } @Article{Adewale:2008:PAM, author = "A. J. Adewale and I. Dinu and J. D. Potter and Q. Liu and Y. Yasui", title = "Pathway Analysis of Microarray Data via Regression", journal = j-J-COMPUT-BIOL, volume = "15", number = "3", pages = "269--277", month = apr, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0002; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0002", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2008", } @Article{Wu:2008:CBD, author = "Jing Wu and Jun Xie", title = "Computation-Based Discovery of {{\em Cis\/}}-Regulatory Modules by Hidden {Markov} Model", journal = j-J-COMPUT-BIOL, volume = "15", number = "3", pages = "279--290", month = apr, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0024", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0024; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0024", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2008", } @Article{Boden:2008:DNA, author = "Mikael Bod{\'e}n and Rohan D. Teasdale", title = "Determining Nucleolar Association from Sequence by Leveraging Protein-Protein Interactions", journal = j-J-COMPUT-BIOL, volume = "15", number = "3", pages = "291--304", month = apr, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2008", } @Article{Khanin:2008:CMP, author = "Raya Khanin and Veronica Vinciotti", title = "Computational Modeling of Post-Transcriptional Gene Regulation by {MicroRNAs}", journal = j-J-COMPUT-BIOL, volume = "15", number = "3", pages = "305--316", month = apr, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0184", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0184; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0184", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2008", } @Article{Wrabl:2008:SRP, author = "James O. Wrabl and Nick V. Grishin", title = "Statistics of Random Protein Superpositions: $p$-Values for Pairwise Structure Alignment", journal = j-J-COMPUT-BIOL, volume = "15", number = "3", pages = "317--355", month = apr, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0161", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:48:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0161; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0161", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2008", } @Article{Ohlebusch:2008:SEC, author = "Enno Ohlebusch and Stefan Kurtz", title = "Space Efficient Computation of Rare Maximal Exact Matches between Multiple Sequences", journal = j-J-COMPUT-BIOL, volume = "15", number = "4", pages = "357--377", month = may, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0105", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0105; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0105", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2008", } @Article{Polyanovsky:2008:RGP, author = "Valery Polyanovsky and Mikhail A. Roytberg and Vladimir G. Tumanyan", title = "Reconstruction of Genuine Pair-Wise Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "15", number = "4", pages = "379--391", month = may, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0145", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0145; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0145", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2008", } @Article{Filkov:2008:SMM, author = "Vladimir Filkov and Nameeta Shah", title = "A Simple Model of the Modular Structure of Transcriptional Regulation in Yeast", journal = j-J-COMPUT-BIOL, volume = "15", number = "4", pages = "393--405", month = may, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0020", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0020; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0020", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 May 2008", } @Article{Keith:2008:DSR, author = "Jonathan M. Keith and Peter Adams and Stuart Stephen and John S. Mattick", title = "Delineating Slowly and Rapidly Evolving Fractions of the \bioname{Drosophila} Genome", journal = j-J-COMPUT-BIOL, volume = "15", number = "4", pages = "407--430", month = may, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2008", } @Article{Ma:2008:UAC, author = "Patrick C. H. Ma and Keith C. C. Chan", title = "{UPSEC}: an Algorithm for Classifying Unaligned Protein Sequences into Functional Families", journal = j-J-COMPUT-BIOL, volume = "15", number = "4", pages = "431--443", month = may, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2008", } @Article{Tcheremenskaia:2008:PAI, author = "Olga Tcheremenskaia and Alessandro Giuliani and Maurizio Tomasi", title = "{PROFALIGN} Algorithm Identifies the Regions Containing Folding Determinants by Scoring Pairs of Hydrophobic Profiles of Remotely Related Proteins", journal = j-J-COMPUT-BIOL, volume = "15", number = "4", pages = "445--455", month = may, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0100; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0100", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 April 2008", } @Article{Feng:2008:CDA, author = "Jian Feng and Daniel Q. Naiman and Bret Cooper", title = "Combined Dynamic Arrays for Storing and Searching Semi-Ordered Tandem Mass Spectrometry Data", journal = j-J-COMPUT-BIOL, volume = "15", number = "4", pages = "457--468", month = may, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0011", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0011; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0011", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2008", } @Article{Do:2008:SBN, author = "Huy Hoang Do and Kwok Pui Choi and Franco P. Preparata and Wing Kin Sung and Louxin Zhang", title = "Spectrum-Based {{\em {De} Novo\/}} Repeat Detection in Genomic Sequences", journal = j-J-COMPUT-BIOL, volume = "15", number = "5", pages = "469--488", month = jun, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0013", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0013; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0013", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 June 2008", } @Article{Han:2008:SAP, author = "Buhm Han and Banu Dost and Vineet Bafna and Shaojie Zhang", title = "Structural Alignment of Pseudoknotted {RNA}", journal = j-J-COMPUT-BIOL, volume = "15", number = "5", pages = "489--504", month = jun, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0214", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0214; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0214", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 June 2008", } @Article{Zhao:2008:FAW, author = "Zhiyu Zhao and Bin Fu and Francisco J. Alanis and Christopher M. Summa", title = "Feedback Algorithm and {Web}-Server for Protein Structure Alignment", journal = j-J-COMPUT-BIOL, volume = "15", number = "5", pages = "505--524", month = jun, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0075", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0075; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0075", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 June 2008", } @Article{Macula:2008:NIP, author = "Anthony J. Macula and Alexander Schliep and Morgan A. Bishop and Thomas E. Renz", title = "New, Improved, and Practical $k$-Stem Sequence Similarity Measures for Probe Design", journal = j-J-COMPUT-BIOL, volume = "15", number = "5", pages = "525--534", month = jun, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0208", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0208; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0208", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 June 2008", } @Article{Chen:2008:LTP, author = "Zhixiang Chen and Bin Fu and Robert Schweller and Boting Yang and Zhiyu Zhao and Binhai Zhu", title = "Linear Time Probabilistic Algorithms for the Singular Haplotype Reconstruction Problem from {SNP} Fragments", journal = j-J-COMPUT-BIOL, volume = "15", number = "5", pages = "535--546", month = jun, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0003", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:03 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0003; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0003", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 June 2008", } @Article{Pape:2008:CPA, author = "Utz J. Pape and Sven Rahmann and Fengzhu Sun and Martin Vingron", title = "Compound {Poisson} Approximation of the Number of Occurrences of a Position Frequency Matrix {(PFM)} on Both Strands", journal = j-J-COMPUT-BIOL, volume = "15", number = "6", pages = "547--564", month = jul, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2008", } @Article{Blum:2008:UAM, author = "Torsten Blum and Oliver Kohlbacher", title = "Using Atom Mapping Rules for an Improved Detection of Relevant Routes in Weighted Metabolic Networks", journal = j-J-COMPUT-BIOL, volume = "15", number = "6", pages = "565--576", month = jul, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0044", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0044; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0044", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2008", } @Article{Kupczok:2008:EAG, author = "Anne Kupczok and Arndt {Von Haeseler} and Steffen Klaere", title = "An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "15", number = "6", pages = "577--591", month = jul, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0068", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0068; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0068", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2008", } @Article{Ling:2008:EIM, author = "Xu Ling and Xin He and Dong Xin and Jiawei Han", title = "Efficiently Identifying Max-Gap Clusters in Pairwise Genome Comparison", journal = j-J-COMPUT-BIOL, volume = "15", number = "6", pages = "593--609", month = jul, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0010", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0010; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0010", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2008", } @Article{Gold:2008:RTG, author = "David Gold and Bani Mallick and Kevin Coombes", title = "Real-Time Gene Expression: Statistical Challenges in Design and Inference", journal = j-J-COMPUT-BIOL, volume = "15", number = "6", pages = "611--623", month = jul, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0220", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0220; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0220", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2008", } @Article{Wong:2008:DHO, author = "Andrew K. C. Wong and Wai-Ho Au and Keith C. C. Chan", title = "Discovering High-Order Patterns of Gene Expression Levels", journal = j-J-COMPUT-BIOL, volume = "15", number = "6", pages = "625--637", month = jul, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0147", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0147; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0147", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2008", } @Article{Huber:2008:CDM, author = "Katharina T. Huber and Martin Lott and Vincent Moulton and Andreas Spillner", title = "The Complexity of Deriving Multi-Labeled Trees from Bipartitions", journal = j-J-COMPUT-BIOL, volume = "15", number = "6", pages = "639--651", month = jul, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0088", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0088; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0088", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2008", } @Article{Speed:2008:P, author = "Terry Speed", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "653--653", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.P001", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.P001", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 September 2008", } @Article{Philippakis:2008:DCU, author = "Anthony A. Philippakis and Aaron M. Qureshi and Michael F. Berger and Martha L. Bulyk", title = "Design of Compact, Universal {DNA} Microarrays for Protein Binding Microarray Experiments", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "655--665", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0114", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0114; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0114", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 July 2008", } @Article{Wu:2008:AMC, author = "Yufeng Wu", title = "Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "667--684", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0116", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0116; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0116", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 July 2008", } @Article{Schulz-Trieglaff:2008:CQP, author = "Ole Schulz-Trieglaff and Rene Hussong and Clemens Gr{\"o}pl and Andreas Leinenbach and Andreas Hildebrandt and Christian Huber and Knut Reinert", title = "Computational Quantification of Peptides from {LC-MS} Data", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "685--704", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0117", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0117; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0117", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2008", } @Article{Bern:2008:IRF, author = "Marshall Bern and David Goldberg", title = "Improved Ranking Functions for Protein and Modification-Site Identifications", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "705--719", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0119", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0119; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0119", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 July 2008", } @Article{Wexler:2008:VUL, author = "Ydo Wexler and Dan Geiger", title = "Variational Upper and Lower Bounds for Probabilistic Graphical Models", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "721--735", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2008", } @Article{Schneidman-Duhovny:2008:DPD, author = "Dina Schneidman-Duhovny and Oranit Dror and Yuval Inbar and Ruth Nussinov and Haim J. Wolfson", title = "Deterministic Pharmacophore Detection via Multiple Flexible Alignment of Drug-Like Molecules", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "737--754", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0130", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0130; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0130", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2008", } @Article{Kamisetty:2008:FEE, author = "Hetunandan Kamisetty and Eric P. Xing and Christopher J. Langmead", title = "Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "755--766", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0131", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0131; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0131", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2008", } @Article{Lu:2008:MSA, author = "Yue Lu and Sing-Hoi Sze", title = "Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "767--777", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0132", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0132; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0132", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2008", } @Article{Kuwahara:2008:PPT, author = "Hiroyuki Kuwahara and Chris J. Myers", title = "Production-Passage-Time Approximation: a New Approximation Method to Accelerate the Simulation Process of Enzymatic Reactions", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "779--792", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0135", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0135; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0135", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2008", } @Article{Ozery-Flato:2008:SGC, author = "Michal Ozery-Flato and Ron Shamir", title = "Sorting Genomes with Centromeres by Translocations", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "793--812", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0136", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0136; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0136", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2008", } @Article{Nigham:2008:PCF, author = "Anshul Nigham and David Hsu", title = "Protein Conformational Flexibility Analysis with Noisy Data", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "813--828", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0138", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0138; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0138", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2008", } @Article{Murali:2008:NLB, author = "T. M. Murali and Corban G. Rivera", title = "Network {Legos}: Building Blocks of Cellular Wiring Diagrams", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "829--844", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0139", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0139; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0139", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2008", } @Article{Piccolboni:2008:MSA, author = "Antonio Piccolboni", title = "Multivariate Segmentation in the Analysis of Transcription Tiling Array Data", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "845--856", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0141", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0141; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0141", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2008", } @Article{Wang:2008:EGW, author = "Wenyi Wang and Benilton Carvalho and Nathaniel D. Miller and Jonathan Pevsner and Aravinda Chakravarti and Rafael A. Irizarry", title = "Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "857--866", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0148", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0148; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0148", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2008", } @Article{Yu:2008:SVT, author = "Chun-Nam John Yu and Thorsten Joachims and Ron Elber and Jaroslaw Pillardy", title = "Support Vector Training of Protein Alignment Models", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "867--880", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0152", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0152; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0152", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2008", } @Article{Lee:2008:RFI, author = "Wah-Heng Lee and Wing-Kin Sung", title = "{RB-Finder}: an Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "881--898", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0154", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0154; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0154", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2008", } @Article{Yanover:2008:MLE, author = "Chen Yanover and Ora Schueler-Furman and Yair Weiss", title = "Minimizing and Learning Energy Functions for Side-Chain Prediction", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "899--911", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0158", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0158; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0158", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2008", } @Article{Dost:2008:QTQ, author = "Banu Dost and Tomer Shlomi and Nitin Gupta and Eytan Ruppin and Vineet Bafna and Roded Sharan", title = "{QNet}: a Tool for Querying Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "913--925", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0172; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2008", } @Article{Zaitlen:2008:SIA, author = "Noah Zaitlen and Manuel Reyes-Gomez and David Heckerman and Nebojsa Jojic", title = "Shift-Invariant Adaptive Double Threading: Learning {MHC} {II--Peptide} Binding", journal = j-J-COMPUT-BIOL, volume = "15", number = "7", pages = "927--942", month = sep, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0183", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0183; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0183", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 September 2008", } @Article{Tesler:2008:P, author = "Glenn Tesler and Dannie Durand", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "943--946", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.P002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.P002; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.P002", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2008", } @Article{Zheng:2008:DWG, author = "Chunfang Zheng and Qian Zhu and David Sankoff", title = "Descendants of Whole Genome Duplication within Gene Order Phylogeny", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "947--964", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0118", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0118; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0118", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 September 2008", } @Article{Xia:2008:RAA, author = "Ai Xia and Maria V. Sharakhova and Igor V. Sharakhov", title = "Reconstructing Ancestral Autosomal Arrangements in the \bioname{Anopheles gambiae} Complex", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "965--980", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0076", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0076; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0076", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 September 2008", } @Article{Vernot:2008:RNB, author = "Benjamin Vernot and Maureen Stolzer and Aiton Goldman and Dannie Durand", title = "Reconciliation with Non-Binary Species Trees", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "981--1006", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0092", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0092; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0092", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2008", } @Article{Ma:2008:DRC, author = "Jian Ma and Aakrosh Ratan and Brian J. Raney and Bernard B. Suh and Louxin Zhang and Webb Miller and David Haussler", title = "{DUPCAR}: Reconstructing Contiguous Ancestral Regions with Duplications", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "1007--1027", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0069", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0069; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0069", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 September 2008", } @Article{Gog:2008:FAT, author = "Simon Gog and Martin Bader", title = "Fast Algorithms for Transforming Back and Forth between a Signed Permutation and Its Equivalent Simple Permutation", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "1029--1041", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0040", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0040; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0040", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2008", } @Article{Chauve:2008:GFE, author = "Cedric Chauve and Jean-Philippe Doyon and Nadia El-Mabrouk", title = "Gene Family Evolution by Duplication, Speciation, and Loss", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "1043--1062", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0054", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0054; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0054", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2008", } @Article{Bertrand:2008:IAG, author = "Denis Bertrand and Mathieu Lajoie and Nadia El-Mabrouk", title = "Inferring Ancestral Gene Orders for a Family of Tandemly Arrayed Genes", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "1063--1077", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0025", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0025; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0025", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2008", } @Article{Arndt:2008:IRM, author = "William Arndt and Jijun Tang", title = "Improving Reversal Median Computation Using Commuting Reversals and Cycle Information", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "1079--1092", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0116", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0116; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0116", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 September 2008", } @Article{Angibaud:2008:ETC, author = "S{\'e}bastien Angibaud and Guillaume Fertin and Irena Rusu and Annelyse Th{\'e}venin and St{\'e}phane Vialette", title = "Efficient Tools for Computing the Number of Breakpoints and the Number of Adjacencies between Two Genomes with Duplicate Genes", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "1093--1115", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0061", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0061; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0061", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 September 2008", } @Article{Alekseyev:2008:MBR, author = "Max A. Alekseyev", title = "Multi-Break Rearrangements and Breakpoint Re-Uses: From Circular to Linear Genomes", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "1117--1131", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0080", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0080; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0080", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 September 2008", } @Article{Anonymous:2008:C, author = "Anonymous", title = "Correction", journal = j-J-COMPUT-BIOL, volume = "15", number = "8", pages = "1132--1132", month = oct, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.C002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.C002", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2008", } @Article{Parida:2008:EAR, author = "Laxmi Parida and Marta Mel{\'e} and Francesc Calafell and Jaume Bertranpetit", title = "Estimating the Ancestral Recombinations Graph {(ARG)} as Compatible Networks of {SNP} Patterns", journal = j-J-COMPUT-BIOL, volume = "15", number = "9", pages = "1133--1153", month = nov, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0065", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0065; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0065", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 October 2008", } @Article{Kennedy:2008:GED, author = "Justin Kennedy and Ion M{\u{a}}ndoiu and Bogdan Pa{\c{s}}aniuc", title = "Genotype Error Detection Using Hidden {Markov} Models of Haplotype Diversity", journal = j-J-COMPUT-BIOL, volume = "15", number = "9", pages = "1155--1171", month = nov, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0133", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0133; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0133", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2008", } @Article{Andrecut:2008:HAS, author = "M. Andrecut and S. Huang and S. A. Kauffman", title = "Heuristic Approach to Sparse Approximation of Gene Regulatory Networks", journal = j-J-COMPUT-BIOL, volume = "15", number = "9", pages = "1173--1186", month = nov, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0087", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0087; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0087", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 October 2008", } @Article{Newberg:2008:SGS, author = "Lee A. Newberg", title = "Significance of Gapped Sequence Alignments", journal = j-J-COMPUT-BIOL, volume = "15", number = "9", pages = "1187--1194", month = nov, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2008", } @Article{Han:2008:PRS, author = "Hillary S. W. Han and Christian M. Reidys", title = "Pseudoknot {RNA} Structures with Arc-Length $ \geq 4 $", journal = j-J-COMPUT-BIOL, volume = "15", number = "9", pages = "1195--1208", month = nov, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0051", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0051; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0051", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2008", } @Article{Mardia:2008:SVP, author = "Kanti V. Mardia and Vysaul B. Nyirongo", title = "Simulating Virtual Protein {$ C_\alpha $} Traces with Applications", journal = j-J-COMPUT-BIOL, volume = "15", number = "9", pages = "1209--1220", month = nov, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0092", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0092; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0092", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2008", } @Article{Diaz:2008:APP, author = "Mar{\'\i}a Elena D{\'\i}az and Guillermo Ayala and Teresa Le{\'o}n and Roberto Zoncu and Derek Toomre", title = "Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets", journal = j-J-COMPUT-BIOL, volume = "15", number = "9", pages = "1221--1236", month = nov, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0055", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0055; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0055", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2008", } @Article{Jiang:2008:CRP, author = "Xianyang Jiang and Dominique Lavenier and Stephen S.-T. Yau", title = "Coding Region Prediction Based on a Universal {DNA} Sequence Representation Method", journal = j-J-COMPUT-BIOL, volume = "15", number = "10", pages = "1237--1256", month = dec, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0041", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0041; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0041", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2008", } @Article{Ma:2008:CRP, author = "Gang Ma and Christian M. Reidys", title = "Canonical {RNA} Pseudoknot Structures", journal = j-J-COMPUT-BIOL, volume = "15", number = "10", pages = "1257--1273", month = dec, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0121", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0121; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0121", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2008", } @Article{Xiao:2008:EVA, author = "Jing Xiao and Lusheng Wang and Xiaowen Liu and Tao Jiang", title = "An Efficient Voting Algorithm for Finding Additive Biclusters with Random Background", journal = j-J-COMPUT-BIOL, volume = "15", number = "10", pages = "1275--1293", month = dec, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0219", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0219; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0219", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 October 2010", } @Article{Yang:2008:RPS, author = "Jialiang Yang and Louxin Zhang", title = "Run Probabilities of Seed-Like Patterns and Identifying Good Transition Seeds", journal = j-J-COMPUT-BIOL, volume = "15", number = "10", pages = "1295--1313", month = dec, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0209", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0209; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0209", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2008", } @Article{Lijoi:2008:BNA, author = "Antonio Lijoi and Rams{\'e}s H. Mena and Igor Pr{\"u}nster", title = "A {Bayesian} Nonparametric Approach for Comparing Clustering Structures in {EST} Libraries", journal = j-J-COMPUT-BIOL, volume = "15", number = "10", pages = "1315--1327", month = dec, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0043", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0043; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0043", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2008", } @Article{vanUitert:2008:BSB, author = "Miranda van Uitert and Wouter Meuleman and Lodewyk Wessels", title = "Biclustering Sparse Binary Genomic Data", journal = j-J-COMPUT-BIOL, volume = "15", number = "10", pages = "1329--1345", month = dec, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0066", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0066; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0066", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2008", } @Article{Tang:2008:BFB, author = "Man-Hung Eric Tang and Anders Krogh and Ole Winther", title = "{BayesMD}: Flexible Biological Modeling for Motif Discovery", journal = j-J-COMPUT-BIOL, volume = "15", number = "10", pages = "1347--1363", month = dec, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0176", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0176; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0176", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2008", } @Article{Porreca:2008:SIP, author = "Riccardo Porreca and Samuel Drulhe and Hidde de Jong and Giancarlo Ferrari-Trecate", title = "Structural Identification of Piecewise-Linear Models of Genetic Regulatory Networks", journal = j-J-COMPUT-BIOL, volume = "15", number = "10", pages = "1365--1380", month = dec, year = "2008", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0109", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0109; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0109", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2008", } @Article{Newberg:2009:ECD, author = "Lee A. Newberg and Charles E. Lawrence", title = "Exact Calculation of Distributions on Integers, with Application to Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "16", number = "1", pages = "1--18", month = jan, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0137", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0137; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0137", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2009", } @Article{Khodabakhshi:2009:SSA, author = "Alireza Hadj Khodabakhshi and J{\'a}n Ma{\v{n}}uch and Arash Rafiey and Arvind Gupta", title = "Stable Structure-Approximating Inverse Protein Folding in {$2$D} Hydrophobic-Polar-Cysteine {(HPC)} Model", journal = j-J-COMPUT-BIOL, volume = "16", number = "1", pages = "19--30", month = jan, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0096; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0096", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 December 2008", } @Article{Kong:2009:SDP, author = "Yong Kong", title = "Statistical Distributions of Pyrosequencing", journal = j-J-COMPUT-BIOL, volume = "16", number = "1", pages = "31--42", month = jan, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0106", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0106; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0106", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 December 2008", } @Article{Bonizzoni:2009:DAG, author = "Paola Bonizzoni and Giancarlo Mauri and Graziano Pesole and Ernesto Picardi and Yuri Pirola and Raffaella Rizzi", title = "Detecting Alternative Gene Structures from Spliced {ESTs}: a Computational Approach", journal = j-J-COMPUT-BIOL, volume = "16", number = "1", pages = "43--66", month = jan, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0028", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0028; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0028", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2009", } @Article{Passos:2009:ODO, author = "Val{\'e}ria Lima Passos and Frans E. S. Tan and Bjorn Winkens and Martijn P. F. Berger", title = "Optimal Designs for One- and Two-Color Microarrays Using Mixed Models: a Comparative Evaluation of Their Efficiencies", journal = j-J-COMPUT-BIOL, volume = "16", number = "1", pages = "67--83", month = jan, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0048", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0048; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0048", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 December 2008", } @Article{Hoque:2009:EHM, author = "Tamjidul Hoque and Madhu Chetty and Abdul Sattar", title = "Extended {HP} Model for Protein Structure Prediction", journal = j-J-COMPUT-BIOL, volume = "16", number = "1", pages = "85--103", month = jan, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0082", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0082; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0082", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2009", } @Article{Libeskind-Hadas:2009:CCR, author = "Ran Libeskind-Hadas and Michael A. Charleston", title = "On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem", journal = j-J-COMPUT-BIOL, volume = "16", number = "1", pages = "105--117", month = jan, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2009", } @Article{Ge:2009:BNA, author = "Hao Ge and Min Qian", title = "{Boolean} Network Approach to Negative Feedback Loops of the p53 Pathways: Synchronized Dynamics and Stochastic Limit Cycles", journal = j-J-COMPUT-BIOL, volume = "16", number = "1", pages = "119--132", month = jan, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0181", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0181; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0181", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2009", } @Article{Leung:2009:PPC, author = "Henry C. M. Leung and Qian Xiang and S. M. Yiu and Francis Y. L. Chin", title = "Predicting Protein Complexes from {PPI} Data: a Core-Attachment Approach", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "133--144", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.01TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.01TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.01TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2009", } @Article{Qian:2009:QPP, author = "Xiaoning Qian and Sing-Hoi Sze and Byung-Jun Yoon", title = "Querying Pathways in Protein Interaction Networks Based on Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "145--157", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.02TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.02TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.02TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2009", } @Article{Hormozdiari:2009:EID, author = "Fereydoun Hormozdiari and Raheleh Salari and Michael Hsing and Alexander Sch{\"o}nhuth and Simon K. Chan and S. Cenk Sahinalp and Artem Cherkasov", title = "The Effect of Insertions and Deletions on Wirings in Protein-Protein Interaction Networks: a Large-Scale Study", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "159--167", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.03TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.03TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.03TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2009", } @Article{McDermott:2009:BHI, author = "Jason E. McDermott and Ronald C. Taylor and Hyunjin Yoon and Fred Heffron", title = "Bottlenecks and Hubs in Inferred Networks Are Important for Virulence in \bioname{Salmonella typhimurium}", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "169--180", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.04TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.04TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.04TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2009", } @Article{Karni:2009:NBM, author = "Shaul Karni and Hermona Soreq and Roded Sharan", title = "A Network-Based Method for Predicting Disease-Causing Genes", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "181--189", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.05TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.05TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.05TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2009", } @Article{Borenstein:2009:TSS, author = "Elhanan Borenstein and Marcus W. Feldman", title = "Topological Signatures of Species Interactions in Metabolic Networks", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "191--200", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.06TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.06TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.06TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2009", } @Article{Sachs:2009:LSN, author = "Karen Sachs and Solomon Itani and Jennifer Carlisle and Garry P. Nolan and Dana Pe'er and Douglas A. Lauffenburger", title = "Learning Signaling Network Structures with Sparsely Distributed Data", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "201--212", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.07TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.07TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.07TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2009", } @Article{Castelo:2009:REM, author = "Robert Castelo and Alberto Roverato", title = "Reverse Engineering Molecular Regulatory Networks from Microarray Data with qp-Graphs", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "213--227", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.08TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.08TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.08TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2009", } @Article{Marbach:2009:GRS, author = "Daniel Marbach and Thomas Schaffter and Claudio Mattiussi and Dario Floreano", title = "Generating Realistic {{\em In Silico\/}} Gene Networks for Performance Assessment of Reverse Engineering Methods", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "229--239", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.09TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.09TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.09TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 January 2009", } @Article{Iorio:2009:IND, author = "Francesco Iorio and Roberto Tagliaferri and Diego di Bernardo", title = "Identifying Network of Drug Mode of Action by Gene Expression Profiling", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "241--251", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.10TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.10TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.10TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 January 2009", } @Article{Navlakha:2009:RBM, author = "Saket Navlakha and Michael C. Schatz and Carl Kingsford", title = "Revealing Biological Modules via Graph Summarization", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "253--264", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.11TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.11TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.11TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 January 2009", } @Article{Chen:2009:IBK, author = "Xi Chen and Lily Wang", title = "Integrating Biological Knowledge with Gene Expression Profiles for Survival Prediction of Cancer", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "265--278", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.12TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.12TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.12TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 January 2009", } @Article{Chechik:2009:TGE, author = "Gal Chechik and Daphne Koller", title = "Timing of Gene Expression Responses to Environmental Changes", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "279--290", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.13TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.13TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.13TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2009", } @Article{Veeramani:2009:MFC, author = "Balaji Veeramani and Joel S. Bader", title = "Metabolic Flux Correlations, Genetic Interactions, and Disease", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "291--302", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.14TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.14TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.14TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 January 2009", } @Article{Tuller:2009:HOG, author = "Tamir Tuller and Udi Rubinstein and Dani Bar and Michael Gurevitch and Eytan Ruppin and Martin Kupiec", title = "Higher-Order Genomic Organization of Cellular Functions in Yeast", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "303--316", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.15TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.15TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.15TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2009", } @Article{Li:2009:GGA, author = "Leping Li", title = "{GADEM}: a Genetic Algorithm Guided Formation of Spaced Dyads Coupled with an {EM} Algorithm for Motif Discovery", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "317--329", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.16TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.16TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.16TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2009", } @Article{Lee:2009:SLE, author = "J. William Lee and Tomasz Zemojtel and Eugene Shakhnovich", title = "Systems-Level Evidence of Transcriptional Co-Regulation of Yeast Protein Complexes", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "331--339", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.17TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.17TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.17TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2009", } @Article{Yuan:2009:TRH, author = "Guo-Cheng Yuan", title = "Targeted Recruitment of Histone Modifications in Humans Predicted by Genomic Sequences", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "341--355", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.18TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.18TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.18TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2009", } @Article{Yeo:2009:ITF, author = "Zhen Xuan Yeo and Hock Chuan Yeo and Joan Keng Suan Yeo and Ai Li Yeo and Ye Li and Neil D. Clarke", title = "Inferring Transcription Factor Targets from Gene Expression Changes and Predicted Promoter Occupancy", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "357--368", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.19TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.19TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.19TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2009", } @Article{Erives:2009:NHS, author = "Albert Erives", title = "Non-Homologous Structured {CRMs} from the \bioname{Ciona} Genome", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "369--377", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.20TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.20TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.20TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2009", } @Article{Russo:2009:HSB, author = "G. Russo and M. {Di Bernardo}", title = "How to Synchronize Biological Clocks", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "379--393", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.21TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.21TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.21TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 January 2009", } @Article{Kluge:2009:MEA, author = "Bogusaw Kluge and Anna Gambin and Wojciech Niemiro", title = "Modeling Exopeptidase Activity from {LC-MS} Data", journal = j-J-COMPUT-BIOL, volume = "16", number = "2", pages = "395--406", month = feb, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.22TT", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.22TT; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.22TT", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 January 2009", } @Article{Shojaie:2009:AGS, author = "Ali Shojaie and George Michailidis", title = "Analysis of Gene Sets Based on the Underlying Regulatory Network", journal = j-J-COMPUT-BIOL, volume = "16", number = "3", pages = "407--426", month = mar, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0081", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0081; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0081", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 October 2010", } @Article{Gu:2009:OEP, author = "Junfeng Gu and Honglin Li and Hualiang Jiang and Xicheng Wang", title = "Optimizing Energy Potential for Protein Fold Recognition with Parametric Evaluation Function", journal = j-J-COMPUT-BIOL, volume = "16", number = "3", pages = "427--442", month = mar, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0128", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0128; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0128", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2009", } @Article{Lacey:2009:SEP, author = "Michelle R. Lacey and Jason Calmes", title = "A Sharp Error Probability Estimate for the Reconstruction of Phylogenetic Quartets by the Four-Point Method", journal = j-J-COMPUT-BIOL, volume = "16", number = "3", pages = "443--456", month = mar, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0123", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0123; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0123", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2009", } @Article{Min:2009:LRW, author = "Renqiang Min and Anthony Bonner and Jingjing Li and Zhaolei Zhang", title = "Learned Random-Walk Kernels and Empirical-Map Kernels for Protein Sequence Classification", journal = j-J-COMPUT-BIOL, volume = "16", number = "3", pages = "457--474", month = mar, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0031", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0031; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0031", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2009", } @Article{Blanchet:2009:MBA, author = "Juliette Blanchet and Matthieu Vignes", title = "A Model-Based Approach to Gene Clustering with Missing Observation Reconstruction in a {Markov} Random Field Framework", journal = j-J-COMPUT-BIOL, volume = "16", number = "3", pages = "475--486", month = mar, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2009", } @Article{Grandison:2009:AZM, author = "Scott Grandison and Carl Roberts and Richard J. Morris", title = "The Application of {$3$D} {Zernike} Moments for the Description of ``Model-Free'' Molecular Structure, Functional Motion, and Structural Reliability", journal = j-J-COMPUT-BIOL, volume = "16", number = "3", pages = "487--500", month = mar, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0083", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0083; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0083", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2009", } @Article{Soloveichik:2009:RSC, author = "David Soloveichik", title = "Robust Stochastic Chemical Reaction Networks and Bounded {Tau}-Leaping", journal = j-J-COMPUT-BIOL, volume = "16", number = "3", pages = "501--522", month = mar, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0063", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0063; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0063", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2009", } @Article{Dynerman:2009:CCG, author = "David Dynerman and Erick Butzlaff and Julie C. Mitchell", title = "{CUSA} and {CUDE}: {GPU-Accelerated} Methods for Estimating Solvent Accessible Surface Area and Desolvation", journal = j-J-COMPUT-BIOL, volume = "16", number = "4", pages = "523--537", month = apr, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0157", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0157; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0157", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2009", } @Article{Ribeiro:2009:DSM, author = "Andre S. Ribeiro and Olli-Pekka Smolander and Tiina Rajala and Antti H{\"a}kkinen and Olli Yli-Harja", title = "Delayed Stochastic Model of Transcription at the Single Nucleotide Level", journal = j-J-COMPUT-BIOL, volume = "16", number = "4", pages = "539--553", month = apr, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2009", } @Article{Ilatovskiy:2009:GWS, author = "Andrey Ilatovskiy and Michael Petukhov", title = "Genome-Wide Search for Local {DNA} Segments with Anomalous {GC-Content}", journal = j-J-COMPUT-BIOL, volume = "16", number = "4", pages = "555--564", month = apr, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0159", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0159; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0159", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2009", } @Article{Tembe:2009:SCF, author = "Waibhav D. Tembe and John V. Pearson and Nils Homer and James Lowey and Edward Suh and David W. Craig", title = "Statistical Comparison Framework and Visualization Scheme for Ranking-Based Algorithms in High-Throughput Genome-Wide Studies", journal = j-J-COMPUT-BIOL, volume = "16", number = "4", pages = "565--577", month = apr, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2009", } @Article{Stojmirovic:2009:GAB, author = "Aleksandar Stojmirovi{\'c} and Yi-Kuo Yu", title = "Geometric Aspects of Biological Sequence Comparison", journal = j-J-COMPUT-BIOL, volume = "16", number = "4", pages = "579--610", month = apr, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0100; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0100", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2009", } @Article{Dombi:2009:AFT, author = "J{\'o}zsef Dombi and Attila Kert{\'e}sz-Farkas", title = "Applying Fuzzy Technologies to Equivalence Learning in Protein Classification", journal = j-J-COMPUT-BIOL, volume = "16", number = "4", pages = "611--623", month = apr, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0147", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0147; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0147", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2009", } @Article{Southworth:2009:PBP, author = "Lucinda K. Southworth and Stuart K. Kim and Art B. Owen", title = "Properties of Balanced Permutations", journal = j-J-COMPUT-BIOL, volume = "16", number = "4", pages = "625--638", month = apr, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0144", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0144; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0144", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2009", } @Article{Liu:2009:CGM, author = "Yan Liu and Jaime Carbonell and Vanathi Gopalakrishnan and Peter Weigele", title = "Conditional Graphical Models for Protein Structural Motif Recognition", journal = j-J-COMPUT-BIOL, volume = "16", number = "5", pages = "639--657", month = may, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0176", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0176; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0176", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2009", } @Article{Seok:2009:FAC, author = "Sang-Cheol Seok and Michael Evans and Veronica J. Vieland", title = "Fast and Accurate Calculation of a Computationally Intensive Statistic for Mapping Disease Genes", journal = j-J-COMPUT-BIOL, volume = "16", number = "5", pages = "659--676", month = may, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0175", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0175; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0175", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2009", } @Article{DeMol:2009:RMS, author = "Christine {De Mol} and Sofia Mosci and Magali Traskine and Alessandro Verri", title = "A Regularized Method for Selecting Nested Groups of Relevant Genes from Microarray Data", journal = j-J-COMPUT-BIOL, volume = "16", number = "5", pages = "677--690", month = may, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0171", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0171; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0171", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2009", } @Article{Yang:2009:PCH, author = "Zheng Rong Yang", title = "Predict Collagen Hydroxyproline Sites Using Support Vector Machines", journal = j-J-COMPUT-BIOL, volume = "16", number = "5", pages = "691--702", month = may, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0167", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0167; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0167", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2009", } @Article{Georgiev:2009:IND, author = "Alexander G. Georgiev", title = "Interpretable Numerical Descriptors of Amino Acid Space", journal = j-J-COMPUT-BIOL, volume = "16", number = "5", pages = "703--723", month = may, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2009", } @Article{Haus:2009:LIP, author = "Utz-Uwe Haus and Kathrin Niermann and Klaus Truemper and Robert Weismantel", title = "Logic Integer Programming Models for Signaling Networks", journal = j-J-COMPUT-BIOL, volume = "16", number = "5", pages = "725--743", month = may, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2009", } @Article{Chang:2009:MSC, author = "Ye-In Chang and Jiun-Rung Chen and Yueh-Chi Tsai", title = "Mining Subspace Clusters from {DNA} Microarray Data Using Large Itemset Techniques", journal = j-J-COMPUT-BIOL, volume = "16", number = "5", pages = "745--768", month = may, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0161", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0161; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0161", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2009", } @Article{Khodabakhshi:2009:IPF, author = "Alireza Hadj Khodabakhshi and J{\'a}n Ma{\v{n}}uch and Arash Rafiey and Arvind Gupta", title = "Inverse Protein Folding in {$3$D} Hexagonal Prism Lattice under {HPC} Model", journal = j-J-COMPUT-BIOL, volume = "16", number = "6", pages = "769--802", month = jun, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0202", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0202; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0202", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2009", } @Article{Chen:2009:AMP, author = "Ho-Lin Chen and Anne Condon and Hosna Jabbari", title = "An {$O$} ( $ n^5$ ) Algorithm for {MFE} Prediction of Kissing Hairpins and $4$-Chains in Nucleic Acids", journal = j-J-COMPUT-BIOL, volume = "16", number = "6", pages = "803--815", month = jun, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0219", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0219; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0219", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2009", } @Article{Kong:2009:SDS, author = "Yong Kong", title = "Statistical Distributions of Sequencing by Synthesis with Probabilistic Nucleotide Incorporation", journal = j-J-COMPUT-BIOL, volume = "16", number = "6", pages = "817--827", month = jun, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0215", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0215; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0215", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2009", } @Article{Behre:2009:MST, author = "J{\"o}rn Behre and Stefan Schuster", title = "Modeling Signal Transduction in Enzyme Cascades with the Concept of Elementary Flux Modes", journal = j-J-COMPUT-BIOL, volume = "16", number = "6", pages = "829--844", month = jun, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0177", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0177; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0177", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2009", } @Article{Hansen:2009:SML, author = "Niels Richard Hansen", title = "Statistical Models for Local Occurrences of {RNA} Structures", journal = j-J-COMPUT-BIOL, volume = "16", number = "6", pages = "845--858", month = jun, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0180", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0180; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0180", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2009", } @Article{Geraci:2009:KBS, author = "Filippo Geraci and Mauro Leoncini and Manuela Montangero and Marco Pellegrini and M. Elena Renda", title = "{K-Boost}: a Scalable Algorithm for High-Quality Clustering of Microarray Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "16", number = "6", pages = "859--873", month = jun, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0201", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0201; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0201", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2009", } @Article{August:2009:NCT, author = "Elias August and Antonis Papachristodoulou", title = "A New Computational Tool for Establishing Model Parameter Identifiability", journal = j-J-COMPUT-BIOL, volume = "16", number = "6", pages = "875--885", month = jun, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0211", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0211; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0211", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2009", } @Article{Anonymous:2009:C, author = "Anonymous", title = "Correction", journal = j-J-COMPUT-BIOL, volume = "16", number = "6", pages = "886--886", month = jun, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.00C1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.00C1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2009", } @Article{Huang:2009:MSN, author = "Xiaoqiu Huang and Martin Vingron", title = "Maximum Similarity: a New Formulation of Phylogenetic Reconstruction", journal = j-J-COMPUT-BIOL, volume = "16", number = "7", pages = "887--896", month = jul, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0232", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0232; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0232", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2009", } @Article{Nagarajan:2009:PCS, author = "Niranjan Nagarajan and Mihai Pop", title = "Parametric Complexity of Sequence Assembly: Theory and Applications to Next Generation Sequencing", journal = j-J-COMPUT-BIOL, volume = "16", number = "7", pages = "897--908", month = jul, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0005", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0005; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0005", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2009", } @Article{Andrecut:2009:MIT, author = "M. Andrecut and D. Foster and H. Carteret and S. A. Kauffman", title = "Maximal Information Transfer and Behavior Diversity in Random Threshold Networks", journal = j-J-COMPUT-BIOL, volume = "16", number = "7", pages = "909--916", month = jul, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0007", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0007; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0007", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2009", } @Article{Cai:2009:SMS, author = "Xiaodong Cai and Zhi-Min Yuan", title = "Stochastic Modeling and Simulation of the {p53-MDM2/MDMX} Loop", journal = j-J-COMPUT-BIOL, volume = "16", number = "7", pages = "917--933", month = jul, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0231", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0231; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0231", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2009", } @Article{Qiu:2009:SCD, author = "Peng Qiu and Sylvia K. Plevritis", title = "Simultaneous Class Discovery and Classification of Microarray Data Using Spectral Analysis", journal = j-J-COMPUT-BIOL, volume = "16", number = "7", pages = "935--944", month = jul, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0227", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0227; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0227", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2009", } @Article{Kato:2009:DPA, author = "Yuki Kato and Tatsuya Akutsu and Hiroyuki Seki", title = "Dynamic Programming Algorithms and Grammatical Modeling for Protein Beta-Sheet Prediction", journal = j-J-COMPUT-BIOL, volume = "16", number = "7", pages = "945--957", month = jul, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0228", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0228; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0228", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2009", } @Article{Bartholome:2009:EGI, author = "Kilian Bartholom{\'e} and Clemens Kreutz and Jens Timmer", title = "Estimation of Gene Induction Enables a Relevance-Based Ranking of Gene Sets", journal = j-J-COMPUT-BIOL, volume = "16", number = "7", pages = "959--967", month = jul, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0226", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0226; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0226", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2009", } @Article{Anonymous:2009:SRI, author = "Anonymous", title = "Special {RECOMB 2008} Issue", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "969--969", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.001P", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.001P", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2009", } @Article{Friedel:2009:BIU, author = "Caroline C. Friedel and Jan Krumsiek and Ralf Zimmer", title = "Bootstrapping the Interactome: Unsupervised Identification of Protein Complexes in Yeast", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "971--987", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0023; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0023", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2009", } @Article{Kalaev:2009:FAA, author = "Maxim Kalaev and Vineet Bafna and Roded Sharan", title = "Fast and Accurate Alignment of Multiple Protein Networks", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "989--999", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0136", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0136; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0136", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 July 2009", } @Article{Flannick:2009:APL, author = "Jason Flannick and Antal Novak and Chuong B. Do and Balaji S. Srinivasan and Serafim Batzoglou", title = "Automatic Parameter Learning for Multiple Local Network Alignment", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1001--1022", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0099", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0099; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0099", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2009", } @Article{Mehan:2009:INA, author = "Michael R. Mehan and Juan Nunez-Iglesias and Mrinal Kalakrishnan and Michael S. Waterman and Xianghong Jasmine Zhou", title = "An Integrative Network Approach to Map the Transcriptome to the Phenome", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1023--1034", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0037", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0037; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0037", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2009", } @Article{Shi:2009:CEI, author = "Yanxin Shi and Michael Klutstein and Itamar Simon and Tom Mitchell and Ziv Bar-Joseph", title = "A Combined Expression-Interaction Model for Inferring the Temporal Activity of Transcription Factors", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1035--1049", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0024", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0024; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0024", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2009", } @Article{Zhang:2009:EHR, author = "Yu Zhang and Giltae Song and Tom{\'a}{\v{s}} Vina{\v{r}} and Eric D. Green and Adam Siepel and Webb Miller", title = "Evolutionary History Reconstruction for Mammalian Complex Gene Clusters", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1051--1070", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0040", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0040; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0040", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2009", } @Article{Burleigh:2009:LLS, author = "J. G. Burleigh and M. S. Bansal and A. Wehe and O. Eulenstein", title = "Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1071--1083", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0139", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0139; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0139", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2009", } @Article{Bocker:2009:CMG, author = "Sebastian B{\"o}cker and Katharina Jahn and Julia Mixtacki and Jens Stoye", title = "Computation of Median Gene Clusters", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1085--1099", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0098", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0098; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0098", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2009", } @Article{Medvedev:2009:MLG, author = "Paul Medvedev and Michael Brudno", title = "Maximum Likelihood Genome Assembly", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1101--1116", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0047", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0047; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0047", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2009", } @Article{Sammeth:2009:CAS, author = "Michael Sammeth", title = "Complete Alternative Splicing Events Are Bubbles in Splicing Graphs", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1117--1140", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0108; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0108", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2009", } @Article{Bercovici:2009:IAE, author = "Sivan Bercovici and Dan Geiger", title = "Inferring Ancestries Efficiently in Admixed Populations with Linkage Disequilibrium", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1141--1150", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0105", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0105; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0105", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2009", } @Article{Zheng:2009:AJO, author = "Wei Zheng and Alan M. Friedman and Chris Bailey-Kellogg", title = "Algorithms for Joint Optimization of Stability and Diversity in Planning Combinatorial Libraries of Chimeric Proteins", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1151--1168", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0090", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0090; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0090", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2009", } @Article{Datta:2009:SFU, author = "Ritendra Datta and Marshall Bern", title = "Spectrum Fusion: Using Multiple Mass Spectra for {De} {Novo} Peptide Sequencing", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1169--1182", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0122", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0122; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0122", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2009", } @Article{Li:2009:BAP, author = "Yong Fuga Li and Randy J. Arnold and Yixue Li and Predrag Radivojac and Quanhu Sheng and Haixu Tang", title = "A {Bayesian} Approach to Protein Inference Problem in Shotgun Proteomics", journal = j-J-COMPUT-BIOL, volume = "16", number = "8", pages = "1183--1193", month = aug, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0018", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0018; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0018", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2009", } @Article{Sehl:2009:ASS, author = "Mary Sehl and Alexander V. Alekseyenko and Kenneth L. Lange", title = "Accurate Stochastic Simulation via the Step Anticipation $ \tau $-Leaping {(SAL)} Algorithm", journal = j-J-COMPUT-BIOL, volume = "16", number = "9", pages = "1195--1208", month = sep, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0249", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0249; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0249", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Jensen:2009:NLM, author = "Jens Ledet Jensen", title = "A Note on the Linear Memory {Baum--Welch} Algorithm", journal = j-J-COMPUT-BIOL, volume = "16", number = "9", pages = "1209--1210", month = sep, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0178", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0178; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0178", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Eng:2009:NDM, author = "Catherine Eng and Charu Asthana and Bertrand Aigle and S{\'e}bastien Hergalant and Jean-Fran{\c{c}}ois Mari and Pierre Leblond", title = "A New Data Mining Approach for the Detection of Bacterial Promoters Combining Stochastic and Combinatorial Methods", journal = j-J-COMPUT-BIOL, volume = "16", number = "9", pages = "1211--1225", month = sep, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0122", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0122; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0122", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{BenHassen:2009:IST, author = "Hanen {Ben Hassen} and Afif Masmoudi and Ahmed Rebai", title = "Inference in Signal Transduction Pathways Using {EM} Algorithm and an Implicit Algorithm: Incomplete Data Case", journal = j-J-COMPUT-BIOL, volume = "16", number = "9", pages = "1227--1240", month = sep, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Cheng:2009:SOM, author = "Qiang Cheng and Jie Cheng", title = "Sparsity Optimization Method for Multivariate Feature Screening for Gene Expression Analysis", journal = j-J-COMPUT-BIOL, volume = "16", number = "9", pages = "1241--1252", month = sep, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0034", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0034; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0034", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Jun:2009:DMD, author = "Jin Jun and Paul Ryvkin and Edward Hemphill and Craig Nelson", title = "Duplication Mechanism and Disruptions in Flanking Regions Determine the Fate of Mammalian Gene Duplicates", journal = j-J-COMPUT-BIOL, volume = "16", number = "9", pages = "1253--1266", month = sep, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0074", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0074; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0074", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Jean:2009:MSG, author = "G{\'e}raldine Jean and David James Sherman and Macha Nikolski", title = "Mining the Semantics of Genome Super-Blocks to Infer Ancestral Architectures", journal = j-J-COMPUT-BIOL, volume = "16", number = "9", pages = "1267--1284", month = sep, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0046", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0046; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0046", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Nelson:2009:RCG, author = "Craig Nelson and St{\'e}phane Vialette", title = "{RECOMB--Comparative} Genomics Special Issue", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1285--1286", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.002P", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.002P", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2009", } @Article{Berard:2009:CPD, author = "S{\`e}verine B{\'e}rard and Annie Chateau and Cedric Chauve and Christophe Paul and Eric Tannier", title = "Computation of Perfect {DCJ} Rearrangement Scenarios with Linear and Circular Chromosomes", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1287--1309", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0088", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0088; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0088", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 October 2009", } @Article{Yancopoulos:2009:DPF, author = "Sophia Yancopoulos and Richard Friedberg", title = "{DCJ} Path Formulation for Genome Transformations which Include Insertions, Deletions, and Duplications", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1311--1338", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0092", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0092; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0092", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 October 2009", } @Article{Swenson:2009:HSI, author = "Krister M. Swenson and Yu Lin and Vaibhav Rajan and Bernard M. E. Moret", title = "Hurdles and Sorting by Inversions: Combinatorial, Statistical, and Experimental Results", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1339--1351", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0156; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0156", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 September 2009", } @Article{Sankoff:2009:TIR, author = "David Sankoff and Chunfang Zheng and P. Kerr Wall and Claude dePamphilis and Jim Leebens-Mack and Victor A. Albert", title = "Towards Improved Reconstruction of Ancestral Gene Order in Angiosperm Phylogeny", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1353--1367", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 October 2009", } @Article{Xu:2009:FEA, author = "Andrew Wei Xu", title = "A Fast and Exact Algorithm for the Median of Three Problem: a Graph Decomposition Approach", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1369--1381", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0087", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0087; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0087", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 September 2009", } @Article{Zhang:2009:GTT, author = "Melvin Zhang and Hon Wai Leong", title = "Gene Team Tree: a Hierarchical Representation of Gene Teams for All Gap Lengths", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1383--1398", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0093", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0093; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0093", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 October 2009", } @Article{Doyon:2009:SGS, author = "Jean-Philippe Doyon and Cedric Chauve and Sylvie Hamel", title = "Space of Gene/Species Trees Reconciliations and Parsimonious Models", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1399--1418", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0095", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0095; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0095", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2009", } @Article{Schrider:2009:AHS, author = "Daniel R. Schrider and James C. Costello and Matthew W. Hahn", title = "All Human-Specific Gene Losses Are Present in the Genome as Pseudogenes", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1419--1427", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0085", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0085; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0085", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2009", } @Article{Jun:2009:BNG, author = "Jin Jun and Paul Ryvkin and Edward Hemphill and Ion Mandoiu and Craig Nelson", title = "The Birth of New Genes by {RNA}- and {DNA}-Mediated Duplication during Mammalian Evolution", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1429--1444", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 October 2009", } @Article{Ozery-Flato:2009:SCK, author = "Michal Ozery-Flato and Ron Shamir", title = "Sorting Cancer Karyotypes by Elementary Operations", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1445--1460", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0083", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0083; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0083", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2009", } @Article{Diallo:2009:WGS, author = "Abdoulaye Banir{\'e} Diallo and Dunarel Badescu and Mathieu Blanchette and Vladimir Makarenkov", title = "A Whole Genome Study and Identification of Specific Carcinogenic Regions of the Human Papilloma Viruses", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1461--1473", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0091", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0091; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0091", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2009", } @Article{Bertrand:2009:GMR, author = "Denis Bertrand and Mathieu Blanchette and Nadia El-Mabrouk", title = "Genetic Map Refinement Using a Comparative Genomic Approach", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1475--1486", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0094", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0094; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0094", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2009", } @Article{Haubold:2009:EMD, author = "Bernhard Haubold and Peter Pfaffelhuber and Mirjana Domazet-Los{\=o} and Thomas Wiehe", title = "Estimating Mutation Distances from Unaligned Genomes", journal = j-J-COMPUT-BIOL, volume = "16", number = "10", pages = "1487--1500", month = oct, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0106", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0106; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0106", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 October 2009", } @Article{Sui:2009:BAD, author = "Yunxia Sui and Xiaoyue Zhao and Terence P. Speed and Zhijin Wu", title = "Background Adjustment for {DNA} Microarrays Using a Database of Microarray Experiments", journal = j-J-COMPUT-BIOL, volume = "16", number = "11", pages = "1501--1515", month = nov, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0063", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0063; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0063", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2009", } @Article{McCrow:2009:APU, author = "John P. McCrow", title = "Alignment of Phylogenetically Unambiguous Indels in \bioname{Shewanella}", journal = j-J-COMPUT-BIOL, volume = "16", number = "11", pages = "1517--1528", month = nov, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0188", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0188; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0188", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2009", } @Article{Cheng:2009:PCP, author = "Yongxi Cheng and Ding-Zhu Du and Ker-I Ko and Guohui Lin", title = "On the Parameterized Complexity of Pooling Design", journal = j-J-COMPUT-BIOL, volume = "16", number = "11", pages = "1529--1537", month = nov, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0224", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0224; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0224", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Su:2009:CHD, author = "Ming-Wei Su and Hsiu-Man Lin and Hanna S. Yuan and Woei-Chyn Chu", title = "Categorizing Host-Dependent {RNA} Viruses by Principal Component Analysis of Their Codon Usage Preferences", journal = j-J-COMPUT-BIOL, volume = "16", number = "11", pages = "1539--1547", month = nov, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0046", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0046; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0046", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2009", } @Article{Huang:2009:FNR, author = "Fenix W. D. Huang and Wade W. J. Peng and Christian M. Reidys", title = "Folding $3$-Noncrossing {RNA} Pseudoknot Structures", journal = j-J-COMPUT-BIOL, volume = "16", number = "11", pages = "1549--1575", month = nov, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0194", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0194; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0194", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2009", } @Article{Comin:2009:BBF, author = "Matteo Comin and Concettina Guerra and Frank Dellaert", title = "Binding Balls: Fast Detection of Binding Sites Using a Property of Spherical {Fourier} Transform", journal = j-J-COMPUT-BIOL, volume = "16", number = "11", pages = "1577--1591", month = nov, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0045", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0045; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0045", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2009", } @Article{Andrecut:2009:PGI, author = "M. Andrecut", title = "Parallel {GPU} Implementation of Iterative {PCA} Algorithms", journal = j-J-COMPUT-BIOL, volume = "16", number = "11", pages = "1593--1599", month = nov, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0221", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0221; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0221", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Kimura:2009:CRS, author = "Kouichi Kimura and Yutaka Suzuki and Sumio Sugano and Asako Koike", title = "Computation of Rank and Select Functions on Hierarchical Binary String and Its Application to Genome Mapping Problems for Short-Read {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "16", number = "11", pages = "1601--1613", month = nov, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0146", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0146; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0146", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Reinert:2009:AFS, author = "Gesine Reinert and David Chew and Fengzhu Sun and Michael S. Waterman", title = "Alignment-Free Sequence Comparison (I): Statistics and Power", journal = j-J-COMPUT-BIOL, volume = "16", number = "12", pages = "1615--1634", month = dec, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0198", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0198; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0198", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 December 2009", } @Article{Pisanti:2009:REN, author = "Nadia Pisanti and Henry Soldano and Mathilde Carpentier and Joel Pothier", title = "A Relational Extension of the Notion of Motifs: Application to the Common {$3$D} Protein Substructures Searching Problem", journal = j-J-COMPUT-BIOL, volume = "16", number = "12", pages = "1635--1660", month = dec, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0019", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0019; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0019", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2010", } @Article{Liu:2009:SPG, author = "Zhenqiu Liu and Ronald B. Gartenhaus and Xue-Wen Chen and Charles D. Howell and Ming Tan", title = "Survival Prediction and Gene Identification with Penalized Global {AUC} Maximization", journal = j-J-COMPUT-BIOL, volume = "16", number = "12", pages = "1661--1670", month = dec, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0188", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0188; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0188", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Hong:2009:APP, author = "Huixiao Hong and Qilong Hong and Roger Perkins and Leming Shi and Hong Fang and Zhenqiang Su and Yvonne Dragan and James C. Fuscoe and Weida Tong", title = "The Accurate Prediction of Protein Family from Amino Acid Sequence by Measuring Features of Sequence Fragments", journal = j-J-COMPUT-BIOL, volume = "16", number = "12", pages = "1671--1688", month = dec, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0115; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0115", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2010", } @Article{Chuang:2009:TSB, author = "Li-Yeh Chuang and Cheng-Huei Yang and Cheng-Hong Yang", title = "Tabu Search and Binary Particle Swarm Optimization for Feature Selection Using Microarray Data", journal = j-J-COMPUT-BIOL, volume = "16", number = "12", pages = "1689--1703", month = dec, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0211", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0211; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0211", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2010", } @Article{Rodin:2009:UWA, author = "Andrei S. Rodin and Anatoliy Litvinenko and Kathy Klos and Alanna C. Morrison and Trevor Woodage and Josef Coresh and Eric Boerwinkle", title = "Use of Wrapper Algorithms Coupled with a Random Forests Classifier for Variable Selection in Large-Scale Genomic Association Studies", journal = j-J-COMPUT-BIOL, volume = "16", number = "12", pages = "1705--1718", month = dec, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0037", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0037; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0037", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2010", } @Article{He:2009:URU, author = "Yi He and Changjun Chen and Yi Xiao", title = "United-Residue {(UNRES)} {Langevin} Dynamics Simulations of trpzip2 Folding", journal = j-J-COMPUT-BIOL, volume = "16", number = "12", pages = "1719--1730", month = dec, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0070", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0070; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0070", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2010", } @Article{Wu:2009:CIA, author = "Li-Ching Wu and Jorng-Tzong Horng and Yong-An Chen", title = "A Computation to Integrate the Analysis of Genetic Variations Occurring within Regulatory Elements and Their Possible Effects", journal = j-J-COMPUT-BIOL, volume = "16", number = "12", pages = "1731--1747", month = dec, year = "2009", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0247", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0247; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0247", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2010", } @Article{Schonhuth:2010:TIA, author = "Alexander Sch{\"o}nhuth and Raheleh Salari and Fereydoun Hormozdiari and Artem Cherkasov and S. Cenk Sahinalp", title = "Towards Improved Assessment of Functional Similarity in Large-Scale Screens: a Study on Indel Length", journal = j-J-COMPUT-BIOL, volume = "17", number = "1", pages = "1--20", month = jan, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0031", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0031; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0031", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2010", } @Article{Liu:2010:EGW, author = "Lan Liu and Yonghui Wu and Stefano Lonardi and Tao Jiang", title = "Efficient Genome-Wide {TagSNP} Selection Across Populations via the Linkage Disequilibrium Criterion", journal = j-J-COMPUT-BIOL, volume = "17", number = "1", pages = "21--37", month = jan, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2007.0228", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2007.0228; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2007.0228", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2010", } @Article{Samaga:2010:CCI, author = "Regina Samaga and Axel {Von Kamp} and Steffen Klamt", title = "Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks", journal = j-J-COMPUT-BIOL, volume = "17", number = "1", pages = "39--53", month = jan, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0121", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0121; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0121", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2010", } @Article{Vacic:2010:GKP, author = "Vladimir Vacic and Lilia M. Iakoucheva and Stefano Lonardi and Predrag Radivojac", title = "Graphlet Kernels for Prediction of Functional Residues in Protein Structures", journal = j-J-COMPUT-BIOL, volume = "17", number = "1", pages = "55--72", month = jan, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0029", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0029; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0029", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2010", } @Article{Bandyopadhyay:2010:GMO, author = "Nirmalya Bandyopadhyay and Tamer Kahveci", title = "{GBA} Manager: an Online Tool for Querying Low-Complexity Regions in Proteins", journal = j-J-COMPUT-BIOL, volume = "17", number = "1", pages = "73--77", month = jan, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0006", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0006; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0006", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2010", } @Article{Mann:2010:IBG, author = "Scott Mann and Jinyan Li and Yi-Ping Phoebe Chen", title = "Insights into Bacterial Genome Composition through Variable Target {GC} Content Profiling", journal = j-J-COMPUT-BIOL, volume = "17", number = "1", pages = "79--96", month = jan, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0058", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0058; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0058", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2010", } @Article{Jung:2010:PEM, author = "Juhyun Jung and Taewoo Ryu and Yongdeuk Hwang and Eunjung Lee and Doheon Lee", title = "Prediction of Extracellular Matrix Proteins Based on Distinctive Sequence and Domain Characteristics", journal = j-J-COMPUT-BIOL, volume = "17", number = "1", pages = "97--105", month = jan, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0236", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0236; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0236", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2010", } @Article{Jevremovic:2010:APE, author = "Dimitrije Jevremovic and Cong T. Trinh and Friedrich Srienc and Daniel Boley", title = "On Algebraic Properties of Extreme Pathways in Metabolic Networks", journal = j-J-COMPUT-BIOL, volume = "17", number = "2", pages = "107--119", month = feb, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0020", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0020; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0020", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2010", } @Article{Choi:2010:DLM, author = "Hyungwon Choi and Zhaohui S. Qin and Debashis Ghosh", title = "A Double-Layered Mixture Model for the Joint Analysis of {DNA} Copy Number and Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "17", number = "2", pages = "121--137", month = feb, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0019", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0019; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0019", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2010", } @Article{Nguyen:2010:SWP, author = "Nha Nguyen and Heng Huang and Soontorn Oraintara and An Vo", title = "Stationary Wavelet Packet Transform and Dependent {Laplacian} Bivariate Shrinkage Estimator for {Array-CGH} Data Smoothing", journal = j-J-COMPUT-BIOL, volume = "17", number = "2", pages = "139--152", month = feb, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0013", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0013; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0013", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 January 2010", } @Article{Karakas:2010:BCL, author = "Mert Karaka{\c{s}} and Nils Woetzel and Jens Meiler", title = "{BCL::Contact} --- Low Confidence Fold Recognition Hits Boost Protein Contact Prediction and {{\em {De} Novo\/}} Structure Determination", journal = j-J-COMPUT-BIOL, volume = "17", number = "2", pages = "153--168", month = feb, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0030", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0030; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0030", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2009", } @Article{Qiu:2010:RCC, author = "Peng Qiu and Andrew J. Gentles and Sylvia K. Plevritis", title = "Reducing the Computational Complexity of Information Theoretic Approaches for Reconstructing Gene Regulatory Networks", journal = j-J-COMPUT-BIOL, volume = "17", number = "2", pages = "169--176", month = feb, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0052", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0052; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0052", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 January 2010", } @Article{Jiao:2010:EPE, author = "Shuo Jiao and Shunpu Zhang", title = "Estimating the Proportion of Equivalently Expressed Genes in Microarray Data Based on Transformed Test Statistics", journal = j-J-COMPUT-BIOL, volume = "17", number = "2", pages = "177--187", month = feb, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0060", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0060; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0060", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 January 2010", } @Article{Steijaert:2010:CSD, author = "M. N. Steijaert and J. H. K. {Van Den Brink} and A. M. L. Liekens and P. A. J. Hilbers and H. M. M. {Ten Eikelder}", title = "Computing the Stochastic Dynamics of Phosphorylation Networks", journal = j-J-COMPUT-BIOL, volume = "17", number = "2", pages = "189--199", month = feb, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0059", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0059; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0059", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2010", } @Article{Anonymous:2010:RMC, author = "Anonymous", title = "{RECOMB Main Conference 2009}", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "201--201", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.Pr01", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.Pr01", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Shibuya:2010:SPD, author = "Tetsuo Shibuya", title = "Searching Protein {$3$-D} Structures in Linear Time", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "203--219", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0148", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0148; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0148", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{He:2010:OBP, author = "Zengyou He and Chao Yang and Can Yang and Robert Z. Qi and Jason Po-Ming Tam and Weichuan Yu", title = "Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "221--235", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0160", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0160; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0160", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Bruckner:2010:TFQ, author = "Sharon Bruckner and Falk H{\"u}ffner and Richard M. Karp and Ron Shamir and Roded Sharan", title = "Topology-Free Querying of Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "237--252", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0170", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0170; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0170", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Lu:2010:CSE, author = "Yong Lu and Roni Rosenfeld and Gerard J. Nau and Ziv Bar-Joseph", title = "Cross Species Expression Analysis of Innate Immune Response", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "253--268", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0147", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0147; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0147", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Kirkpatrick:2010:HIC, author = "Bonnie Kirkpatrick and Eran Halperin and Richard M. Karp", title = "Haplotype Inference in Complex Pedigrees", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "269--280", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0174", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0174; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0174", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Makinen:2010:SRH, author = "Veli M{\"a}kinen and Gonzalo Navarro and Jouni Sir{\'e}n and Niko V{\"a}lim{\"a}ki", title = "Storage and Retrieval of Highly Repetitive Sequence Collections", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "281--308", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0169", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0169; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0169", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Ramanathan:2010:OAM, author = "Arvind Ramanathan and Pratul K. Agarwal and Maria Kurnikova and Christopher J. Langmead", title = "An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "309--324", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0167", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0167; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0167", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Donze:2010:PSN, author = "Alexandre Donz{\'e} and Gilles Clermont and Christopher J. Langmead", title = "Parameter Synthesis in Nonlinear Dynamical Systems: Application to Systems Biology", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "325--336", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0172; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Pattengale:2010:HMB, author = "Nicholas D. Pattengale and Masoud Alipour and Olaf R. P. Bininda-Emonds and Bernard M. E. Moret and Alexandros Stamatakis", title = "How Many Bootstrap Replicates Are Necessary?", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "337--354", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0179", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0179; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0179", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Stegle:2010:RBT, author = "Oliver Stegle and Katherine J. Denby and Emma J. Cooke and David L. Wild and Zoubin Ghahramani and Karsten M. Borgwardt", title = "A Robust {Bayesian} Two-Sample Test for Detecting Intervals of Differential Gene Expression in Microarray Time Series", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "355--367", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0175", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0175; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0175", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Bashir:2010:OPA, author = "Ali Bashir and Qing Lu and Dennis Carson and Benjamin J. Raphael and Yu-Tsueng Liu and Vineet Bafna", title = "Optimizing {PCR} Assays for {DNA-Based} Cancer Diagnostics", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "369--381", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0203", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0203; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0203", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Gusfield:2010:MSP, author = "Dan Gusfield", title = "The Multi-State Perfect Phylogeny Problem with Missing and Removable Data: Solutions via Integer-Programming and Chordal Graph Theory", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "383--399", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0200", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0200; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0200", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Zhang:2010:CGA, author = "Xiang Zhang and Feng Pan and Yuying Xie and Fei Zou and Wei Wang", title = "{COE}: a General Approach for Efficient Genome-Wide Two-Locus Epistasis Test in Disease Association Study", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "401--415", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0155", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0155; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0155", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Zagordi:2010:DSG, author = "Osvaldo Zagordi and Lukas Geyrhofer and Volker Roth and Niko Beerenwinkel", title = "Deep Sequencing of a Genetically Heterogeneous Sample: Local Haplotype Reconstruction and Read Error Correction", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "417--428", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0164", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0164; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0164", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Mohl:2010:LPA, author = "Mathias M{\"o}hl and Sebastian Will and Rolf Backofen", title = "Lifting Prediction to Alignment of {RNA} Pseudoknots", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "429--442", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0168", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0168; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0168", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Lavallee-Adam:2010:DLR, author = "Mathieu Lavall{\'e}e-Adam and Benoit Coulombe and Mathieu Blanchette", title = "Detection of Locally Over-Represented {GO} Terms in Protein-Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "443--457", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Zheng:2010:PFS, author = "Wei Zheng and Karl E. Griswold and Chris Bailey-Kellogg", title = "Protein Fragment Swapping: a Method for Asymmetric, Selective Site-Directed Recombination", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "459--475", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0189; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Hescott:2010:EBP, author = "B. J. Hescott and M. D. M. Leiserson and L. J. Cowen and D. K. Slonim", title = "Evaluating Between-Pathway Models with Expression Data", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "477--487", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0178", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0178; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0178", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Swenson:2010:SSP, author = "Krister M. Swenson and Vaibhav Rajan and Yu Lin and Bernard M. E. Moret", title = "Sorting Signed Permutations by Inversions in {$ O(n \log n) $} Time", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "489--501", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0184", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0184; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0184", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Navlakha:2010:FBA, author = "Saket Navlakha and James White and Niranjan Nagarajan and Mihai Pop and Carl Kingsford", title = "Finding Biologically Accurate Clusterings in Hierarchical Tree Decompositions Using the Variation of Information", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "503--516", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Sindi:2010:IFE, author = "Suzanne S. Sindi and Benjamin J. Raphael", title = "Identification and Frequency Estimation of Inversion Polymorphisms from Haplotype Data", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "517--531", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Kang:2010:DPA, author = "Eun Yong Kang and Chun Ye and Ilya Shpitser and Eleazar Eskin", title = "Detecting the Presence and Absence of Causal Relationships between Expression of Yeast Genes with Very Few Samples", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "533--546", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0176", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0176; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0176", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Kang:2010:EAM, author = "Hyun Min Kang and Noah A. Zaitlen and Eleazar Eskin", title = "{EMINIM}: an Adaptive and Memory-Efficient Algorithm for Genotype Imputation", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "547--560", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0199", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0199; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0199", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Kececioglu:2010:APS, author = "John Kececioglu and Eagu Kim and Travis Wheeler", title = "Aligning Protein Sequences with Predicted Secondary Structure", journal = j-J-COMPUT-BIOL, volume = "17", number = "3", pages = "561--580", month = mar, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0222", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0222; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0222", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2010", } @Article{Zhai:2010:PDE, author = "Zhiyuan Zhai and Shih-Yen Ku and Yihui Luan and Gesine Reinert and Michael S. Waterman and Fengzhu Sun", title = "The Power of Detecting Enriched Patterns: an {HMM} Approach", journal = j-J-COMPUT-BIOL, volume = "17", number = "4", pages = "581--592", month = apr, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0218", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0218; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0218", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 April 2010", } @Article{Shibuya:2010:SPT, author = "Tetsuo Shibuya", title = "Searching Protein Three-Dimensional Structures in Faster Than Linear Time", journal = j-J-COMPUT-BIOL, volume = "17", number = "4", pages = "593--602", month = apr, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0217", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0217; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0217", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 April 2010", } @Article{Shi:2010:PAE, author = "Haixiang Shi and Bertil Schmidt and Weiguo Liu and Wolfgang M{\"u}ller-Wittig", title = "A Parallel Algorithm for Error Correction in High-Throughput Short-Read Data on {CUDA-Enabled} Graphics Hardware", journal = j-J-COMPUT-BIOL, volume = "17", number = "4", pages = "603--615", month = apr, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0062", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0062; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0062", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 April 2010", } @Article{Boden:2010:BNM, author = "Mikael Bod{\'e}n and Graham Dellaire and Kevin Burrage and Timothy L. Bailey", title = "A {Bayesian} Network Model of Proteins' Association with Promyelocytic Leukemia {(PML)} Nuclear Bodies", journal = j-J-COMPUT-BIOL, volume = "17", number = "4", pages = "617--630", month = apr, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0140", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0140; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0140", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 April 2010", } @Article{Wu:2010:KSA, author = "Gang Wu and Ying Zhang and Yimin Wei", title = "{Krylov} Subspace Algorithms for Computing {GeneRank} for the Analysis of Microarray Data Mining", journal = j-J-COMPUT-BIOL, volume = "17", number = "4", pages = "631--646", month = apr, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0004", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/pagerank.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0004; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0004", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 April 2010", } @Article{Ahn:2010:FUB, author = "Namsu Ahn and Sungsoo Park", title = "Finding an Upper Bound for the Number of Contacts in Hydrophobic-Hydrophilic Protein Structure Prediction Model", journal = j-J-COMPUT-BIOL, volume = "17", number = "4", pages = "647--656", month = apr, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0009", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0009; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0009", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 April 2010", } @Article{Yang:2010:IGC, author = "Qingwu Yang and Gangman Yi and Fenghui Zhang and Michael R. Thon and Sing-Hoi Sze", title = "Identifying Gene Clusters within Localized Regions in Multiple Genomes", journal = j-J-COMPUT-BIOL, volume = "17", number = "5", pages = "657--668", month = may, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0116", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0116; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0116", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Hormozdiari:2010:PPI, author = "Fereydoun Hormozdiari and Raheleh Salari and Vineet Bafna and S. Cenk Sahinalp", title = "Protein-Protein Interaction Network Evaluation for Identifying Potential Drug Targets", journal = j-J-COMPUT-BIOL, volume = "17", number = "5", pages = "669--684", month = may, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0032", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0032; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0032", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Huang:2010:SRG, author = "Yen-Lin Huang and Chin Lung Lu", title = "Sorting by Reversals, Generalized Transpositions, and Translocations Using Permutation Groups", journal = j-J-COMPUT-BIOL, volume = "17", number = "5", pages = "685--705", month = may, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0025", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0025; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0025", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Cardone:2010:EIC, author = "Antonio Cardone and R. Wayne Albers and Ram D. Sriram and Harish C. Pant", title = "Evaluation of the Interaction of Cyclin-Dependent Kinase 5 with Activator p25 and with p25-Derived Inhibitor {CIP}", journal = j-J-COMPUT-BIOL, volume = "17", number = "5", pages = "707--721", month = may, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0202", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0202; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0202", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Berge:2010:MFM, author = "Claude Berge and Nicolas Froloff and Ravi Kiran Reddy Kalathur and Myriam Maumy and Olivier Poch and Wolfgang Raffelsberger and Nicolas Wicker", title = "Multidimensional Fitting for Multivariate Data Analysis", journal = j-J-COMPUT-BIOL, volume = "17", number = "5", pages = "723--732", month = may, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0126", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0126; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0126", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2010", } @Article{Ma:2010:DIM, author = "Patrick C. H. Ma and Keith C. C. Chan", title = "Discovering Interesting Motif-Sets for Multi-Class Protein Sequence Classification", journal = j-J-COMPUT-BIOL, volume = "17", number = "5", pages = "733--743", month = may, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0213", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0213; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0213", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Chung:2010:NRM, author = "Myung-Hoon Chung and Chul Koo Kim", title = "Non-Random Mating Involving Inheritance of Social Status", journal = j-J-COMPUT-BIOL, volume = "17", number = "5", pages = "745--754", month = may, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0152", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0152; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0152", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Molineris:2010:NAI, author = "Ivan Molineris and Gabriele Sales and Federico Bianchi and Ferdinando {Di Cunto} and Michele Caselle", title = "A New Approach for the Identification of Processed Pseudogenes", journal = j-J-COMPUT-BIOL, volume = "17", number = "5", pages = "755--765", month = may, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0027", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0027; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0027", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Lam:2010:IAR, author = "Fumei Lam and Ryan Tarpine and Sorin Istrail", title = "The Imperfect Ancestral Recombination Graph Reconstruction Problem: Upper Bounds for Recombination and Homoplasy", journal = j-J-COMPUT-BIOL, volume = "17", number = "6", pages = "767--781", month = jun, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0249", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0249; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0249", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 June 2010", } @Article{Zhao:2010:PCM, author = "Feng Zhao and Jian Peng and Joe Debartolo and Karl F. Freed and Tobin R. Sosnick and Jinbo Xu", title = "A Probabilistic and Continuous Model of Protein Conformational Space for Template-Free Modeling", journal = j-J-COMPUT-BIOL, volume = "17", number = "6", pages = "783--798", month = jun, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0235", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0235; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0235", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 June 2010", } @Article{Matsen:2010:CAR, author = "Frederick A. Matsen", title = "{constNJ}: an Algorithm to Reconstruct Sets of Phylogenetic Trees Satisfying Pairwise Topological Constraints", journal = j-J-COMPUT-BIOL, volume = "17", number = "6", pages = "799--818", month = jun, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0201", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0201; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0201", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Aspnas:2010:COS, author = "Mats Aspn{\"a}s and Kimmo Mattila and Kristoffer Osowski and Jan Westerholm", title = "Code Optimization of the Subroutine to Remove Near Identical Matches in the Sequence Database Homology Search Tool {PSI-BLAST}", journal = j-J-COMPUT-BIOL, volume = "17", number = "6", pages = "819--823", month = jun, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0053", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0053; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0053", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 June 2010", } @Article{Jow:2010:IGM, author = "Howsun Jow and Madhuchhanda Bhattacharjee and Richard Boys and Darren Wilkinson", title = "The Integration of Genetic Maps Using {Bayesian} Inference", journal = j-J-COMPUT-BIOL, volume = "17", number = "6", pages = "825--840", month = jun, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0243; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0243", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 June 2010", } @Article{Manuch:2010:TLB, author = "J{\'a}n Ma{\v{n}}uch and Ladislav Stacho and Christine Stoll", title = "Two Lower Bounds for Self-Assemblies at Temperature 1", journal = j-J-COMPUT-BIOL, volume = "17", number = "6", pages = "841--852", month = jun, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0067", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0067; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0067", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2010", } @Article{Dimitrova:2010:DTS, author = "Elena S. Dimitrova and M. Paola Vera Licona and John McGee and Reinhard Laubenbacher", title = "Discretization of Time Series Data", journal = j-J-COMPUT-BIOL, volume = "17", number = "6", pages = "853--868", month = jun, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0023; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0023", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 June 2010", } @Article{LopezGarciaDeLomana:2010:SAG, author = "Adri{\'a}n {L{\'o}pez Garc{\'\i}a De Lomana} and Qasim K. Beg and G. {De Fabritiis} and Jordi Vill{\`a}-Freixa", title = "Statistical Analysis of Global Connectivity and Activity Distributions in Cellular Networks", journal = j-J-COMPUT-BIOL, volume = "17", number = "7", pages = "869--878", month = jul, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0240", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0240; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0240", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2010", } @Article{Huang:2010:SIS, author = "Shuguang Huang", title = "Statistical Issues in Subpopulation Analysis of High Content Imaging Data", journal = j-J-COMPUT-BIOL, volume = "17", number = "7", pages = "879--894", month = jul, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0071", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0071; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0071", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2010", } @Article{James:2010:MAG, author = "Scott C. James and Varun Boriah", title = "Modeling Algae Growth in an Open-Channel Raceway", journal = j-J-COMPUT-BIOL, volume = "17", number = "7", pages = "895--906", month = jul, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2010", } @Article{Wang:2010:TMS, author = "Lusheng Wang and Binhai Zhu", title = "On the Tractability of Maximal Strip Recovery", journal = j-J-COMPUT-BIOL, volume = "17", number = "7", pages = "907--914", month = jul, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2010", } @Article{Jiang:2010:PRS, author = "Minghui Jiang and Pedro J. Tejada and Ramoni O. Lasisi and Shanhong Cheng and D. Scott Fechser", title = "{$K$}-Partite {RNA} Secondary Structures", journal = j-J-COMPUT-BIOL, volume = "17", number = "7", pages = "915--925", month = jul, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0119", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0119; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0119", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2010", } @Article{Chang:2010:ICP, author = "Huilan Chang and Hong-Bin Chen and Hung-Lin Fu", title = "Identification and Classification Problems on Pooling Designs for Inhibitor Models", journal = j-J-COMPUT-BIOL, volume = "17", number = "7", pages = "927--941", month = jul, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0138", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0138; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0138", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2010", } @Article{Betancourt:2010:CBM, author = "Marcos R. Betancourt", title = "Comparison between Molecular Dynamic Based and Knowledge Based Potentials for Protein Side Chains", journal = j-J-COMPUT-BIOL, volume = "17", number = "7", pages = "943--952", month = jul, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0152", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0152; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0152", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2010", } @Article{Szczurek:2010:IKD, author = "Ewa Szczurek and Przemys{\l}aw Biecek and Jerzy Tiuryn and Martin Vingron", title = "Introducing Knowledge into Differential Expression Analysis", journal = j-J-COMPUT-BIOL, volume = "17", number = "8", pages = "953--967", month = aug, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0034", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0034; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0034", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 August 2010", } @Article{Graca:2010:HIP, author = "Ana Gra{\c{c}}a and In{\^e}s Lynce and Jo{\~a}o Marques-Silva and Arlindo L. Oliveira", title = "Haplotype Inference by Pure Parsimony: a Survey", journal = j-J-COMPUT-BIOL, volume = "17", number = "8", pages = "969--992", month = aug, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0101; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0101", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 August 2010", } @Article{Minary:2010:CON, author = "Peter Minary and Michael Levitt", title = "Conformational Optimization with Natural Degrees of Freedom: a Novel Stochastic Chain Closure Algorithm", journal = j-J-COMPUT-BIOL, volume = "17", number = "8", pages = "993--1010", month = aug, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0016", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0016; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0016", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 August 2010", } @Article{Apostolico:2010:SCP, author = "Alberto Apostolico and Fabio Cunial", title = "The Subsequence Composition of Polypeptides", journal = j-J-COMPUT-BIOL, volume = "17", number = "8", pages = "1011--1049", month = aug, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2010", } @Article{Ziv-Ukelson:2010:FAS, author = "Michal Ziv-Ukelson and Irit Gat-Viks and Ydo Wexler and Ron Shamir", title = "A Faster Algorithm for Simultaneous Alignment and Folding of {RNA}", journal = j-J-COMPUT-BIOL, volume = "17", number = "8", pages = "1051--1065", month = aug, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 July 2010", } @Article{Kim:2010:WBF, author = "Bong-Rae Kim and Timothy McMurry and Wei Zhao and Rongling Wu and Arthur Berg", title = "Wavelet-Based Functional Clustering for Patterns of High-Dimensional Dynamic Gene Expression", journal = j-J-COMPUT-BIOL, volume = "17", number = "8", pages = "1067--1080", month = aug, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0270", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0270; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0270", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 August 2010", } @Article{Pang:2010:MMP, author = "Xiaodong Pang and Linxiang Zhou and Mingjun Zhang and Fang Xie and Long Yu and Lili Zhang and Lina Xu and Xinyi Zhang", title = "A Mathematical Model for Peptide Inhibitor Design", journal = j-J-COMPUT-BIOL, volume = "17", number = "8", pages = "1081--1093", month = aug, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0272", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:49:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0272; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0272", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 August 2010", } @Article{Anonymous:2010:P, author = "Anonymous", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1095--1096", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.004p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.004p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Chauve:2010:YAG, author = "Cedric Chauve and Haris Gavranovic and Aida Ouangraoua and Eric Tannier", title = "Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods {II}", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1097--1112", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0092", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0092; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0092", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Yang:2010:NPV, author = "Zhenyu Yang and David Sankoff", title = "Natural Parameter Values for Generalized Gene Adjacency", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1113--1128", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0099", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0099; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0099", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Ouangraoua:2010:CSG, author = "A{\"\i}da Ouangraoua and Anne Bergeron", title = "Combinatorial Structure of Genome Rearrangements Scenarios", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1129--1144", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0126", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0126; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0126", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Braga:2010:SSS, author = "Mar{\'\i}lia D. V. Braga and Jens Stoye", title = "The Solution Space of Sorting by {DCJ}", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1145--1165", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0109", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0109; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0109", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Chauve:2010:MCS, author = "Cedric Chauve and Utz-Uwe Haus and Tamon Stephen and Vivija P. You", title = "Minimal Conflicting Sets for the Consecutive Ones Property in Ancestral Genome Reconstruction", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1167--1181", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Blin:2010:FNC, author = "Guillaume Blin and David Faye and Jens Stoye", title = "Finding Nested Common Intervals Efficiently", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1183--1194", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0089", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0089; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0089", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Xu:2010:MPL, author = "Andrew Wei Xu", title = "The Median Problems on Linear Multichromosomal Genomes: Graph Representation and Fast Exact Solutions", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1195--1211", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0106", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0106; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0106", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Bergeron:2010:RMS, author = "Anne Bergeron and Paul Medvedev and Jens Stoye", title = "Rearrangement Models and Single-Cut Operations", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1213--1225", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0091", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0091; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0091", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Song:2010:CCA, author = "Giltae Song and Louxin Zhang and Tomas Vinar and Webb Miller", title = "{CAGE}: Combinatorial Analysis of Gene-Cluster Evolution", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1227--1242", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0094", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0094; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0094", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Delgado:2010:CSA, author = "Jo{\~a}o Delgado and In{\^e}s Lynce and Vasco Manquinho", title = "Computing the Summed Adjacency Disruption Number between Two Genomes with Duplicate Genes", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1243--1265", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0098", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0098; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0098", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Vinar:2010:RHC, author = "Tom{\'a}{\v{s}} Vina{\v{r}} and Bro{\v{n}}a Brejov{\'a} and Giltae Song and Adam Siepel", title = "Reconstructing Histories of Complex Gene Clusters on a Phylogeny", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1267--1279", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0090", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0090; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0090", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Hsu:2010:EMD, author = "Chih-Hao Hsu and Yu Zhang and Ross C. Hardison and Eric D. Green and Webb Miller", title = "An Effective Method for Detecting Gene Conversion Events in Whole Genomes", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1281--1297", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Adam:2010:SFC, author = "Zaky Adam and David Sankoff", title = "A Statistically Fair Comparison of Ancestral Genome Reconstructions, Based on Breakpoint and Rearrangement Distances", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1299--1314", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0121", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0121; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0121", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Belcaid:2010:MGC, author = "Mahdi Belcaid and Anne Bergeron and Guylaine Poisson", title = "{Mosaic} Graphs and Comparative Genomics in Phage Communities", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1315--1326", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0108; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0108", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Tuller:2010:RAG, author = "Tamir Tuller and Hadas Birin and Martin Kupiec and Eytan Ruppin", title = "Reconstructing Ancestral Genomic Sequences by Co-Evolution: Formal Definitions, Computational Issues, and Biological Examples", journal = j-J-COMPUT-BIOL, volume = "17", number = "9", pages = "1327--1344", month = sep, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0112", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:01 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0112; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0112", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2010", } @Article{Parida:2010:ARG, author = "Laxmi Parida", title = "Ancestral Recombinations Graph: a Reconstructability Perspective Using Random-Graphs Framework", journal = j-J-COMPUT-BIOL, volume = "17", number = "10", pages = "1345--1370", month = oct, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0243; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0243", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2010", } @Article{Grainger:2010:RER, author = "Ben Grainger and Michael I. Sadowski and William R. Taylor", title = "Re-Evaluating the ``Rules'' of Protein Topology", journal = j-J-COMPUT-BIOL, volume = "17", number = "10", pages = "1371--1384", month = oct, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0265", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0265; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0265", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 July 2010", } @Article{Wu:2010:SQN, author = "Zhijin Wu and Martin J. Aryee", title = "Subset Quantile Normalization Using Negative Control Features", journal = j-J-COMPUT-BIOL, volume = "17", number = "10", pages = "1385--1395", month = oct, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0049", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0049; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0049", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2010", } @Article{Giladi:2010:ETI, author = "Eldar Giladi and John Healy and Gene Myers and Chris Hart and Philipp Kapranov and Doron Lipson and Steve Roels and Edward Thayer and Stan Letovsky", title = "Error Tolerant Indexing and Alignment of Short Reads with Covering Template Families", journal = j-J-COMPUT-BIOL, volume = "17", number = "10", pages = "1397--1411", month = oct, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0005", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0005; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0005", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2010", } @Article{Li:2010:EEC, author = "Zengti Li and Suogang Gao and Hongjie Du and Feng Zou and Weili Wu", title = "Efficient Error-Correcting Pooling Designs Constructed from Pseudo-Symplectic Spaces Over a Finite Field", journal = j-J-COMPUT-BIOL, volume = "17", number = "10", pages = "1413--1423", month = oct, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0206", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0206; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0206", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 July 2010", } @Article{Zhang:2010:MIS, author = "Haiying Zhang and Bing Zhou", title = "On the Maximal Interval Subgraph of a Tree", journal = j-J-COMPUT-BIOL, volume = "17", number = "10", pages = "1425--1433", month = oct, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0039", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0039; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0039", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2010", } @Article{Gupta:2010:HIG, author = "Arvind Gupta and Mohammad M. Karimi and J{\'a}n Ma{\v{n}}uch and Ladislav Stacho and Xiaohong Zhao", title = "Haplotype Inferring via Galled-Tree Networks Is {NP-Complete}", journal = j-J-COMPUT-BIOL, volume = "17", number = "10", pages = "1435--1449", month = oct, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0117", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0117; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0117", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2010", } @Article{Doan:2010:NLT, author = "Duong D. Doan and Patricia A. Evans and Joseph D. Horton", title = "A Near-Linear Time Algorithm for Haplotype Determination on General Pedigrees", journal = j-J-COMPUT-BIOL, volume = "17", number = "10", pages = "1451--1465", month = oct, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0133", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0133; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0133", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2010", } @Article{Wan:2010:AFS, author = "Lin Wan and Gesine Reinert and Fengzhu Sun and Michael S. Waterman", title = "Alignment-Free Sequence Comparison {(II)}: Theoretical Power of Comparison Statistics", journal = j-J-COMPUT-BIOL, volume = "17", number = "11", pages = "1467--1490", month = nov, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0056", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0056; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0056", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2010", } @Article{Sakhanenko:2010:MLN, author = "Nikita A. Sakhanenko and David J. Galas", title = "{Markov} Logic Networks in the Analysis of Genetic Data", journal = j-J-COMPUT-BIOL, volume = "17", number = "11", pages = "1491--1508", month = nov, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0044", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0044; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0044", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 October 2010", } @Article{Gronau:2010:ADM, author = "Ilan Gronau and Shlomo Moran and Irad Yavneh", title = "Adaptive Distance Measures for Resolving {K2P} Quartets: Metric Separation versus Stochastic Noise", journal = j-J-COMPUT-BIOL, volume = "17", number = "11", pages = "1509--1518", month = nov, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0236", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0236; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0236", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2010", } @Article{Boisvert:2010:RSA, author = "S{\'e}bastien Boisvert and Fran{\c{c}}ois Laviolette and Jacques Corbeil", title = "{Ray}: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies", journal = j-J-COMPUT-BIOL, volume = "17", number = "11", pages = "1519--1533", month = nov, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0238", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0238; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0238", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 October 2010", } @Article{Snir:2010:NTD, author = "Sagi Snir and Edward Trifonov", title = "A Novel Technique for Detecting Putative Horizontal Gene Transfer in the Sequence Space", journal = j-J-COMPUT-BIOL, volume = "17", number = "11", pages = "1535--1548", month = nov, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0095", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0095; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0095", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2010", } @Article{Zhao:2010:EEE, author = "Xiaohong Zhao and Lance E. Palmer and Randall Bolanos and Cristian Mircean and Dan Fasulo and Gayle M. Wittenberg", title = "{EDAR}: an Efficient Error Detection and Removal Algorithm for Next Generation Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "17", number = "11", pages = "1549--1560", month = nov, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0127", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0127; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0127", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2010", } @Article{Chen:2010:CCG, author = "Xin Chen and Jian-Yi Yang", title = "Constructing Consensus Genetic Maps in Comparative Analysis", journal = j-J-COMPUT-BIOL, volume = "17", number = "11", pages = "1561--1573", month = nov, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0268", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0268; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0268", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 October 2010", } @Article{Reidys:2010:SRP, author = "Christian M. Reidys and Rita R. Wang", title = "Shapes of {RNA} Pseudoknot Structures", journal = j-J-COMPUT-BIOL, volume = "17", number = "11", pages = "1575--1590", month = nov, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0006", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0006; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0006", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 September 2010", } @Article{Behrens:2010:SEP, author = "Sarah Behrens and Martin Vingron", title = "Studying the Evolution of Promoter Sequences: a Waiting Time Problem", journal = j-J-COMPUT-BIOL, volume = "17", number = "12", pages = "1591--1606", month = dec, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2010", } @Article{Ye:2010:CAD, author = "Xugang Ye and Yi-Kuo Yu and Stephen F. Altschul", title = "Compositional Adjustment of {Dirichlet} Mixture Priors", journal = j-J-COMPUT-BIOL, volume = "17", number = "12", pages = "1607--1620", month = dec, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0117", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0117; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0117", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2010", } @Article{Zhou:2010:WMF, author = "Qing Zhou", title = "On Weight Matrix and Free Energy Models for Sequence Motif Detection", journal = j-J-COMPUT-BIOL, volume = "17", number = "12", pages = "1621--1638", month = dec, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0142", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0142; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0142", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2010", } @Article{Herant:2010:CTD, author = "Marc Herant and Micah Dembo", title = "{Cytopede}: a Three-Dimensional Tool for Modeling Cell Motility on a Flat Surface", journal = j-J-COMPUT-BIOL, volume = "17", number = "12", pages = "1639--1677", month = dec, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0271", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0271; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0271", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 October 2010", } @Article{Liu:2010:SMR, author = "Xin Liu and Ya-Pu Zhao", title = "Substitution Matrices of Residue Triplets Derived from Protein Blocks", journal = j-J-COMPUT-BIOL, volume = "17", number = "12", pages = "1679--1687", month = dec, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0035", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0035; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0035", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2010", } @Article{Zhang:2010:PIV, author = "Xinan Zhang and Yingdong Zhao and Avidan U. Neumann", title = "Partial Immunity and Vaccination for Influenza", journal = j-J-COMPUT-BIOL, volume = "17", number = "12", pages = "1689--1696", month = dec, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0003", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0003; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0003", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2010", } @Article{Chan:2010:ISW, author = "Hock Peng Chan and Nancy Ruonan Zhang and Louis H. Y. Chen", title = "Importance Sampling of Word Patterns in {DNA} and Protein Sequences", journal = j-J-COMPUT-BIOL, volume = "17", number = "12", pages = "1697--1709", month = dec, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0233", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0233; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0233", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2010", } @Article{Luaces:2010:EGB, author = "Oscar Luaces and Jos{\'e} R. Quevedo and Miguel P{\'e}rez-Enciso and Jorge D{\'\i}ez and Juan Jos{\'e} {Del Coz} and Antonio Bahamonde", title = "Explaining the Genetic Basis of Complex Quantitative Traits through Prediction Models", journal = j-J-COMPUT-BIOL, volume = "17", number = "12", pages = "1711--1723", month = dec, year = "2010", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0161", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0161; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0161", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2010", } @Article{Than:2011:CPS, author = "Cuong V. Than and Noah A. Rosenberg", title = "Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "1--15", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0102; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0102", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Day:2011:RPG, author = "Ryan Day and Xiaotao Qu and Rosemarie Swanson and Zach Bohannan and Robert Bliss and Jerry Tsai", title = "Relative Packing Groups in Template-Based Structure Prediction: Cooperative Effects of True Positive Constraints", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "17--26", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Andonov:2011:MCM, author = "Rumen Andonov and No{\"e}l Malod-Dognin and Nicola Yanev", title = "Maximum Contact Map Overlap Revisited", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "27--41", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0196", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0196; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0196", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Heinonen:2011:CAM, author = "Markus Heinonen and Sampsa Lappalainen and Taneli Mielik{\"a}inen and Juho Rousu", title = "Computing Atom Mappings for Biochemical Reactions without Subgraph Isomorphism", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "43--58", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0216", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0216; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0216", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Ovadia:2011:CRP, author = "Y. Ovadia and D. Fielder and C. Conow and R. Libeskind-Hadas", title = "The Cophylogeny Reconstruction Problem Is {NP-Complete}", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "59--65", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0240", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0240; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0240", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2010", } @Article{Weng:2011:MPS, author = "J. F. Weng and D. A. Thomas and I. Mareels", title = "Maximum Parsimony, Substitution Model, and Probability Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "67--80", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0232", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0232; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0232", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 July 2010", } @Article{Marras:2011:MLP, author = "Elisabetta Marras and Antonella Travaglione and Enrico Capobianco", title = "Manifold Learning in Protein Interactomes", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "81--96", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0258", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0258; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0258", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 July 2010", } @Article{Wong:2011:SAR, author = "Thomas K. F. Wong and T. W. Lam and Wing-Kin Sung and Brenda W. Y. Cheung and S. M. Yiu", title = "Structural Alignment of {RNA} with Complex Pseudoknot Structure", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "97--108", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0275", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0275; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0275", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Jenkins:2011:ISD, author = "Paul A. Jenkins and Robert C. Griffiths", title = "Inference from Samples of {DNA} Sequences Using a Two-Locus Model", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "109--127", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0231", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0231; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0231", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Anonymous:2011:C, author = "Anonymous", title = "Correction", journal = j-J-COMPUT-BIOL, volume = "18", number = "1", pages = "129--129", month = jan, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.cor1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.cor1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Kellis:2011:P, author = "Manolis Kellis and Andrea Califano and Ziv Bar-Joseph", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "18", number = "2", pages = "131--131", month = feb, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.005p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.005p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2011", } @Article{Perlman:2011:CDG, author = "Liat Perlman and Assaf Gottlieb and Nir Atias and Eytan Ruppin and Roded Sharan", title = "Combining Drug and Gene Similarity Measures for Drug-Target Elucidation", journal = j-J-COMPUT-BIOL, volume = "18", number = "2", pages = "133--145", month = feb, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0213", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0213; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0213", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2011", } @Article{Bandaru:2011:MCI, author = "Pradeep Bandaru and Mukesh Bansal and Ilya Nemenman", title = "Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data", journal = j-J-COMPUT-BIOL, volume = "18", number = "2", pages = "147--154", month = feb, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0222", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0222; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0222", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2011", } @Article{Ng:2011:ACS, author = "Patrick Ng and Uri Keich", title = "Alignment Constrained Sampling", journal = j-J-COMPUT-BIOL, volume = "18", number = "2", pages = "155--168", month = feb, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0220", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0220; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0220", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2011", } @Article{Quo:2011:ACM, author = "Chang F. Quo and Richard A. Moffitt and Alfred H. {Merrill, Jr.} and May D. Wang", title = "Adaptive Control Model Reveals Systematic Feedback and Key Molecules in Metabolic Pathway Regulation", journal = j-J-COMPUT-BIOL, volume = "18", number = "2", pages = "169--182", month = feb, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0215", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0215; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0215", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2011", } @Article{Corradin:2011:SAR, author = "Alberto Corradin and Barbara {Di Camillo} and Vincenzo Ciminale and Gianna Toffolo and Claudio Cobelli", title = "Sensitivity Analysis of Retrovirus {HTLV-1} Transactivation", journal = j-J-COMPUT-BIOL, volume = "18", number = "2", pages = "183--193", month = feb, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0219", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0219; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0219", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2011", } @Article{Polynikis:2011:DCV, author = "Athanasios Polynikis and Giulia Cuccato and Stefania Criscuolo and Stephen J. Hogan and Mario {Di Bernardo} and Diego {Di Bernardo}", title = "Design and Construction of a Versatile Synthetic Network for Bistable Gene Expression in Mammalian Systems", journal = j-J-COMPUT-BIOL, volume = "18", number = "2", pages = "195--203", month = feb, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0208", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0208; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0208", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2011", } @Article{Berger:2011:PIC, author = "Bonnie Berger", title = "Preface: {14$^{th}$ International Conference on Research in Computational Molecular Biology (RECOMB 2010)}", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "205--205", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.006p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.006p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Atias:2011:AFP, author = "Nir Atias and Roded Sharan", title = "An Algorithmic Framework for Predicting Side Effects of Drugs", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "207--218", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0255", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0255; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0255", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Ay:2011:SAM, author = "Ferhat Ay and Manolis Kellis and Tamer Kahveci", title = "{SubMAP}: Aligning Metabolic Pathways with Subnetwork Mappings", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "219--235", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0280", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0280; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0280", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Bercovici:2011:AAA, author = "Sivan Bercovici and Dan Geiger", title = "Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled {DNA}", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "237--249", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0250", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0250; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0250", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Caldas:2011:HGB, author = "Jos{\'e} Caldas and Samuel Kaski", title = "Hierarchical Generative Biclustering for {MicroRNA} Expression Analysis", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "251--261", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0256", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0256; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0256", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Chowdhury:2011:SSF, author = "Salim A. Chowdhury and Rod K. Nibbe and Mark R. Chance and Mehmet Koyut{\"u}rk", title = "Subnetwork State Functions Define Dysregulated Subnetworks in Cancer", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "263--281", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0269", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0269; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0269", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Claassen:2011:PCP, author = "Manfred Claassen and Ruedi Aebersold and Joachim M. Buhmann", title = "Proteome Coverage Prediction for Integrated Proteomics Datasets", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "283--293", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0261", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0261; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0261", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Danford:2011:DRO, author = "Timothy Danford and Robin Dowell and Sudeep Agarwala and Paula Grisafi and Gerald Fink and David Gifford", title = "Discovering Regulatory Overlapping {RNA} Transcripts", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "295--303", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0267", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0267; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0267", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Feng:2011:IIS, author = "Jianxing Feng and Wei Li and Tao Jiang", title = "Inference of Isoforms from Short Sequence Reads", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "305--321", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0243; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0243", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Halldorsson:2011:CPS, author = "Bjarni V. Halld{\'o}rsson and Derek Aguiar and Ryan Tarpine and Sorin Istrail", title = "The {Clark} Phaseable Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in {GWAS}", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "323--333", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0288", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0288; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0288", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Hirsch:2011:BDA, author = "Michael Hirsch and Bernhard Sch{\"o}lkopf and Michael Habeck", title = "A Blind Deconvolution Approach for Improving the Resolution of {Cryo-EM} Density Maps", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "335--346", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0264", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0264; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0264", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Jang:2011:TFA, author = "Richard Jang and Xin Gao and Ming Li", title = "Towards Fully Automated Structure-Based {NMR} Resonance Assignment of {$^{15}$N}-Labeled Proteins From Automatically Picked Peaks", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "347--363", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0251", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0251; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0251", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Kao:2011:NEM, author = "Wei-Chun Kao and Yun S. Song", title = "{naiveBayesCall}: an Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "365--377", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0247", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0247; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0247", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Kelley:2011:EBP, author = "David R. Kelley and Carl Kingsford", title = "Extracting Between-Pathway Models from {E-MAP} Interactions Using Expected Graph Compression", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "379--390", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0268", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0268; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0268", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Kowalczyk:2011:PMT, author = "Adam Kowalczyk and Justin Bedo and Thomas Conway and Bryan Beresford-Smith", title = "The {Poisson} Margin Test for Normalization-Free Significance Analysis of {NGS} Data", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "391--400", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0272", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0272; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0272", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Kozanitis:2011:CGS, author = "Christos Kozanitis and Chris Saunders and Semyon Kruglyak and Vineet Bafna and George Varghese", title = "Compressing Genomic Sequence Fragments Using {SlimGene}", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "401--413", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0253", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0253; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0253", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Lam:2011:GAD, author = "Fumei Lam and Charles H. Langley and Yun S. Song", title = "On the Genealogy of Asexual Diploids", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "415--428", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0270", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0270; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0270", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Laserson:2011:GNA, author = "Jonathan Laserson and Vladimir Jojic and Daphne Koller", title = "{Genovo}: {{\em {De} Novo\/}} Assembly for Metagenomes", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "429--443", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0244; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0244", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Misra:2011:GBP, author = "Navodit Misra and Guy Blelloch and R. Ravi and Russell Schwartz", title = "Generalized {Buneman} Pruning for Inferring the Most Parsimonious Multi-State Phylogeny", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "445--457", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0254", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0254; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0254", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Pasaniuc:2011:AEE, author = "Bogdan Pa{\c{s}}aniuc and Noah Zaitlen and Eran Halperin", title = "Accurate Estimation of Expression Levels of Homologous Genes in {RNA-seq} Experiments", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "459--468", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0259", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0259; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0259", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Paten:2011:CGG, author = "Benedict Paten and Mark Diekhans and Dent Earl and John {St.John} and Jian Ma and Bernard Suh and David Haussler", title = "Cactus Graphs for Genome Comparisons", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "469--481", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0252", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0252; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0252", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Setty:2011:HTI, author = "Manu N. Setty and Alexander Gusev and Itsik Pe'er", title = "{HLA} Type Inference via Haplotypes Identical by Descent", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "483--493", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0258", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0258; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0258", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Sharon:2011:PBF, author = "Itai Sharon and Sivan Bercovici and Ron Y. Pinter and Tomer Shlomi", title = "Pathway-Based Functional Analysis of Metagenomes", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "495--505", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0260", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0260; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0260", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Vandin:2011:ADS, author = "Fabio Vandin and Eli Upfal and Benjamin J. Raphael", title = "Algorithms for Detecting Significantly Mutated Pathways in Cancer", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "507--522", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0265", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0265; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0265", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Wu:2011:NAB, author = "Yu-Wei Wu and Yuzhen Ye", title = "A Novel Abundance-Based Algorithm for Binning Metagenomic Sequences Using $l$-tuples", journal = j-J-COMPUT-BIOL, volume = "18", number = "3", pages = "523--534", month = mar, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0245", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0245; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0245", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2011", } @Article{Grossi:2011:MSM, author = "Roberto Grossi and Andrea Pietracaprina and Nadia Pisanti and Geppino Pucci and Eli Upfal and Fabio Vandin", title = "{MADMX}: a Strategy for Maximal Dense Motif Extraction", journal = j-J-COMPUT-BIOL, volume = "18", number = "4", pages = "535--545", month = apr, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0177", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0177; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0177", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 March 2011", } @Article{Noy:2011:SBF, author = "Karin Noy and Fadi Towfic and Gayle M. Wittenberg and Daniel Fasulo", title = "Shape-Based Feature Matching Improves Protein Identification via {LC-MS} and Tandem {MS}", journal = j-J-COMPUT-BIOL, volume = "18", number = "4", pages = "547--557", month = apr, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0155", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0155; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0155", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 March 2011", } @Article{Graudenzi:2011:RAB, author = "A. Graudenzi and R. Serra and M. Villani and A. Colacci and S. A. Kauffman", title = "Robustness Analysis of a {Boolean} Model of Gene Regulatory Network with Memory", journal = j-J-COMPUT-BIOL, volume = "18", number = "4", pages = "559--577", month = apr, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0224", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0224; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0224", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 March 2011", } @Article{Grusea:2011:CPA, author = "S. Grusea and E. Pardoux and O. Chabrol and P. Pontarotti", title = "Compound {Poisson} Approximation and Testing for Gene Clusters with Multigene Families", journal = j-J-COMPUT-BIOL, volume = "18", number = "4", pages = "579--594", month = apr, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0043", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0043; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0043", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 March 2011", } @Article{Fionda:2011:BNQ, author = "Valeria Fionda and Luigi Palopoli", title = "Biological Network Querying Techniques: Analysis and Comparison", journal = j-J-COMPUT-BIOL, volume = "18", number = "4", pages = "595--625", month = apr, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0144", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0144; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0144", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 March 2011", } @Article{Zhang:2011:PIB, author = "Shu-Bo Zhang and Song-Yu Zhou and Jian-Guo He and Jian-Huang Lai", title = "Phylogeny Inference Based on Spectral Graph Clustering", journal = j-J-COMPUT-BIOL, volume = "18", number = "4", pages = "627--637", month = apr, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0028", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0028; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0028", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 February 2011", } @Article{Marhon:2011:GPB, author = "Sajid A. Marhon and Stefan C. Kremer", title = "Gene Prediction Based on {DNA} Spectral Analysis: a Literature Review", journal = j-J-COMPUT-BIOL, volume = "18", number = "4", pages = "639--676", month = apr, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0184", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:18 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0184; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0184", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 March 2011", } @Article{Meng:2011:SAH, author = "Lu Meng and Fengzhu Sun and Xuegong Zhang and Michael S. Waterman", title = "Sequence Alignment as Hypothesis Testing", journal = j-J-COMPUT-BIOL, volume = "18", number = "5", pages = "677--691", month = may, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0328", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0328; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0328", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2011", } @Article{Li:2011:FNO, author = "Shuai Cheng Li and Dongbo Bu and Jinbo Xu and Ming Li", title = "Finding Nearly Optimal {GDT} Scores", journal = j-J-COMPUT-BIOL, volume = "18", number = "5", pages = "693--704", month = may, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0123", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0123; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0123", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2011", } @Article{Belal:2011:TMW, author = "Nahla A. Belal and Lenwood S. Heath", title = "A Theoretical Model for Whole Genome Alignment", journal = j-J-COMPUT-BIOL, volume = "18", number = "5", pages = "705--728", month = may, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0101; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0101", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Wieringen:2011:EFA, author = "Wessel N. Van Wieringen and Mark A. {Van De Wiel}", title = "Exploratory Factor Analysis of Pathway Copy Number Data with an Application Towards the Integration with Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "18", number = "5", pages = "729--741", month = may, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0209", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0209; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0209", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2011", } @Article{Kannan:2011:PTA, author = "Lavanya Kannan and Hua Li and Arcady Mushegian", title = "A Polynomial-Time Algorithm Computing Lower and Upper Bounds of the Rooted Subtree Prune and Regraft Distance", journal = j-J-COMPUT-BIOL, volume = "18", number = "5", pages = "743--757", month = may, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0045", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0045; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0045", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 December 2010", } @Article{Zhao:2011:MFD, author = "Xiaoyan Zhao and Sing-Hoi Sze", title = "Motif Finding in {DNA} Sequences Based on Skipping Nonconserved Positions in Background {Markov} Chains", journal = j-J-COMPUT-BIOL, volume = "18", number = "5", pages = "759--770", month = may, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2011", } @Article{Kucherov:2011:RLC, author = "Gregory Kucherov and Tamar Pinhas and Michal Ziv-Ukelson", title = "Regular Language Constrained Sequence Alignment Revisited", journal = j-J-COMPUT-BIOL, volume = "18", number = "5", pages = "771--781", month = may, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0291", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0291; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0291", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2011", } @Article{Veliz-Cuba:2011:BMC, author = "Alan Veliz-Cuba and Brandilyn Stigler", title = "{Boolean} Models Can Explain Bistability in the \bioname{lac} Operon", journal = j-J-COMPUT-BIOL, volume = "18", number = "6", pages = "783--794", month = jun, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0031", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0031; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0031", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2011", } @Article{Souaiaia:2011:CSC, author = "Tade Souaiaia and Zach Frazier and Ting Chen", title = "{ComB}: {SNP} Calling and Mapping Analysis for Color and Nucleotide Space Platforms", journal = j-J-COMPUT-BIOL, volume = "18", number = "6", pages = "795--807", month = jun, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0027", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0027; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0027", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2011", } @Article{Dojer:2011:BBS, author = "Norbert Dojer and Przemys{\l}aw Biecek and Jerzy Tiuryn", title = "{Bi}-Billboard: Symmetrization and Careful Choice of Informant Species Results in Higher Accuracy of Regulatory Element Prediction", journal = j-J-COMPUT-BIOL, volume = "18", number = "6", pages = "809--819", month = jun, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0299", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0299; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0299", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2011", } @Article{Blazewicz:2011:RPD, author = "Jacek Blazewicz and Marek Figlerowicz and Marta Kasprzak and Martyna Nowacka and Agnieszka Rybarczyk", title = "{RNA} Partial Degradation Problem: Motivation, Complexity, Algorithm", journal = j-J-COMPUT-BIOL, volume = "18", number = "6", pages = "821--834", month = jun, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2011", } @Article{Tan:2011:OCF, author = "Frans E. S. Tan and Val{\'e}ria Lima Passos", title = "On the {$A$}-Optimality Criterion for Finding Two-Color Microarray Optimal Designs", journal = j-J-COMPUT-BIOL, volume = "18", number = "6", pages = "835--841", month = jun, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0009", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0009; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0009", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 January 2011", } @Article{Pacholczyk:2011:ELP, author = "Marcin Pacholczyk and Marek Kimmel", title = "Exploring the Landscape of Protein-Ligand Interaction Energy Using Probabilistic Approach", journal = j-J-COMPUT-BIOL, volume = "18", number = "6", pages = "843--850", month = jun, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0017", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0017; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0017", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 November 2010", } @Article{Chen:2011:AOA, author = "Hong-Bin Chen and Annalisa {De Bonis}", title = "An Almost Optimal Algorithm for Generalized Threshold Group Testing with Inhibitors", journal = j-J-COMPUT-BIOL, volume = "18", number = "6", pages = "851--864", month = jun, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0030", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:22 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0030; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0030", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Pevzner:2011:PSM, author = "Pavel A. Pevzner and Ron Shamir", title = "Preface: {2$^{nd}$ Satellite Meeting on Bioinformatics Education, Research in Computational Molecular Biology (RECOMB--BE 2010)}", journal = j-J-COMPUT-BIOL, volume = "18", number = "7", pages = "865--865", month = jul, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.007p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.007p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2011", } @Article{Elhai:2011:HCR, author = "Jeff Elhai", title = "Humans, Computers, and the Route to Biological Insights: Regaining Our Capacity for Surprise", journal = j-J-COMPUT-BIOL, volume = "18", number = "7", pages = "867--878", month = jul, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0194", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0194; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0194", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2011", } @Article{Ma:2011:RHL, author = "Jian Ma", title = "Reconstructing the History of Large-Scale Genomic Changes: Biological Questions and Computational Challenges", journal = j-J-COMPUT-BIOL, volume = "18", number = "7", pages = "879--893", month = jul, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0189; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2011", } @Article{Sul:2011:BCP, author = "Seung-Jin Sul and Tiffani L. Williams", title = "Big Cat Phylogenies, Consensus Trees, and Computational Thinking", journal = j-J-COMPUT-BIOL, volume = "18", number = "7", pages = "895--906", month = jul, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0199", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0199; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0199", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2011", } @Article{Taneri:2011:TRE, author = "Bahar Taneri", title = "Is there Room for Ethics within Bioinformatics Education?", journal = j-J-COMPUT-BIOL, volume = "18", number = "7", pages = "907--916", month = jul, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0187", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0187; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0187", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2011", } @Article{Koonin:2011:CPT, author = "Eugene V. Koonin and Pere Puigb{\`o} and Yuri I. Wolf", title = "Comparison of Phylogenetic Trees and Search for a Central Trend in the ``Forest of Life''", journal = j-J-COMPUT-BIOL, volume = "18", number = "7", pages = "917--924", month = jul, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:24 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2011", } @Article{Yu:2011:CDM, author = "Yi-Kuo Yu and Stephen F. Altschul", title = "The Complexity of the {Dirichlet} Model for Multiple Alignment Data", journal = j-J-COMPUT-BIOL, volume = "18", number = "8", pages = "925--939", month = aug, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0039", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0039; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0039", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2011", } @Article{Ye:2011:IDM, author = "Xugang Ye and Yi-Kuo Yu and Stephen F. Altschul", title = "On the Inference of {Dirichlet} Mixture Priors for Protein Sequence Comparison", journal = j-J-COMPUT-BIOL, volume = "18", number = "8", pages = "941--954", month = aug, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0040", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0040; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0040", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2011", } @Article{Halldorsson:2011:ADH, author = "Bjarni V. Halld{\'o}rsson and Dan{\'\i}el F. Gudbjartsson", title = "An Algorithm for Detecting High Frequency Copy Number Polymorphisms Using {SNP} Arrays", journal = j-J-COMPUT-BIOL, volume = "18", number = "8", pages = "955--966", month = aug, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0317", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0317; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0317", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2011", } @Article{Snir:2011:TMP, author = "Sagi Snir and Lior Pachter", title = "Tracing the Most Parsimonious Indel History", journal = j-J-COMPUT-BIOL, volume = "18", number = "8", pages = "967--986", month = aug, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0325", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0325; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0325", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2011", } @Article{Freschi:2011:IBN, author = "Valerio Freschi", title = "Improved Biological Network Reconstruction Using Graph {Laplacian} Regularization", journal = j-J-COMPUT-BIOL, volume = "18", number = "8", pages = "987--996", month = aug, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0232", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0232; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0232", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2011", } @Article{Knapp:2011:ICD, author = "B. Knapp and S. Frantal and M. Cibena and W. Schreiner and P. Bauer", title = "Is an Intuitive Convergence Definition of Molecular Dynamics Simulations Solely Based on the Root Mean Square Deviation Possible?", journal = j-J-COMPUT-BIOL, volume = "18", number = "8", pages = "997--1005", month = aug, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0237", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0237; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0237", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2011", } @Article{Firoz:2011:AAS, author = "Jesun Sahariar Firoz and Masud Hasan and Ashik Zinnat Khan and M. Sohel Rahman", title = "The 1.375 Approximation Algorithm for Sorting by Transpositions Can Run in {$ O(n \log n) $} Time", journal = j-J-COMPUT-BIOL, volume = "18", number = "8", pages = "1007--1011", month = aug, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0042", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0042; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0042", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2011", } @Article{Kuo:2011:DDC, author = "Hsien-Chi Kuo and Po-Yu Lin and Ting-Chiun Chung and Chin-Mei Chao and Liang-Chuan Lai and Mong-Hsun Tsai and Eric Y. Chuang", title = "{DBCAT}: Database of {CpG} Islands and Analytical Tools for Identifying Comprehensive Methylation Profiles in Cancer Cells", journal = j-J-COMPUT-BIOL, volume = "18", number = "8", pages = "1013--1017", month = aug, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0038", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:26 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0038; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0038", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 January 2011", } @Article{Anonymous:2011:PSW, author = "Anonymous", title = "Preface: {Satellite Workshop on Comparative Genomics, Research in Computational Molecular Biology (RECOMB-CG 2010)}", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1019--1021", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.008p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.008p; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.008p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Wittler:2011:CSB, author = "Roland Wittler and J{\'a}n Ma{\v{n}}uch and Murray Patterson and Jens Stoye", title = "Consistency of Sequence-Based Gene Clusters", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1023--1039", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0083", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0083; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0083", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Ouangraoua:2011:AMD, author = "A{\"\i}da Ouangraoua and Krister M. Swenson and Cedric Chauve", title = "A $2$-Approximation for the Minimum Duplication Speciation Problem", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1041--1053", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0108; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0108", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Lin:2011:NGE, author = "Yu Lin and Bernard M. E. Moret", title = "A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses that Applies across Eukaryotes and Prokaryotes", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1055--1064", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0098", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0098; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0098", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Warren:2011:GAR, author = "Robert Warren and David Sankoff", title = "Genome Aliquoting Revisited", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1065--1075", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0087", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0087; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0087", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Jiang:2011:ZED, author = "Minghui Jiang", title = "The Zero Exemplar Distance Problem", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1077--1086", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0097", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0097; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0097", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Bansal:2011:DHH, author = "Mukul S. Bansal and Guy Banay and J. Peter Gogarten and Ron Shamir", title = "Detecting Highways of Horizontal Gene Transfer", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1087--1114", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0066", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0066; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0066", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Mongin:2011:MAB, author = "Emmanuel Mongin and Ken Dewar and Mathieu Blanchette", title = "Mapping Association between Long-Range {\em cis\/}-Regulatory Regions and Their Target Genes Using Synteny", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1115--1130", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0088", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0088; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0088", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Lin:2011:FAP, author = "Y. Lin and V. Rajan and B. M. E. Moret", title = "Fast and Accurate Phylogenetic Reconstruction from High-Resolution Whole-Genome Data and a Novel Robustness Estimator", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1131--1139", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0114", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0114; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0114", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Uricaru:2011:NDA, author = "Raluca Uricaru and Alban Mancheron and Eric Rivals", title = "Novel Definition and Algorithm for Chaining Fragments with Proportional Overlaps", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1141--1154", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0126", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0126; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0126", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Devillers:2011:RAW, author = "Hugo Devillers and H{\'e}l{\`e}ne Chiapello and Sophie Schbath and Meriem {El Karoui}", title = "Robustness Assessment of Whole Bacterial Genome Segmentations", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1155--1165", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0115; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0115", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Braga:2011:DCJ, author = "Mar{\'\i}lia D. V. Braga and Eyla Willing and Jens Stoye", title = "Double Cut and Join with Insertions and Deletions", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1167--1184", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0118", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0118; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0118", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Savard:2011:GHD, author = "Olivier Tremblay Savard and Yves Gagnon and Denis Bertrand and Nadia El-Mabrouk", title = "Genome Halving and Double Distance with Losses", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1185--1199", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0136", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0136; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0136", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Badr:2011:LAP, author = "Ghada Badr and Krister M. Swenson and David Sankoff", title = "Listing All Parsimonious Reversal Sequences: New Algorithms and Perspectives", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1201--1210", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0133", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0133; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0133", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Matroud:2011:ASM, author = "Atheer A. Matroud and Christopher P. Tuffley and Michael D. Hendy", title = "An Algorithm to Solve the Motif Alignment Problem for Approximate Nested Tandem Repeats in Biological Sequences", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1211--1218", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0101; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0101", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Ouangraoua:2011:TPU, author = "A{\"\i}da Ouangraoua and Anne Bergeron and Krister M. Swenson", title = "Theory and Practice of Ultra-Perfection", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1219--1230", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0086", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0086; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0086", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Kovac:2011:RDM, author = "Jakub Kov{\'a}{\v{c}} and Robert Warren and Mar{\'\i}lia D. V. Braga and Jens Stoye", title = "Restricted {DCJ} Model: Rearrangement Problems with Chromosome Reincorporation", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1231--1241", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0116", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0116; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0116", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Manuch:2011:CGC, author = "J{\'a}n Ma{\v{n}}uch and Murray Patterson", title = "The Complexity of the Gapped Consecutive-Ones Property Problem for Matrices of Bounded Maximum Degree", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1243--1253", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0128", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0128; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0128", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Jahn:2011:ECA, author = "Katharina Jahn", title = "Efficient Computation of Approximate Gene Clusters Based on Reference Occurrences", journal = j-J-COMPUT-BIOL, volume = "18", number = "9", pages = "1255--1274", month = sep, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0132", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0132; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0132", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2011", } @Article{Akutsu:2011:DSA, author = "Tatsuya Akutsu and Avraham A. Melkman and Takeyuki Tamura and Masaki Yamamoto", title = "Determining a Singleton Attractor of a {Boolean} Network with Nested Canalyzing Functions", journal = j-J-COMPUT-BIOL, volume = "18", number = "10", pages = "1275--1290", month = oct, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0281", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0281; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0281", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2011", } @Article{Graudenzi:2011:DPB, author = "Alex Graudenzi and Roberto Serra and Marco Villani and Chiara Damiani and Annamaria Colacci and Stuart A. Kauffman", title = "Dynamical Properties of a {Boolean} Model of Gene Regulatory Network with Memory", journal = j-J-COMPUT-BIOL, volume = "18", number = "10", pages = "1291--1303", month = oct, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0069", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0069; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0069", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2011", } @Article{Collins:2011:QHR, author = "Joshua Collins and Simone Linz and Charles Semple", title = "Quantifying Hybridization in Realistic Time", journal = j-J-COMPUT-BIOL, volume = "18", number = "10", pages = "1305--1318", month = oct, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0166", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0166; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0166", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Barreto-Hernadez:2011:PPO, author = "Emiliano Barreto-Hernadez and Margarida Gama-Carvalho and Lisete Sousa", title = "Pre-Processing Optimization of {RNA} Immunoprecipitation Microarray Data", journal = j-J-COMPUT-BIOL, volume = "18", number = "10", pages = "1319--1328", month = oct, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0020", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0020; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0020", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 July 2011", } @Article{Kim:2011:BDU, author = "Hoon Kim and John Watkinson and Dimitris Anastassiou", title = "Biomarker Discovery Using Statistically Significant Gene Sets", journal = j-J-COMPUT-BIOL, volume = "18", number = "10", pages = "1329--1338", month = oct, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0085", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0085; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0085", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2011", } @Article{Saule:2011:CRP, author = "C{\'e}dric Saule and Mireille R{\'e}gnier and Jean-Marc Steyaert and Alain Denise", title = "Counting {RNA} Pseudoknotted Structures", journal = j-J-COMPUT-BIOL, volume = "18", number = "10", pages = "1339--1351", month = oct, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0086", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0086; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0086", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2011", } @Article{Lopes:2011:GEC, author = "Fabr{\'\i}cio M. Lopes and Roberto M. {Cesar, Jr.} and Luciano {Da F.Costa}", title = "Gene Expression Complex Networks: Synthesis, Identification, and Analysis", journal = j-J-COMPUT-BIOL, volume = "18", number = "10", pages = "1353--1367", month = oct, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0118", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0118; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0118", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2011", } @Article{Bafna:2011:PRC, author = "Vineet Bafna", title = "Preface: {Research in Computational Molecular Biology (RECOMB 2011)}", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1369--1369", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.009p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.009p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 November 2011", } @Article{Mohimani:2011:MNS, author = "Hosein Mohimani and Wei-Ting Liu and Yu-Liang Yang and Susana P. Gaud{\^e}ncio and William Fenical and Pieter C. Dorrestein and Pavel A. Pevzner", title = "Multiplex {De} {Novo} Sequencing of Peptide Antibiotics", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1371--1381", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0158", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0158; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0158", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Scheubert:2011:CFT, author = "Kerstin Scheubert and Franziska Hufsky and Florian Rasche and Sebastian B{\"o}cker", title = "Computing Fragmentation Trees from Metabolite Multiple Mass Spectrometry Data", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1383--1397", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0168", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0168; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0168", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Leiserson:2011:IMC, author = "Mark D. M. Leiserson and Diana Tatar and Lenore J. Cowen and Benjamin J. Hescott", title = "Inferring Mechanisms of Compensation from {E-MAP} and {SGA} Data Using Local Search Algorithms for Max Cut", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1399--1409", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0191", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0191; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0191", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 September 2011", } @Article{Li:2011:HRL, author = "Xin Li and Jing Li", title = "Haplotype Reconstruction in Large Pedigrees with Untyped Individuals through {IBD} Inference", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1411--1421", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0167", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0167; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0167", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 September 2011", } @Article{Petri:2011:ESE, author = "Tobias Petri and Robert K{\"u}ffner and Ralf Zimmer", title = "Experiment Specific Expression Patterns", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1423--1435", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0159", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0159; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0159", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2011", } @Article{Silverbush:2011:OOP, author = "Dana Silverbush and Michael Elberfeld and Roded Sharan", title = "Optimally Orienting Physical Networks", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1437--1448", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 October 2011", } @Article{Hickey:2011:PMS, author = "Glenn Hickey and Mathieu Blanchette", title = "A Probabilistic Model for Sequence Alignment with Context-Sensitive Indels", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1449--1464", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0157", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0157; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0157", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 September 2011", } @Article{Waldispuhl:2011:UAS, author = "J{\'e}r{\^o}me Waldisp{\"u}hl and Yann Ponty", title = "An Unbiased Adaptive Sampling Algorithm for the Exploration of {RNA} Mutational Landscapes Under Evolutionary Pressure", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1465--1479", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0181", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0181; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0181", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Kirkpatrick:2011:PRU, author = "Bonnie Kirkpatrick and Shuai Cheng Li and Richard M. Karp and Eran Halperin", title = "Pedigree Reconstruction Using Identity by Descent", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1481--1493", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0156; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0156", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Newkirk:2011:AAS, author = "Daniel Newkirk and Jacob Biesinger and Alvin Chon and Kyoko Yokomori and Xiaohui Xie", title = "{AREM}: Aligning Short Reads from {ChIP-Sequencing} by Expectation Maximization", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1495--1505", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Martin:2011:GAA, author = "Jeffrey W. Martin and Anthony K. Yan and Chris Bailey-Kellogg and Pei Zhou and Bruce R. Donald", title = "A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from {NOEs} and {RDCs}", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1507--1523", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Zakov:2011:RPI, author = "Shay Zakov and Yoav Goldberg and Michael Elhadad and Michal Ziv-ukelson", title = "Rich Parameterization Improves {RNA} Structure Prediction", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1525--1542", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0184", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0184; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0184", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Yu:2011:AMB, author = "Yun Yu and Tandy Warnow and Luay Nakhleh", title = "Algorithms for {MDC-Based} Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1543--1559", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0174", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0174; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0174", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Erten:2011:VAP, author = "Sinan Erten and Gurkan Bebek and Mehmet Koyut{\"u}rk", title = "{Vavien}: an Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1561--1574", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0154", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0154; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0154", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 October 2011", } @Article{Heath:2011:AEI, author = "Allison P. Heath and George N. Bennett and Lydia E. Kavraki", title = "An Algorithm for Efficient Identification of Branched Metabolic Pathways", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1575--1597", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 October 2011", } @Article{Misra:2011:OBS, author = "Navodit Misra and Guy Blelloch and R. Ravi and Russell Schwartz", title = "An Optimization-Based Sampling Scheme for Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1599--1609", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0164", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0164; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0164", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 September 2011", } @Article{Sul:2011:IPG, author = "Jae Hoon Sul and Buhm Han and Eleazar Eskin", title = "Increasing Power of Groupwise Association Test with Likelihood Ratio Test", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1611--1624", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0161", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0161; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0161", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2011", } @Article{Medvedev:2011:PBG, author = "Paul Medvedev and Son Pham and Mark Chaisson and Glenn Tesler and Pavel Pevzner", title = "Paired {de Bruijn} Graphs: a Novel Approach for Incorporating Mate Pair Information into Genome Assemblers", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1625--1634", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 October 2011", } @Article{Shenker:2011:ETB, author = "Solomon Shenker and Charles W. O'Donnell and Srinivas Devadas and Bonnie Berger and J{\'e}r{\^o}me Waldisp{\"u}hl", title = "Efficient Traversal of Beta-Sheet Protein Folding Pathways Using Ensemble Models", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1635--1647", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0176", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0176; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0176", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 September 2011", } @Article{Wauthier:2011:NCS, author = "Fabian L. Wauthier and Michael I. Jordan and Nebojsa Jojic", title = "Nonparametric Combinatorial Sequence Models", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1649--1660", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0175", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0175; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0175", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 November 2011", } @Article{Zeng:2011:BAD, author = "Jianyang Zeng and Kyle E. Roberts and Pei Zhou and Bruce Randall Donald", title = "A {Bayesian} Approach for Determining Protein Side-Chain Rotamer Conformations Using Unassigned {NOE} Data", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1661--1679", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0172; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2011", } @Article{Gao:2011:ORO, author = "Song Gao and Wing-Kin Sung and Niranjan Nagarajan", title = "{Opera}: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1681--1691", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0170", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0170; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0170", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 September 2011", } @Article{Li:2011:ILR, author = "Wei Li and Jianxing Feng and Tao Jiang", title = "{IsoLasso}: a {LASSO} Regression Approach to {RNA-Seq} Based Transcriptome Assembly", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1693--1707", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0171", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0171; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0171", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 September 2011", } @Article{Lin:2011:LCS, author = "Tien-Ho Lin and Ziv Bar-Joseph and Robert F. Murphy", title = "Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1709--1722", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0193", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0193; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0193", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 October 2011", } @Article{Amir:2011:BCR, author = "Amnon Amir and Or Zuk", title = "Bacterial Community Reconstruction Using Compressed Sensing", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1723--1741", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0189; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 October 2011", } @Article{Parker:2011:OCM, author = "Andrew S. Parker and Karl E. Griswold and Chris Bailey-Kellogg", title = "Optimization of Combinatorial Mutagenesis", journal = j-J-COMPUT-BIOL, volume = "18", number = "11", pages = "1743--1756", month = nov, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0152", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0152; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0152", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 September 2011", } @Article{Chandola:2011:NSI, author = "Himanshu Chandola and Anthony K. Yan and Shobha Potluri and Bruce R. Donald and Chris Bailey-Kellogg", title = "{NMR} Structural Inference of Symmetric Homo-Oligomers", journal = j-J-COMPUT-BIOL, volume = "18", number = "12", pages = "1757--1775", month = dec, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0327", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0327; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0327", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 June 2011", } @Article{Chen:2011:BPA, author = "Jiun-Rung Chen and Ye-In Chang", title = "An Up-Down Bit Pattern Approach to Coregulated and Negative-Coregulated Gene Clustering of Microarray Data", journal = j-J-COMPUT-BIOL, volume = "18", number = "12", pages = "1777--1791", month = dec, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0212", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0212; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0212", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Nebel:2011:LCR, author = "Markus E. Nebel and Christian M. Reidys and Rita R. Wang", title = "Loops in Canonical {RNA} Pseudoknot Structures", journal = j-J-COMPUT-BIOL, volume = "18", number = "12", pages = "1793--1806", month = dec, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0022", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0022; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0022", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 March 2011", } @Article{Adamczak:2011:FGC, author = "Rafa{\l} Adamczak and Jaroslaw Pillardy and Brinda K. Vallat and Jaroslaw Meller", title = "Fast Geometric Consensus Approach for Protein Model Quality Assessment", journal = j-J-COMPUT-BIOL, volume = "18", number = "12", pages = "1807--1818", month = dec, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0170", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0170; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0170", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2011", } @Article{Comin:2011:ICM, author = "Matteo Comin and Davide Verzotto", title = "The Irredundant Class Method for Remote Homology Detection of Protein Sequences", journal = j-J-COMPUT-BIOL, volume = "18", number = "12", pages = "1819--1829", month = dec, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0171", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0171; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0171", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2011", } @Article{Li:2011:FMM, author = "Meng-Rong Li and Yu-Ju Lin and Tzong-Hann Shieh", title = "The Flux Model of the Movement of Tumor Cells and Healthy Cells Using a System of Nonlinear Heat Equations", journal = j-J-COMPUT-BIOL, volume = "18", number = "12", pages = "1831--1839", month = dec, year = "2011", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0050", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0050; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0050", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Devillers:2012:SSM, author = "Hugo Devillers and Sophie Schbath", title = "Separating Significant Matches from Spurious Matches in {DNA} Sequences", journal = j-J-COMPUT-BIOL, volume = "19", number = "1", pages = "1--12", month = jan, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0070", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0070; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0070", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 December 2011", } @Article{Movaghar:2012:SST, author = "Afshin Fayyaz Movaghar and Guillaume Launay and Sophie Schbath and Jean-Fran{\c{c}}ois Gibrat and Fran{\c{c}}ois Rodolphe", title = "Statistical Significance of Threading Scores", journal = j-J-COMPUT-BIOL, volume = "19", number = "1", pages = "13--29", month = jan, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0236", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0236; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0236", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 December 2011", } @Article{Karlebach:2012:CLM, author = "Guy Karlebach and Ron Shamir", title = "Constructing Logical Models of Gene Regulatory Networks by Integrating Transcription {Factor--DNA} Interactions with Expression Data: an Entropy-Based Approach", journal = j-J-COMPUT-BIOL, volume = "19", number = "1", pages = "30--41", month = jan, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0100; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0100", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2012", } @Article{Yuan:2012:OPG, author = "Xiguo Yuan and David J. Miller and Junying Zhang and David Herrington and Yue Wang", title = "An Overview of Population Genetic Data Simulation", journal = j-J-COMPUT-BIOL, volume = "19", number = "1", pages = "42--54", month = jan, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0188", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0188; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0188", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 December 2011", } @Article{Onuki:2012:PMB, author = "Ritsuko Onuki and Ryo Yamada and Rui Yamaguchi and Minoru Kanehisa and Tetsuo Shibuya", title = "Population Model--Based Inter-Diplotype Similarity Measure for Accurate Diplotype Clustering", journal = j-J-COMPUT-BIOL, volume = "19", number = "1", pages = "55--67", month = jan, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0227", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0227; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0227", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 December 2011", } @Article{Chuang:2012:HBC, author = "Li-Yeh Chuang and Cheng-Huei Yang and Jung-Chike Li and Cheng-Hong Yang", title = "A Hybrid {BPSO-CGA} Approach for Gene Selection and Classification of Microarray Data", journal = j-J-COMPUT-BIOL, volume = "19", number = "1", pages = "68--82", month = jan, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0064; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0064", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{Winter:2012:ACT, author = "Pawe{\l} Winter and Rasmus Fonseca", title = "Adjustable Chain Trees for Proteins", journal = j-J-COMPUT-BIOL, volume = "19", number = "1", pages = "83--99", month = jan, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0320", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0320; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0320", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2011", } @Article{Califano:2012:PRS, author = "Andrea Califano and Manolis Kellis and Gustavo Stolovitzky", title = "Preface: {RECOMB Systems Biology, Regulatory Genomics, and DREAM 2011} Special Issue", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "101--101", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.010p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.010p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Goncalves:2012:OAS, author = "Emanuel Gon{\c{c}}alves and Rui Pereira and Isabel Rocha and Miguel Rocha", title = "Optimization Approaches for the {{\em In Silico\/}} Discovery of Optimal Targets for Gene Over/Underexpression", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "102--114", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0265", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0265; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0265", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Amit:2012:ACC, author = "Roee Amit", title = "Anti-Cooperative and Cooperative Protein-Protein Interactions between {TetR} Isoforms on Synthetic Enhancers", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "115--125", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0257", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0257; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0257", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Sakoparnig:2012:BPC, author = "Thomas Sakoparnig and Tobias Kockmann and Renato Paro and Christian Beisel and Niko Beerenwinkel", title = "Binding Profiles of Chromatin-Modifying Proteins Are Predictive for Transcriptional Activity and Promoter-Proximal Pausing", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "126--138", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0258", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0258; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0258", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Ihuegbu:2012:FSD, author = "Nnamdi E. Ihuegbu and Gary D. Stormo and Jeremy Buhler", title = "Fast, Sensitive Discovery of Conserved Genome-Wide Motifs", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "139--147", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0249", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0249; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0249", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Cosentino:2012:SBG, author = "Carlo Cosentino and Luca Salerno and Antonio Passanti and Alessio Merola and Declan G. Bates and Francesco Amato", title = "Structural Bistability of the {GAL} Regulatory Network and Characterization of its Domains of Attraction", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "148--162", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0251", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0251; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0251", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Silberberg:2012:LSE, author = "Yael Silberberg and Assaf Gottlieb and Martin Kupiec and Eytan Ruppin and Roded Sharan", title = "Large-Scale Elucidation of Drug Response Pathways in Humans", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "163--174", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0264", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0264; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0264", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Yang:2012:SPE, author = "Xinyi Yang and Jennifer E. Dent and Christine Nardini", title = "An {$S$-System Parameter Estimation Method (SPEM)} for Biological Networks", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "175--187", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0269", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0269; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0269", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Eduati:2012:DMM, author = "Federica Eduati and Barbara di Camillo and Michael Karbiener and Marcel Scheideler and Davide Cor{\`a} and Michele Caselle and Gianna Toffolo", title = "Dynamic Modeling of {miRNA-mediated} Feed-Forward Loops", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "188--199", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0274", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0274; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0274", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Dana:2012:EMS, author = "Alexandra Dana and Tamir Tuller", title = "Efficient Manipulations of Synonymous Mutations for Controlling Translation Rate: an Analytical Approach", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "200--231", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0275", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0275; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0275", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Vardi:2012:LCB, author = "Liram Vardi and Eytan Ruppin and Roded Sharan", title = "A Linearized Constraint-Based Approach for Modeling Signaling Networks", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "232--240", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0277", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0277; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0277", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Wang:2012:MNB, author = "Yi Wang and Henry C. M. Leung and S. M. Yiu and Francis Y. L. Chin", title = "{MetaCluster} 4.0: a Novel Binning Algorithm for {NGS} Reads and Huge Number of Species", journal = j-J-COMPUT-BIOL, volume = "19", number = "2", pages = "241--249", month = feb, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0276", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0276; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0276", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2012", } @Article{Song:2012:CAF, author = "Kai Song and Ze Zhang and Tuo-Peng Tong and Fang Wu", title = "Classifier Assessment and Feature Selection for Recognizing Short Coding Sequences of Human Genes", journal = j-J-COMPUT-BIOL, volume = "19", number = "3", pages = "251--260", month = mar, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2012", } @Article{Ceselli:2012:ADM, author = "Alberto Ceselli and Sandro Luciano Fornili and Giovanni Righini", title = "Algorithms for the Design of Maximum Hydropathic Complementarity Molecules", journal = j-J-COMPUT-BIOL, volume = "19", number = "3", pages = "261--270", month = mar, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2012", } @Article{David:2012:CBD, author = "Olivier David and Catherine Lar{\'e}do and Rapha{\"e}l Leblois and Brigitte Schaeffer and Nicolas Vergne", title = "Coalescent-Based {DNA} Barcoding: Multilocus Analysis and Robustness", journal = j-J-COMPUT-BIOL, volume = "19", number = "3", pages = "271--278", month = mar, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0122", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0122; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0122", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2012", } @Article{Carnevali:2012:CTH, author = "Paolo Carnevali and Jonathan Baccash and Aaron L. Halpern and Igor Nazarenko and Geoffrey B. Nilsen and Krishna P. Pant and Jessica C. Ebert and Anushka Brownley and Matt Morenzoni and Vitali Karpinchyk and Bruce Martin and Dennis G. Ballinger and Radoje Drmanac", title = "Computational Techniques for Human Genome Resequencing Using Mated Gapped Reads", journal = j-J-COMPUT-BIOL, volume = "19", number = "3", pages = "279--292", month = mar, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0201", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0201; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0201", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 December 2011", } @Article{Jewett:2012:IIG, author = "Ethan M. Jewett and Noah A. Rosenberg", title = "{iGLASS}: an Improvement to the {GLASS} Method for Estimating Species Trees from Gene Trees", journal = j-J-COMPUT-BIOL, volume = "19", number = "3", pages = "293--315", month = mar, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0231", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0231; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0231", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2012", } @Article{Sakhanenko:2012:PLM, author = "Nikita A. Sakhanenko and David J. Galas", title = "Probabilistic Logic Methods and Some Applications to Biology and Medicine", journal = j-J-COMPUT-BIOL, volume = "19", number = "3", pages = "316--336", month = mar, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0234", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0234; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0234", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2012", } @Article{Dost:2012:AMS, author = "Banu Dost and Nuno Bandeira and Xiangqian Li and Zhouxin Shen and Steven P. Briggs and Vineet Bafna", title = "Accurate Mass Spectrometry Based Protein Quantification via Shared Peptides", journal = j-J-COMPUT-BIOL, volume = "19", number = "4", pages = "337--348", month = apr, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0267", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0267; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0267", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2012", } @Article{Li-Thiao-Te:2012:FDC, author = "S{\'e}bastien Li-Thiao-T{\'e} and Benno Schwikowski", title = "Feature Detection with Controlled Error Rates in {LC/MS} Images", journal = j-J-COMPUT-BIOL, volume = "19", number = "4", pages = "349--364", month = apr, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2012", } @Article{Wong:2012:SAR, author = "Thomas K. F. Wong and S. M. Yiu", title = "Structural Alignment of {RNA} with Triple Helix Structure", journal = j-J-COMPUT-BIOL, volume = "19", number = "4", pages = "365--378", month = apr, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0052", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0052; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0052", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 April 2012", } @Article{Stojmirovic:2012:IFI, author = "Aleksandar Stojmirovi{\'c} and Yi-kuo Yu", title = "Information Flow in Interaction Networks {II}: Channels, Path Lengths, and Potentials", journal = j-J-COMPUT-BIOL, volume = "19", number = "4", pages = "379--403", month = apr, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0228", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0228; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0228", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 March 2012", } @Article{Chen:2012:PDP, author = "Yen Hung Chen", title = "The $k$ Partition-Distance Problem", journal = j-J-COMPUT-BIOL, volume = "19", number = "4", pages = "404--417", month = apr, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0186", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0186; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0186", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 April 2012", } @Article{Arima:2012:IHM, author = "Serena Arima and Luca Tardella", title = "Improved Harmonic Mean Estimator for Phylogenetic Model Evidence", journal = j-J-COMPUT-BIOL, volume = "19", number = "4", pages = "418--438", month = apr, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0139", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0139; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0139", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2012", } @Article{Gupta:2012:AHI, author = "Arvind Gupta and J{\'a}n Ma{\v{n}}uch and Ladislav Stacho and Xiaohong Zhao", title = "Algorithm for Haplotype Inference via Galled-Tree Networks with Simple Galls", journal = j-J-COMPUT-BIOL, volume = "19", number = "4", pages = "439--454", month = apr, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0145", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0145; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0145", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 April 2012", } @Article{Bankevich:2012:SNG, author = "Anton Bankevich and Sergey Nurk and Dmitry Antipov and Alexey A. Gurevich and Mikhail Dvorkin and Alexander S. Kulikov and Valery M. Lesin and Sergey I. Nikolenko and Son Pham and Andrey D. Prjibelski and Alexey V. Pyshkin and Alexander V. Sirotkin and Nikolay Vyahhi and Glenn Tesler and Max A. Alekseyev and Pavel A. Pevzner", title = "{SPAdes}: a New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing", journal = j-J-COMPUT-BIOL, volume = "19", number = "5", pages = "455--477", month = may, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0021", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0021; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0021", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2012", } @Article{Sarkar:2012:SSO, author = "Deepayan Sarkar and Steve Goldstein and David C. Schwartz and Michael A. Newton", title = "Statistical Significance of Optical Map Alignments", journal = j-J-COMPUT-BIOL, volume = "19", number = "5", pages = "478--492", month = may, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0221", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0221; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0221", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2012", } @Article{Terashi:2012:LPT, author = "Genki Terashi and Tetsuo Shibuya and Mayuko Takeda-Shitaka", title = "{LB3D}: a Protein Three-Dimensional Substructure Search Program Based on the Lower Bound of a Root Mean Square Deviation Value", journal = j-J-COMPUT-BIOL, volume = "19", number = "5", pages = "493--503", month = may, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0230", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0230; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0230", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2012", } @Article{Bar-Yaakov:2012:UIR, author = "Nimrod Bar-Yaakov and Zehava Grossman and Nathan Intrator", title = "Using Iterative Ridge Regression to Explore Associations Between Conditioned Variables", journal = j-J-COMPUT-BIOL, volume = "19", number = "5", pages = "504--518", month = may, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0028", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0028; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0028", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 April 2012", } @Article{Falconnet:2012:AEE, author = "Mikael Falconnet and Sarah Behrens", title = "Accurate Estimations of Evolutionary Times in the Context of Strong {CpG} Hypermutability", journal = j-J-COMPUT-BIOL, volume = "19", number = "5", pages = "519--531", month = may, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0135", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0135; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0135", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 April 2012", } @Article{Hamada:2012:CBA, author = "Michiaki Hamada and Kiyoshi Asai", title = "A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy {(MEA)}", journal = j-J-COMPUT-BIOL, volume = "19", number = "5", pages = "532--549", month = may, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 February 2012", } @Article{Behrens:2012:AAW, author = "Sarah Behrens and Cyril Nicaud and Pierre Nicod{\`e}me", title = "An Automaton Approach for Waiting Times in {DNA} Evolution", journal = j-J-COMPUT-BIOL, volume = "19", number = "5", pages = "550--562", month = may, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0218", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0218; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0218", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 April 2012", } @Article{Ibrahim:2012:TBS, author = "Maysson Al-Haj Ibrahim and Sabah Jassim and Michael Anthony Cawthorne and Kenneth Langlands", title = "A Topology-Based Score for Pathway Enrichment", journal = j-J-COMPUT-BIOL, volume = "19", number = "5", pages = "563--573", month = may, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0182", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0182; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0182", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 April 2012", } @Article{Chen:2012:PSI, author = "Ting Chen and Paul Marjoram and Fengzhu Sun and Jasmine Xianghong Zhou", title = "Preface: Special Issue", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "575--576", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.6pre", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.6pre", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 May 2012", } @Article{Aguiar:2012:HFC, author = "Derek Aguiar and Sorin Istrail", title = "{HapCompass}: a Fast Cycle Basis Algorithm for Accurate Haplotype Assembly of Sequence Data", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "577--590", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Bayzid:2012:EOS, author = "Md. Shamsuzzoha Bayzid and Tandy Warnow", title = "Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "591--605", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0037", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0037; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0037", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Frazier:2012:CAI, author = "Zachary Frazier and Frank Alber", title = "A Computational Approach to Increase Time Scales in {Brownian} Dynamics--Based Reaction-Diffusion Modeling", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "606--618", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0027", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0027; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0027", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Gao:2012:BLP, author = "Qinghui Gao and Christine Ho and Yingmin Jia and Jingyi Jessica Li and Haiyan Huang", title = "Biclustering of Linear Patterns In Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "619--631", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0032", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0032; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0032", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Helmkamp:2012:ICD, author = "Laura J. Helmkamp and Ethan M. Jewett and Noah A. Rosenberg", title = "Improvements to a Class of Distance Matrix Methods for Inferring Species Trees from Gene Trees", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "632--649", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0042", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0042; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0042", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Joyce:2012:ESL, author = "Paul Joyce and Alan Genz and Erkan Ozge Buzbas", title = "Efficient Simulation and Likelihood Methods for Non-Neutral Multi-Allele Models", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "650--661", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0033", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0033; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0033", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Kinsella:2012:CBF, author = "Marcus Kinsella and Vineet Bafna", title = "Combinatorics of the Breakage--Fusion--Bridge Mechanism", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "662--678", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0020", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0020; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0020", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2012", } @Article{Lai:2012:CPA, author = "Yinglei Lai", title = "Change-Point Analysis of Paired Allele-Specific Copy Number Variation Data", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "679--693", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0031", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0031; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0031", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Lavi:2012:NIC, author = "Ofer Lavi and Gideon Dror and Ron Shamir", title = "Network-Induced Classification Kernels for Gene Expression Profile Analysis", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "694--709", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0065", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0065; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0065", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Li:2012:AIF, author = "Wenyuan Li and Chao Dai and Chun-Chi Liu and Xianghong Jasmine Zhou", title = "Algorithm to Identify Frequent Coupled Modules from Two-Layered Network Series: Application to Study Transcription and Splicing Coupling", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "710--730", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0025", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0025; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0025", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Luo:2012:NGI, author = "Li Luo and Yun Zhu and Momiao Xiong", title = "A Novel Genome-Information Content-Based Statistic for Genome-Wide Association Analysis Designed for Next-Generation Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "731--744", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0035", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0035; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0035", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 May 2012", } @Article{Manolopoulou:2012:PAI, author = "Ioanna Manolopoulou and Brent C. Emerson", title = "Phylogeographic Ancestral Inference Using the Coalescent Model on Haplotype Trees", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "745--755", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0038", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0038; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0038", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{McPeek:2012:BGI, author = "Mary Sara McPeek", title = "{BLUP} Genotype Imputation for Case-Control Association Testing with Related Individuals and Missing Data", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "756--765", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0024", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0024; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0024", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Ni:2012:RNM, author = "Shengyu Ni and Martin Vingron", title = "{R2KS}: a Novel Measure for Comparing Gene Expression Based on Ranked Gene Lists", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "766--775", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0026", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0026; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0026", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Grover:2012:BTO, author = "Dhruv Grover and Juan Nunez-Iglesias", title = "{Betamax}: Towards Optimal Sampling Strategies for High-Throughput Screens", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "776--784", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0036", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0036; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0036", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Rito:2012:IAH, author = "Tiago Rito and Charlotte M. Deane and Gesine Reinert", title = "The Importance of Age and High Degree, in Protein-Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "785--795", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0054", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0054; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0054", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Schbath:2012:MRG, author = "Sophie Schbath and V{\'e}ronique Martin and Matthias Zytnicki and Julien Fayolle and Valentin Loux and Jean-Fran{\c{c}}ois Gibrat", title = "Mapping Reads on a Genomic Sequence: an Algorithmic Overview and a Practical Comparative Analysis", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "796--813", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0022", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0022; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0022", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2012", } @Article{Wang:2012:BGA, author = "Mingjie Wang and Yuzhen Ye and Haixu Tang", title = "A {{\em de Bruijn\/}} Graph Approach to the Quantification of Closely-Related Genomes in a Microbial Community", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "814--825", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0058", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0058; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0058", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Xu:2012:GLM, author = "Jialin Xu and Yu Zhang", title = "A Generalized Linear Model for Peak Calling in {ChIP-Seq} Data", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "826--838", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0023; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0023", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 April 2012", } @Article{Zhai:2012:NCP, author = "Zhiyuan Zhai and Gesine Reinert and Kai Song and Michael S. Waterman and Yihui Luan and Fengzhu Sun", title = "Normal and Compound {Poisson} Approximations for Pattern Occurrences in {NGS} Reads", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "839--854", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0029", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0029; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0029", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2012", } @Article{Zhang:2012:VVE, author = "Jing Zhang and C.-C. Jay Kuo and Liang Chen", title = "{VERSE}: a Varying Effect Regression for Splicing Elements Discovery", journal = j-J-COMPUT-BIOL, volume = "19", number = "6", pages = "855--865", month = jun, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0063", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0063; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0063", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 May 2012", } @Article{Han:2012:DRS, author = "Hillary S. W. Han and Christian M. Reidys", title = "The 5'-3' Distance of {RNA} Secondary Structures", journal = j-J-COMPUT-BIOL, volume = "19", number = "7", pages = "867--878", month = jul, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0301", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0301; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0301", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 June 2012", } @Article{Gniewek:2012:OPP, author = "Pawe{\l} Gniewek and Andrzej Kolinski and Dominik Gront", title = "Optimization of Profile-to-Profile Alignment Parameters for One-Dimensional Threading", journal = j-J-COMPUT-BIOL, volume = "19", number = "7", pages = "879--886", month = jul, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0307", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0307; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0307", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 June 2012", } @Article{Tvedebrink:2012:ICD, author = "Torben Tvedebrink and Poul Svante Eriksen and Helle Smidt Mogensen and Niels Morling", title = "Identifying Contributors of {DNA} Mixtures by Means of Quantitative Information of {STR} Typing", journal = j-J-COMPUT-BIOL, volume = "19", number = "7", pages = "887--902", month = jul, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0055", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0055; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0055", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2011", } @Article{He:2012:NAT, author = "Yichao He and Haiyan Tian and Xinlu Zhang and Zhiwei Wang and Suogang Gao", title = "Nonadaptive Algorithms for Threshold Group Testing with Inhibitors and Error-Tolerance", journal = j-J-COMPUT-BIOL, volume = "19", number = "7", pages = "903--910", month = jul, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0229", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0229; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0229", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2012", } @Article{Cunial:2012:PCR, author = "Fabio Cunial and Alberto Apostolico", title = "Phylogeny Construction with Rigid Gapped Motifs", journal = j-J-COMPUT-BIOL, volume = "19", number = "7", pages = "911--927", month = jul, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0060", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0060; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0060", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 June 2012", } @Article{Andersen:2012:TRR, author = "J{\o}rgen E. Andersen and Fenix W. D. Huang and Robert C. Penner and Christian M. Reidys", title = "Topology of {RNA-RNA} Interaction Structures", journal = j-J-COMPUT-BIOL, volume = "19", number = "7", pages = "928--943", month = jul, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0308", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:52 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0308; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0308", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 June 2012", } @Article{Cohen:2012:DPS, author = "Eyal Cohen and Benny Chor", title = "Detecting Phylogenetic Signals in Eukaryotic Whole Genome Sequences", journal = j-J-COMPUT-BIOL, volume = "19", number = "8", pages = "945--956", month = aug, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0122", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0122; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0122", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 August 2012", } @Article{Yi:2012:SPF, author = "Gangman Yi and Michael R. Thon and Sing-Hoi Sze", title = "Supervised Protein Family Classification and New Family Construction", journal = j-J-COMPUT-BIOL, volume = "19", number = "8", pages = "957--967", month = aug, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0044", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0044; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0044", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 August 2012", } @Article{August:2012:UNM, author = "Elias August", title = "Using Noise for Model-Testing", journal = j-J-COMPUT-BIOL, volume = "19", number = "8", pages = "968--977", month = aug, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0134", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0134; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0134", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 August 2012", } @Article{Sperrin:2012:RIA, author = "Matthew Sperrin and Thomas Jaki", title = "Recovering Independent Associations in Genetics: a Comparison", journal = j-J-COMPUT-BIOL, volume = "19", number = "8", pages = "978--987", month = aug, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0141", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:54 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0141; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0141", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 August 2012", } @Article{Bolouri:2012:ICS, author = "Hamid Bolouri and Walter L. Ruzzo", title = "Integration of 198 {ChIP-seq} Datasets Reveals Human {\em cis\/}-Regulatory Regions", journal = j-J-COMPUT-BIOL, volume = "19", number = "9", pages = "989--997", month = sep, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0100; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0100", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 August 2012", } @Article{Kirkpatrick:2012:CPG, author = "Bonnie Kirkpatrick and Yakir Reshef and Hilary Finucane and Haitao Jiang and Binhai Zhu and Richard M. Karp", title = "Comparing Pedigree Graphs", journal = j-J-COMPUT-BIOL, volume = "19", number = "9", pages = "998--1014", month = sep, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0254", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0254; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0254", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 August 2012", } @Article{Gonzalez:2012:EMA, author = "M. Gonz{\'a}lez and C. Guti{\'e}rrez and R. Mart{\'\i}nez", title = "Expectation-Maximization Algorithm for Determining Natural Selection of {Y}-Linked Genes Through Two-Sex Branching Processes", journal = j-J-COMPUT-BIOL, volume = "19", number = "9", pages = "1015--1026", month = sep, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0242", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0242; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0242", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 August 2012", } @Article{Wu:2012:DPC, author = "Min Wu and Xiao-li Li and Chee-Keong Kwoh and See-Kiong Ng and Limsoon Wong", title = "Discovery of Protein Complexes with Core-Attachment Structures from Tandem Affinity Purification {(TAP)} Data", journal = j-J-COMPUT-BIOL, volume = "19", number = "9", pages = "1027--1042", month = sep, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0293", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0293; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0293", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 July 2011", } @Article{Hossain:2012:NNI, author = "M. Shahriar Hossain and Monika Akbar and Nicholas F. Polys", title = "Narratives in the Network: Interactive Methods for Mining Cell Signaling Networks", journal = j-J-COMPUT-BIOL, volume = "19", number = "9", pages = "1043--1059", month = sep, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0244; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0244", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 August 2012", } @Article{Schindler:2012:SAV, author = "Christina Schindler and Wolfgang B. Fischer", title = "Sequence Alignment of Viral Channel Proteins with Cellular Ion Channels", journal = j-J-COMPUT-BIOL, volume = "19", number = "9", pages = "1060--1072", month = sep, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0297", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0297; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0297", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 August 2012", } @Article{Cui:2012:PTA, author = "Yun Cui and Jesper Jansson and Wing-Kin Sung", title = "Polynomial-Time Algorithms for Building a Consensus {MUL-Tree}", journal = j-J-COMPUT-BIOL, volume = "19", number = "9", pages = "1073--1088", month = sep, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:56 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 September 2012", } @Article{Mori:2012:CBM, author = "Tomoya Mori and Takeyuki Tamura and Daiji Fukagawa and Atsuhiro Takasu and Etsuji Tomita and Tatsuya Akutsu", title = "A Clique-Based Method Using Dynamic Programming for Computing Edit Distance Between Unordered Trees", journal = j-J-COMPUT-BIOL, volume = "19", number = "10", pages = "1089--1104", month = oct, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0133", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0133; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0133", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2012", } @Article{Han:2012:PTE, author = "Hillary S. W. Han and Christian M. Reidys", title = "A Phase Transition in Energy-Filtered {RNA} Secondary Structures", journal = j-J-COMPUT-BIOL, volume = "19", number = "10", pages = "1105--1119", month = oct, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2012", } @Article{Saffarian:2012:RLO, author = "Azadeh Saffarian and Mathieu Giraud and Antoine de Monte and H{\'e}l{\`e}ne Touzet", title = "{RNA} Locally Optimal Secondary Structures", journal = j-J-COMPUT-BIOL, volume = "19", number = "10", pages = "1120--1133", month = oct, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2010.0178", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2010.0178; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2010.0178", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2012", } @Article{Nebel:2012:ACP, author = "Markus E. Nebel and Frank Weinberg", title = "Algebraic and Combinatorial Properties of Common {RNA} Pseudoknot Classes with Applications", journal = j-J-COMPUT-BIOL, volume = "19", number = "10", pages = "1134--1150", month = oct, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0094", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0094; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0094", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2012", } @Article{Rabie:2012:SSA, author = "Huwaida S. Rabie and Ian W. Saunders", title = "A Simulation Study to Assess a Variable Selection Method for Selecting Single Nucleotide Polymorphisms Associated with Disease", journal = j-J-COMPUT-BIOL, volume = "19", number = "10", pages = "1151--1161", month = oct, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0105", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0105; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0105", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2012", } @Article{Roy:2012:SSL, author = "Rajat S. Roy and Kevin C. Chen and Anirvan M. Sengupta and Alexander Schliep", title = "{SLIQ}: Simple Linear Inequalities for Efficient Contig Scaffolding", journal = j-J-COMPUT-BIOL, volume = "19", number = "10", pages = "1162--1175", month = oct, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0263", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0263; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0263", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2012", } @Article{Dixit:2012:FPM, author = "Narendra M. Dixit and Piyush Srivastava and Nisheeth K. Vishnoi", title = "A Finite Population Model of Molecular Evolution: Theory and Computation", journal = j-J-COMPUT-BIOL, volume = "19", number = "10", pages = "1176--1202", month = oct, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0064; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0064", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2012", } @Article{Fonseca:2012:BVP, author = "Rasmus Fonseca and Pawe{\l} Winter", title = "Bounding Volumes for Proteins: a Comparative Study", journal = j-J-COMPUT-BIOL, volume = "19", number = "10", pages = "1203--1213", month = oct, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0104", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:50:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0104; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0104", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2012", } @Article{Lu:2012:PSS, author = "I-Lin Lu and Hsiuying Wang", title = "Protein-specific Scoring Method for Ligand Discovery", journal = j-J-COMPUT-BIOL, volume = "19", number = "11", pages = "1215--1226", month = nov, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0188", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0188; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0188", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2012", } @Article{Scornavacca:2012:FST, author = "Celine Scornavacca and Simone Linz and Benjamin Albrecht", title = "A First Step Toward Computing All Hybridization Networks For Two Rooted Binary Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "19", number = "11", pages = "1227--1242", month = nov, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0192", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0192; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0192", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 November 2012", } @Article{Veselsky:2012:OPA, author = "M. Veselsky", title = "Order of Precedence and Age of {Y-DNA} Haplotypes", journal = j-J-COMPUT-BIOL, volume = "19", number = "11", pages = "1243--1250", month = nov, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0193", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0193; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0193", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2012", } @Article{Ehler:2012:LLB, author = "M. Ehler and F. Filbir and H. N. Mhaskar", title = "Locally Learning Biomedical Data Using Diffusion Frames", journal = j-J-COMPUT-BIOL, volume = "19", number = "11", pages = "1251--1264", month = nov, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0187", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0187; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0187", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 October 2012", } @Article{Hamada:2012:DUR, author = "Michiaki Hamada", title = "Direct Updating of an {RNA} Base-Pairing Probability Matrix with Marginal Probability Constraints", journal = j-J-COMPUT-BIOL, volume = "19", number = "12", pages = "1265--1276", month = dec, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0215", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0215; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0215", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2012", } @Article{Toyoizumi:2012:END, author = "Hiroshi Toyoizumi and Hideo Tsubouchi", title = "Estimating the Number of Double-{Strand} Breaks Formed During Meiosis from Partial Observation", journal = j-J-COMPUT-BIOL, volume = "19", number = "12", pages = "1277--1283", month = dec, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0209", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0209; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0209", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2012", } @Article{Fan:2012:ICP, author = "Jia-Hao Fan and Jianer Chen and Sing-Hoi Sze", title = "Identifying Complexes from Protein Interaction Networks According to Different Types of Neighborhood Density", journal = j-J-COMPUT-BIOL, volume = "19", number = "12", pages = "1284--1294", month = dec, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0195", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0195; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0195", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2012", } @Article{Reyes:2012:AGG, author = "R. Reyes and D. Gamermann and A. Montagud and D. Fuente and J. Triana and J. F. Urchuegu{\'\i}a and P. Fern{\'a}ndez de C{\'o}rdoba", title = "Automation on the Generation of Genome-Scale Metabolic Models", journal = j-J-COMPUT-BIOL, volume = "19", number = "12", pages = "1295--1306", month = dec, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0183", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0183; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0183", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2012", } @Article{Chang:2012:OBI, author = "Young Hwan Chang and Joe Gray and Claire Tomlin", title = "Optimization-based Inference for Temporally Evolving Networks with Applications in Biology", journal = j-J-COMPUT-BIOL, volume = "19", number = "12", pages = "1307--1323", month = dec, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0190", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0190; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0190", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2012", } @Article{Pei:2012:RBN, author = "Baikang Pei and Dong-Guk Shin", title = "Reconstruction of Biological Networks by Incorporating Prior Knowledge into {Bayesian} Network Models", journal = j-J-COMPUT-BIOL, volume = "19", number = "12", pages = "1324--1334", month = dec, year = "2012", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0194", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0194; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0194", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2012", } @Article{Nguyen:2013:DMD, author = "Viet-An Nguyen and Jordan Boyd-Graber and Stephen F. Altschul", title = "{Dirichlet} Mixtures, the {Dirichlet} Process, and the Structure of Protein Space", journal = j-J-COMPUT-BIOL, volume = "20", number = "1", pages = "1--18", month = jan, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0244; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0244", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2013", } @Article{Yang:2013:LLA, author = "Lianping Yang and Xiangde Zhang and Tianming Wang and Hegui Zhu", title = "Large Local Analysis of the Unaligned Genome and Its Application", journal = j-J-COMPUT-BIOL, volume = "20", number = "1", pages = "19--29", month = jan, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0052", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0052; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0052", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2013", } @Article{Telles:2013:LP, author = "Guilherme P. Telles and Nalvo F. Almeida and Rosane Minghim and Maria Emilia M. T. Walter", title = "Live Phylogeny", journal = j-J-COMPUT-BIOL, volume = "20", number = "1", pages = "30--37", month = jan, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0219", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0219; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0219", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2013", } @Article{Chen:2013:UTM, author = "Zhi-Zhong Chen and Lusheng Wang", title = "An Ultrafast Tool for Minimum Reticulate Networks", journal = j-J-COMPUT-BIOL, volume = "20", number = "1", pages = "38--41", month = jan, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0240", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0240; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0240", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2013", } @Article{Huang:2013:MVT, author = "Hong Huang and Yongji Li", title = "{MASTtreedist}: Visualization of Tree Space Based on Maximum Agreement Subtree", journal = j-J-COMPUT-BIOL, volume = "20", number = "1", pages = "42--49", month = jan, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0243; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0243", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2013", } @Article{Allman:2013:STI, author = "Elizabeth S. Allman and James H. Degnan and John A. Rhodes", title = "Species Tree Inference by the {STAR} Method and Its Generalizations", journal = j-J-COMPUT-BIOL, volume = "20", number = "1", pages = "50--61", month = jan, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0101; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0101", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2013", } @Article{Chor:2013:PR, author = "Benny Chor", title = "Preface: {RECOMB 2012}", journal = j-J-COMPUT-BIOL, volume = "20", number = "2", pages = "63--63", month = feb, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.007p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.007p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2013", } @Article{Song:2013:AFS, author = "Kai Song and Jie Ren and Zhiyuan Zhai and Xuemei Liu and Minghua Deng and Fengzhu Sun", title = "Alignment-Free Sequence Comparison Based on Next-Generation Sequencing Reads", journal = j-J-COMPUT-BIOL, volume = "20", number = "2", pages = "64--79", month = feb, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0228", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0228; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0228", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2013", } @Article{He:2013:HSO, author = "Dan He and Buhm Han and Eleazar Eskin", title = "{Hap}-seq: an Optimal Algorithm for Haplotype Phasing with Imputation Using Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "20", number = "2", pages = "80--92", month = feb, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0091", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0091; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0091", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2013", } @Article{Roch:2013:RTT, author = "Sebastien Roch and Sagi Snir", title = "Recovering the Treelike Trend of Evolution Despite Extensive Lateral Genetic Transfer: a Probabilistic Analysis", journal = j-J-COMPUT-BIOL, volume = "20", number = "2", pages = "93--112", month = feb, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0234", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0234; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0234", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2013", } @Article{Topfer:2013:PIV, author = "Armin T{\"o}pfer and Osvaldo Zagordi and Sandhya Prabhakaran and Volker Roth and Eran Halperin and Niko Beerenwinkel", title = "Probabilistic Inference of Viral Quasispecies Subject to Recombination", journal = j-J-COMPUT-BIOL, volume = "20", number = "2", pages = "113--123", month = feb, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0232", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0232; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0232", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2013", } @Article{Tuncbag:2013:SRM, author = "Nurcan Tuncbag and Alfredo Braunstein and Andrea Pagnani and Shao-Shan Carol Huang and Jennifer Chayes and Christian Borgs and Riccardo Zecchina and Ernest Fraenkel", title = "Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting {Steiner} Forest Problem", journal = j-J-COMPUT-BIOL, volume = "20", number = "2", pages = "124--136", month = feb, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0092", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0092; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0092", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2013", } @Article{He:2013:BBB, author = "Lu He and Fabio Vandin and Gopal Pandurangan and Chris Bailey-Kellogg", title = "{Ballast}: a Ball-based Algorithm for Structural Motifs", journal = j-J-COMPUT-BIOL, volume = "20", number = "2", pages = "137--151", month = feb, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0246", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0246; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0246", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2013", } @Article{Parker:2013:SGD, author = "Andrew S. Parker and Yoonjoo Choi and Karl E. Griswold and Chris Bailey-Kellogg", title = "Structure-Guided Deimmunization of Therapeutic Proteins", journal = j-J-COMPUT-BIOL, volume = "20", number = "2", pages = "152--165", month = feb, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0251", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0251; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0251", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2013", } @Article{Huang:2013:RMT, author = "Yan Huang and Yin Hu and Corbin D. Jones and James N. MacLeod and Derek Y. Chiang and Yufeng Liu and Jan F. Prins and Jinze Liu", title = "A Robust Method for Transcript Quantification with {RNA-Seq} Data", journal = j-J-COMPUT-BIOL, volume = "20", number = "3", pages = "167--187", month = mar, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0230", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0230; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0230", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2013", } @Article{Canzar:2013:CGP, author = "Stefan Canzar and Mohammed El-Kebir and Ren{\'e} Pool and Khaled Elbassioni and Alpeshkumar K. Malde and Alan E. Mark and Daan P. Geerke and Leen Stougie and Gunnar W. Klau", title = "Charge Group Partitioning in Biomolecular Simulation", journal = j-J-COMPUT-BIOL, volume = "20", number = "3", pages = "188--198", month = mar, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0239", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0239; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0239", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2013", } @Article{Rodriguez:2013:AIC, author = "Jesse M. Rodriguez and Sivan Bercovici and Megan Elmore and Serafim Batzoglou", title = "Ancestry Inference in Complex Admixtures via Variable-length {Markov} Chain Linkage Models", journal = j-J-COMPUT-BIOL, volume = "20", number = "3", pages = "199--211", month = mar, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0088", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0088; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0088", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2013", } @Article{Holtby:2013:LLM, author = "Daniel Holtby and Shuai Cheng Li and Ming Li", title = "{LoopWeaver}: Loop Modeling by the Weighted Scaling of Verified Proteins", journal = j-J-COMPUT-BIOL, volume = "20", number = "3", pages = "212--223", month = mar, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2013", } @Article{Wang:2013:CCN, author = "Zhanyong Wang and Farhad Hormozdiari and Wen-Yun Yang and Eran Halperin and Eleazar Eskin", title = "{CNVeM}: Copy Number Variation Detection Using Uncertainty of Read Mapping", journal = j-J-COMPUT-BIOL, volume = "20", number = "3", pages = "224--236", month = mar, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0258", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0258; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0258", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2013", } @Article{Zhang:2013:SLD, author = "ZhiZhuo Zhang and Cheng Wei Chang and Willy Hugo and Edwin Cheung and Wing-Kin Sung", title = "Simultaneously Learning {DNA} Motif Along with Its Position and Sequence Rank Preferences Through Expectation Maximization Algorithm", journal = j-J-COMPUT-BIOL, volume = "20", number = "3", pages = "237--248", month = mar, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0233", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0233; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0233", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2013", } @Article{Sharan:2013:RBM, author = "Roded Sharan and Richard M. Karp", title = "Reconstructing {Boolean} Models of Signaling", journal = j-J-COMPUT-BIOL, volume = "20", number = "3", pages = "249--257", month = mar, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0241", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:08 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0241; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0241", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2013", } @Article{Kececioglu:2013:AEP, author = "John Kececioglu and Dan DeBlasio", title = "Accuracy Estimation and Parameter Advising for Protein Multiple Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "20", number = "4", pages = "259--279", month = apr, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0007", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0007; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0007", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 March 2013", } @Article{Holloway:2013:AGO, author = "Patrick Holloway and Krister Swenson and David Ardell and Nadia El-Mabrouk", title = "Ancestral Genome Organization: an Alignment Approach", journal = j-J-COMPUT-BIOL, volume = "20", number = "4", pages = "280--295", month = apr, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0292", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0292; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0292", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2013", } @Article{Alipanahi:2013:DPS, author = "Babak Alipanahi and Nathan Krislock and Ali Ghodsi and Henry Wolkowicz and Logan Donaldson and Ming Li", title = "Determining Protein Structures from {NOESY} Distance Constraints by Semidefinite Programming", journal = j-J-COMPUT-BIOL, volume = "20", number = "4", pages = "296--310", month = apr, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0089", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0089; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0089", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 October 2012", } @Article{Rauf:2013:FMC, author = "Imran Rauf and Florian Rasche and Fran{\c{c}}ois Nicolas and Sebastian B{\"o}cker", title = "Finding Maximum Colorful Subtrees in Practice", journal = j-J-COMPUT-BIOL, volume = "20", number = "4", pages = "311--321", month = apr, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0083", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0083; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0083", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 March 2013", } @Article{Wang:2013:FFC, author = "Hua Wang and Heng Huang and Chris Ding", title = "Function--Function Correlated Multi-label Protein Function Prediction over Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "20", number = "4", pages = "322--343", month = apr, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0272", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0272; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0272", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2013", } @Article{Wang:2013:PPP, author = "Hua Wang and Heng Huang and Chris Ding and Feiping Nie", title = "Predicting Protein--Protein Interactions from Multimodal Biological Data Sources via Nonnegative Matrix Tri-Factorization", journal = j-J-COMPUT-BIOL, volume = "20", number = "4", pages = "344--358", month = apr, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0273", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0273; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0273", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 March 2013", } @Article{Pham:2013:PGN, author = "Son K. Pham and Dmitry Antipov and Alexander Sirotkin and Glenn Tesler and Pavel A. Pevzner and Max A. Alekseyev", title = "Pathset Graphs: a Novel Approach for Comprehensive Utilization of Paired Reads in Genome Assembly", journal = j-J-COMPUT-BIOL, volume = "20", number = "4", pages = "359--371", month = apr, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0098", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:11 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0098; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0098", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 July 2012", } @Article{Califano:2013:PRS, author = "Andrea Califano and Manolis Kellis and Gustavo Stolovitzky", title = "Preface: {RECOMB Systems Biology, Regulatory Genomics, and DREAM 2012} Special Issue", journal = j-J-COMPUT-BIOL, volume = "20", number = "5", pages = "373--374", month = may, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.008p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.008p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 May 2013", } @Article{Orenstein:2013:RAF, author = "Yaron Orenstein and Eran Mick and Ron Shamir", title = "{RAP}: Accurate and Fast Motif Finding Based on Protein-Binding Microarray Data", journal = j-J-COMPUT-BIOL, volume = "20", number = "5", pages = "375--382", month = may, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0253", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0253; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0253", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 March 2013", } @Article{Pagliarini:2013:GSM, author = "Roberto Pagliarini and Diego di Bernardo", title = "A Genome-Scale Modeling Approach to Study Inborn Errors of Liver Metabolism: Toward an In Silico Patient", journal = j-J-COMPUT-BIOL, volume = "20", number = "5", pages = "383--397", month = may, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0276", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0276; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0276", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 March 2013", } @Article{Tjarnberg:2013:OSC, author = "Andreas Tj{\"a}rnberg and Torbj{\"o}rn E. M. Nordling and Matthew Studham and Erik L. L. Sonnhammer", title = "Optimal Sparsity Criteria for Network Inference", journal = j-J-COMPUT-BIOL, volume = "20", number = "5", pages = "398--408", month = may, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0268", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0268; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0268", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 May 2013", } @Article{Poirel:2013:TNA, author = "Christopher L. Poirel and Richard R. Rodrigues and Katherine C. Chen and John J. Tyson and T. M. Murali", title = "Top-Down Network Analysis to Drive Bottom-Up Modeling of Physiological Processes", journal = j-J-COMPUT-BIOL, volume = "20", number = "5", pages = "409--418", month = may, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0274", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0274; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0274", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 May 2013", } @Article{Faure:2013:NSP, author = "Emmanuel Faure and Isabelle S. Peter and Eric H. Davidson", title = "A New Software Package for Predictive Gene Regulatory Network Modeling and Redesign", journal = j-J-COMPUT-BIOL, volume = "20", number = "6", pages = "419--423", month = jun, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0297", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0297; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0297", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2013", } @Article{Preparata:2013:CC, author = "Franco P. Preparata", title = "On Contigs and Coverage", journal = j-J-COMPUT-BIOL, volume = "20", number = "6", pages = "424--432", month = jun, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0243; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0243", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 May 2013", } @Article{Antosh:2013:CCR, author = "Michael Antosh and David Fox and Leon N. Cooper and Nicola Neretti", title = "{CORaL}: Comparison of Ranked Lists for Analysis of Gene Expression Data", journal = j-J-COMPUT-BIOL, volume = "20", number = "6", pages = "433--443", month = jun, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0017", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0017; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0017", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 May 2013", } @Article{Wang:2013:BMA, author = "Cong-Jun Wang and Rong-Hua Xu and Qiong-Ying Yuan and Yong-Kun Wang and Dong-Wei Shen and Xu-Jing Wang and Wei Gao and Hui Zhang and Hua Jiang", title = "Bioinformatics Method to Analyze the Mechanism of Pancreatic Cancer Disorder", journal = j-J-COMPUT-BIOL, volume = "20", number = "6", pages = "444--452", month = jun, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0281", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0281; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0281", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2013", } @Article{Prabhakara:2013:MUH, author = "Shruthi Prabhakara and Raunaq Malhotra and Raj Acharya and Mary Poss", title = "{Mutant-Bin}: Unsupervised Haplotype Estimation of Viral Population Diversity Without Reference Genome", journal = j-J-COMPUT-BIOL, volume = "20", number = "6", pages = "453--463", month = jun, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0174", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0174; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0174", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2013", } @Article{Chang:2013:TGT, author = "Huilan Chang and Hung-Lin Fu and ChiH-Huai Shih", title = "Threshold Group Testing on Inhibitor Model", journal = j-J-COMPUT-BIOL, volume = "20", number = "6", pages = "464--470", month = jun, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0224", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0224; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0224", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2013", } @Article{Behnam:2013:GIL, author = "Ehsan Behnam and Michael S. Waterman and Andrew D. Smith", title = "A Geometric Interpretation for Local Alignment-Free Sequence Comparison", journal = j-J-COMPUT-BIOL, volume = "20", number = "7", pages = "471--485", month = jul, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0280", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0280; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0280", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2013", } @Article{Chitsaz:2013:EAU, author = "Hamidreza Chitsaz and Elmirasadat Forouzmand and Gholamreza Haffari", title = "An Efficient Algorithm for Upper Bound on the Partition Function of Nucleic Acids", journal = j-J-COMPUT-BIOL, volume = "20", number = "7", pages = "486--494", month = jul, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0003", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0003; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0003", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 April 2013", } @Article{Qin:2013:TRI, author = "Jing Qin and Christian M. Reidys", title = "On Topological {RNA} Interaction Structures", journal = j-J-COMPUT-BIOL, volume = "20", number = "7", pages = "495--513", month = jul, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0282", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0282; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0282", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2013", } @Article{Wen:2013:CGW, author = "Yalu Wen and Ming Li and Wenjiang J. Fu", title = "Catching the Genomic Wave in Oligonucleotide Single-Nucleotide Polymorphism Arrays by Modeling Sequence Binding", journal = j-J-COMPUT-BIOL, volume = "20", number = "7", pages = "514--523", month = jul, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0102; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0102", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 June 2013", } @Article{Kim:2013:MDD, author = "Jaejik Kim and Jiaxu Li and Srirangapatnam G. Venkatesh and Douglas S. Darling and Grzegorz A. Rempala", title = "Model Discrimination in Dynamic Molecular Systems: Application to Parotid {De}-differentiation Network", journal = j-J-COMPUT-BIOL, volume = "20", number = "7", pages = "524--539", month = jul, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2011.0222", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2011.0222; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2011.0222", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2013", } @Article{Leung:2013:IMN, author = "Henry C. M. Leung and Siu-Ming Yiu and John Parkinson and Francis Y. L. Chin", title = "{IDBA-MT}: {{\em {De} Novo\/}} Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology", journal = j-J-COMPUT-BIOL, volume = "20", number = "7", pages = "540--550", month = jul, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0042", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0042; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0042", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 July 2013", } @Article{Koepke:2013:EIE, author = "Hoyt Koepke and Elizabeth Thompson", title = "Efficient Identification of Equivalences in Dynamic Graphs and Pedigree Structures", journal = j-J-COMPUT-BIOL, volume = "20", number = "8", pages = "551--570", month = aug, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0032", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0032; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0032", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2013", } @Article{Kayano:2013:MOA, author = "Mitsunori Kayano and Seiya Imoto and Rui Yamaguchi and Satoru Miyano", title = "Multi-omics Approach for Estimating Metabolic Networks Using Low-Order Partial Correlations", journal = j-J-COMPUT-BIOL, volume = "20", number = "8", pages = "571--582", month = aug, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0043", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0043; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0043", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2013", } @Article{Flygare:2013:IAI, author = "Steven Flygare and Michael Campbell and Robert Mars Ross and Barry Moore and Mark Yandell", title = "{ImagePlane}: an Automated Image Analysis Pipeline for High-Throughput Screens Using the Planarian \bioname{Schmidtea mediterranea}", journal = j-J-COMPUT-BIOL, volume = "20", number = "8", pages = "583--592", month = aug, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0025", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0025; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0025", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 July 2013", } @Article{Giaquinta:2013:EEA, author = "Emanuele Giaquinta and Laura Pozzi", title = "An Effective Exact Algorithm and a New Upper Bound for the Number of Contacts in the Hydrophobic-Polar Two-Dimensional Lattice Model", journal = j-J-COMPUT-BIOL, volume = "20", number = "8", pages = "593--609", month = aug, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0266", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0266; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0266", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2013", } @Article{Hedjazi:2013:SDA, author = "Lyamine Hedjazi and Marie-Veronique {Le Lann} and Tatiana Kempowsky and Florence Dalenc and Joseph Aguilar-Martin and Gilles Favre", title = "Symbolic Data Analysis to Defy Low Signal-to-Noise Ratio in Microarray Data for Breast Cancer Prognosis", journal = j-J-COMPUT-BIOL, volume = "20", number = "8", pages = "610--620", month = aug, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0249", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0249; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0249", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2013", } @Article{Giaquinta:2013:FMT, author = "Emanuele Giaquinta and Szymon Grabowski and Esko Ukkonen", title = "Fast Matching of Transcription Factor Motifs Using Generalized Position Weight Matrix Models", journal = j-J-COMPUT-BIOL, volume = "20", number = "9", pages = "621--630", month = sep, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0289", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0289; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0289", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 August 2013", } @Article{Dutkowski:2013:PMN, author = "Janusz Dutkowski and Jerzy Tiuryn", title = "A Probabilistic Model of Neutral and Selective Dynamics of Protein Network Evolution", journal = j-J-COMPUT-BIOL, volume = "20", number = "9", pages = "631--642", month = sep, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0295", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0295; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0295", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 August 2013", } @Article{Andreotti:2013:DLS, author = "Sandro Andreotti and Knut Reinert and Stefan Canzar", title = "The Duplication-Loss Small Phylogeny Problem: From Cherries to Trees", journal = j-J-COMPUT-BIOL, volume = "20", number = "9", pages = "643--659", month = sep, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0057", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0057; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0057", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 September 2013", } @Article{Seligmann:2013:TDR, author = "Herv{\'e} Seligmann", title = "Triplex {DNA:RNA}, 3'-to-5' Inverted {RNA} and Protein Coding in Mitochondrial Genomes", journal = j-J-COMPUT-BIOL, volume = "20", number = "9", pages = "660--671", month = sep, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0134", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0134; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0134", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 July 2013", } @Article{Chapuis:2013:GPU, author = "Guillaume Chapuis and Olivier Filangi and Jean-Michel Elsen and Dominique Lavenier and Pascale {Le Roy}", title = "Graphics Processing Unit--Accelerated Quantitative Trait Loci Detection", journal = j-J-COMPUT-BIOL, volume = "20", number = "9", pages = "672--686", month = sep, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0136", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0136; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0136", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 September 2013", } @Article{Nettelblad:2013:FAD, author = "Carl Nettelblad and Behrang Mahjani and Sverker Holmgren", title = "Fast and Accurate Detection of Multiple Quantitative Trait Loci", journal = j-J-COMPUT-BIOL, volume = "20", number = "9", pages = "687--702", month = sep, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0242", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0242; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0242", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 August 2013", } @Article{Rao:2013:NMQ, author = "Xiayu Rao and Dejian Lai and Xuelin Huang", title = "A New Method for Quantitative Real-Time Polymerase Chain Reaction Data Analysis", journal = j-J-COMPUT-BIOL, volume = "20", number = "9", pages = "703--711", month = sep, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0279", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:20 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0279; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0279", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 July 2013", } @Article{Sun:2013:PRC, author = "Fengzhu Sun", title = "Preface: {Research in Computational Molecular Biology (RECOMB 2013)}", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "713--713", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.020p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.020p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2013", } @Article{Nurk:2013:ASC, author = "Sergey Nurk and Anton Bankevich and Dmitry Antipov and Alexey A. Gurevich and Anton Korobeynikov and Alla Lapidus and Andrey D. Prjibelski and Alexey Pyshkin and Alexander Sirotkin and Yakov Sirotkin and Ramunas Stepanauskas and Scott R. Clingenpeel and Tanja Woyke and Jeffrey S. Mclean and Roger Lasken and Glenn Tesler and Max A. Alekseyev and Pavel A. Pevzner", title = "Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric {MDA} Products", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "714--737", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2013", } @Article{Bansal:2013:RRH, author = "Mukul S. Bansal and Eric J. Alm and Manolis Kellis", title = "Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "738--754", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 September 2013", } @Article{Bryant:2013:AME, author = "William A. Bryant and Ali A. Faruqi and John W. Pinney", title = "Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "755--764", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0079", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0079; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0079", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 August 2013", } @Article{Guo:2013:DPC, author = "Fei Guo and Shuai Cheng Li and Wenji Ma and Lusheng Wang", title = "Detecting Protein Conformational Changes in Interactions via Scaling Known Structures", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "765--779", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0069", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0069; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0069", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2013", } @Article{He:2013:IIP, author = "Dan He and Zhanyong Wang and Buhm Han and Laxmi Parida and Eleazar Eskin", title = "{IPED}: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "780--791", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0080", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0080; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0080", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2013", } @Article{Wu:2013:ACP, author = "Yufeng Wu", title = "An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "792--804", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0072", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0072; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0072", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2013", } @Article{Xu:2013:PDC, author = "Dong Xu and Hua Li and Yang Zhang", title = "Protein Depth Calculation and the Use for Improving Accuracy of Protein Fold Recognition", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "805--816", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0071", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0071; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0071", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 August 2013", } @Article{Kostem:2013:EIS, author = "Emrah Kostem and Eleazar Eskin", title = "Efficiently Identifying Significant Associations in Genome-wide Association Studies", journal = j-J-COMPUT-BIOL, volume = "20", number = "10", pages = "817--830", month = oct, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0087", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0087; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0087", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 September 2013", } @Article{Zhang:2013:CMS, author = "ZhiZhuo Zhang and Guoliang Li and Kim-Chuan Toh and Wing-Kin Sung", title = "{$3$D} Chromosome Modeling with Semi-Definite Programming and {Hi-C} Data", journal = j-J-COMPUT-BIOL, volume = "20", number = "11", pages = "831--846", month = nov, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0076", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0076; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0076", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2013", } @Article{Chen:2013:SFM, author = "Shijian Chen and Anqi Wang and Lei M. Li", title = "{SEME}: a Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation", journal = j-J-COMPUT-BIOL, volume = "20", number = "11", pages = "847--860", month = nov, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0111", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0111; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0111", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2013", } @Article{Eskin:2013:EEA, author = "Itamar Eskin and Farhad Hormozdiari and Lucia Conde and Jacques Riby and Christine F. Skibola and Eleazar Eskin and Eran Halperin", title = "{eALPS}: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data", journal = j-J-COMPUT-BIOL, volume = "20", number = "11", pages = "861--877", month = nov, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0105", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0105; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0105", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 October 2013", } @Article{Deng:2013:BPP, author = "Lei Deng and Jihong Guan and Xiaoming Wei and Yuan Yi and Qiangfeng Cliff Zhang and Shuigeng Zhou", title = "Boosting Prediction Performance of Protein--Protein Interaction Hot Spots by Using Structural Neighborhood Properties", journal = j-J-COMPUT-BIOL, volume = "20", number = "11", pages = "878--891", month = nov, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0083", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0083; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0083", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2013", } @Article{Puniyani:2013:NMU, author = "Kriti Puniyani and Eric P. Xing", title = "{NP-MuScL}: Unsupervised Global Prediction of Interaction Networks from Multiple Data Sources", journal = j-J-COMPUT-BIOL, volume = "20", number = "11", pages = "892--904", month = nov, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0093", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0093; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0093", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2013", } @Article{Reinharz:2013:USE, author = "Vladimir Reinharz and Yann Ponty and J{\'e}r{\^o}me Waldisp{\"u}hl", title = "Using Structural and Evolutionary Information to Detect and Correct Pyrosequencing Errors in Noncoding {RNAs}", journal = j-J-COMPUT-BIOL, volume = "20", number = "11", pages = "905--919", month = nov, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0085", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0085; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0085", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2013", } @Article{Sadeh:2013:CUU, author = "Mohammad J. Sadeh and Giusi Moffa and Rainer Spang", title = "Considering Unknown Unknowns: Reconstruction of Nonconfoundable Causal Relations in Biological Networks", journal = j-J-COMPUT-BIOL, volume = "20", number = "11", pages = "920--932", month = nov, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0119", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0119; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0119", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2013", } @Article{Salari:2013:ITP, author = "Raheleh Salari and Syed Shayon Saleh and Dorna Kashef-Haghighi and David Khavari and Daniel E. Newburger and Robert B. West and Arend Sidow and Serafim Batzoglou", title = "Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery", journal = j-J-COMPUT-BIOL, volume = "20", number = "11", pages = "933--944", month = nov, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0106", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0106; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0106", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2013", } @Article{Blokh:2013:ASP, author = "Dima Blokh and Danny Segev and Roded Sharan", title = "The Approximability of Shortest Path-Based Graph Orientations of Protein--Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "20", number = "12", pages = "945--957", month = dec, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0064; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0064", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2013", } @Article{Melkman:2013:ISA, author = "Avraham A. Melkman and Tatsuya Akutsu", title = "An Improved Satisfiability Algorithm for Nested Canalyzing Functions and its Application to Determining a Singleton Attractor of a {Boolean} Network", journal = j-J-COMPUT-BIOL, volume = "20", number = "12", pages = "958--969", month = dec, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0060", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0060; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0060", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2013", } @Article{Hart:2013:CSS, author = "Steven N. Hart and Terry M. Therneau and Yuji Zhang and Gregory A. Poland and Jean-Pierre Kocher", title = "Calculating Sample Size Estimates for {RNA} Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "20", number = "12", pages = "970--978", month = dec, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0283", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0283; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0283", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 August 2013", } @Article{Kirk:2013:BRP, author = "Paul Kirk and Aviva Witkover and Charles R. M. Bangham and Sylvia Richardson and Alexandra M. Lewin and Michael P. H. Stumpf", title = "Balancing the Robustness and Predictive Performance of Biomarkers", journal = j-J-COMPUT-BIOL, volume = "20", number = "12", pages = "979--989", month = dec, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0018", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0018; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0018", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 August 2013", } @Article{Nov:2013:OSA, author = "Yuval Nov and Alexander Fulton and Karl-Erich Jaeger", title = "Optimal Scanning of All Single-Point Mutants of a Protein", journal = j-J-COMPUT-BIOL, volume = "20", number = "12", pages = "990--997", month = dec, year = "2013", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0026", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:27 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0026; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0026", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2013", } @Article{Kovac:2014:CRP, author = "Jakub Kov{\'a}{\v{c}}", title = "On the Complexity of Rearrangement Problems under the Breakpoint Distance", journal = j-J-COMPUT-BIOL, volume = "21", number = "1", pages = "1--15", month = jan, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0004", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:29 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0004; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0004", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 November 2013", } @Article{Beretta:2014:MAS, author = "Stefano Beretta and Paola Bonizzoni and Gianluca Della Vedova and Yuri Pirola and Raffaella Rizzi", title = "Modeling Alternative Splicing Variants from {RNA-Seq} Data with Isoform Graphs", journal = j-J-COMPUT-BIOL, volume = "21", number = "1", pages = "16--40", month = jan, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0112", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:29 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0112; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0112", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 November 2013", } @Article{Burden:2014:DWM, author = "Conrad J. Burden and Paul Leopardi and Sylvain For{\^e}t", title = "The Distribution of Word Matches Between {Markovian} Sequences with Periodic Boundary Conditions", journal = j-J-COMPUT-BIOL, volume = "21", number = "1", pages = "41--63", month = jan, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0277", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:29 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0277; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0277", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 October 2013", } @Article{Ouangraoua:2014:ICC, author = "A{\"\i}da Ouangraoua and Mathieu Raffinot", title = "On the Identification of Conflicting Contiguities in Ancestral Genome Reconstruction", journal = j-J-COMPUT-BIOL, volume = "21", number = "1", pages = "64--79", month = jan, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0086", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:29 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0086; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0086", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 October 2013", } @Article{Li:2014:IRO, author = "Chuan-Xi Li and Ru-Jing Wang and Peng Chen and He Huang and Ya-Ru Su", title = "Interaction Relation Ontology Learning", journal = j-J-COMPUT-BIOL, volume = "21", number = "1", pages = "80--88", month = jan, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0009", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:29 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0009; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0009", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 December 2013", } @Article{Gorecki:2014:DPM, author = "Pawe{\l} G{\'o}recki and Oliver Eulenstein", title = "{DrML}: Probabilistic Modeling of Gene Duplications", journal = j-J-COMPUT-BIOL, volume = "21", number = "1", pages = "89--98", month = jan, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:29 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 September 2013", } @Article{Bartolucci:2014:NCM, author = "Francesco Bartolucci and Silvia Pandolfi", title = "A New Constant Memory Recursion for Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "21", number = "2", pages = "99--117", month = feb, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0096; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0096", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2013", } @Article{Galas:2014:DCS, author = "David J. Galas and Nikita A. Sakhanenko and Alexander Skupin and Tomasz Ignac", title = "Describing the Complexity of Systems: Multivariable ``Set Complexity'' and the Information Basis of Systems Biology", journal = j-J-COMPUT-BIOL, volume = "21", number = "2", pages = "118--140", month = feb, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0039", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0039; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0039", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 December 2013", } @Article{Wang:2014:CMC, author = "Junshan Wang and Ajay Jasra and Maria {De Iorio}", title = "Computational Methods for a Class of Network Models", journal = j-J-COMPUT-BIOL, volume = "21", number = "2", pages = "141--161", month = feb, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0082", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0082; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0082", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 October 2013", } @Article{Dhifli:2014:SPS, author = "Wajdi Dhifli and Rabie Saidi and Engelbert Mephu Nguifo", title = "Smoothing {$3$D} Protein Structure Motifs Through Graph Mining and Amino Acid Similarities", journal = j-J-COMPUT-BIOL, volume = "21", number = "2", pages = "162--172", month = feb, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0092", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0092; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0092", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2013", } @Article{Levtov:2014:DNU, author = "Nissan Levtov and Sandeep Amberkar and Zakharia M. Frenkel and Lars Kaderali and Zeev Volkovich", title = "Detecting Non-Uniform Clusters in Large-Scale Interaction Graphs", journal = j-J-COMPUT-BIOL, volume = "21", number = "2", pages = "173--183", month = feb, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0095", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:31 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0095; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0095", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 September 2013", } @Article{Zheng:2014:JII, author = "Chaozhi Zheng and Mary K. Kuhner and Elizabeth A. Thompson", title = "Joint Inference of Identity by Descent Along Multiple Chromosomes from Population Samples", journal = j-J-COMPUT-BIOL, volume = "21", number = "3", pages = "185--200", month = mar, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0140", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0140; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0140", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 March 2014", } @Article{Ding:2014:CPR, author = "Yang Ding and William A. Lorenz and Ivan Dotu and Evan Senter and Peter Clote", title = "Computing the Probability of {RNA} Hairpin and Multiloop Formation", journal = j-J-COMPUT-BIOL, volume = "21", number = "3", pages = "201--218", month = mar, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0148", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0148; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0148", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2014", } @Article{Lee:2014:DSV, author = "Heewook Lee and Ellen Popodi and Patricia L. Foster and Haixu Tang", title = "Detection of Structural Variants Involving Repetitive Regions in the Reference Genome", journal = j-J-COMPUT-BIOL, volume = "21", number = "3", pages = "219--233", month = mar, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2014", } @Article{Hsieh:2014:FAC, author = "Mu-Fen Hsieh and Sing-Hoi Sze", title = "Finding Alignments of Conserved Graphlets in Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "21", number = "3", pages = "234--246", month = mar, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0130", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0130; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0130", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 February 2014", } @Article{Plewczynski:2014:HSA, author = "Dariusz Plewczynski and Anna Philips and Marcin {Von Grotthuss} and Leszek Rychlewski and Krzysztof Ginalski", title = "{HarmonyDOCK}: The Structural Analysis of Poses in Protein-Ligand Docking", journal = j-J-COMPUT-BIOL, volume = "21", number = "3", pages = "247--256", month = mar, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0111", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0111; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0111", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 November 2010", } @Article{Peris:2014:SSN, author = "Guillermo Peris and Andr{\'e}s Marzal", title = "Statistical Significance of Normalized Global Alignment", journal = j-J-COMPUT-BIOL, volume = "21", number = "3", pages = "257--268", month = mar, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0167", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0167; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0167", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 January 2014", } @Article{Neuwald:2014:BSO, author = "Andrew F. Neuwald", title = "A {Bayesian} Sampler for Optimization of Protein Domain Hierarchies", journal = j-J-COMPUT-BIOL, volume = "21", number = "3", pages = "269--286", month = mar, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0099", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:33 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0099; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0099", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2014", } @Article{Neuwald:2014:ECI, author = "Andrew F. Neuwald", title = "Evaluating, Comparing, and Interpreting Protein Domain Hierarchies", journal = j-J-COMPUT-BIOL, volume = "21", number = "4", pages = "287--302", month = apr, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0098", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0098; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0098", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2014", } @Article{Kannan:2014:ECP, author = "Lavanya Kannan and Ward C. Wheeler", title = "Exactly Computing the Parsimony Scores on Phylogenetic Networks Using Dynamic Programming", journal = j-J-COMPUT-BIOL, volume = "21", number = "4", pages = "303--319", month = apr, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0134", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", note = "See correction \cite{Anonymous:2014:CJC}.", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0134; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0134", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2014", } @Article{Wang:2014:FMD, author = "Xun Wang and Ying Miao and Minquan Cheng", title = "Finding Motifs in {DNA} Sequences Using Low-Dispersion Sequences", journal = j-J-COMPUT-BIOL, volume = "21", number = "4", pages = "320--329", month = apr, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0054", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0054; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0054", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2014", } @Article{Comin:2014:PCF, author = "Matteo Comin and Montse Farreras", title = "Parallel Continuous Flow: a Parallel Suffix Tree Construction Tool for Whole Genomes", journal = j-J-COMPUT-BIOL, volume = "21", number = "4", pages = "330--344", month = apr, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0256", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0256; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0256", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 March 2014", } @Article{Kim:2014:EGS, author = "Seyoung Kim and Eric P. Xing", title = "Exploiting Genome Structure in Association Analysis", journal = j-J-COMPUT-BIOL, volume = "21", number = "4", pages = "345--360", month = apr, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0224", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0224; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0224", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2011", } @Article{Hochberg:2014:DSP, author = "Robert Hochberg and Treena Larrew Milam", title = "Data Structures for Parsimony Correlation and Biosequence Co-Evolution", journal = j-J-COMPUT-BIOL, volume = "21", number = "4", pages = "361--369", month = apr, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2008.0107", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2008.0107; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2008.0107", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 June 2009", } @Article{Califano:2014:RIS, author = "Andrea Califano and Manolis Kellis and Gustavo Stolovitzky", title = "{RECOMB/ISCB} Systems Biology, Regulatory Genomics, and {DREAM} 2013 Special Issue", journal = j-J-COMPUT-BIOL, volume = "21", number = "5", pages = "371--372", month = may, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.009p", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.009p", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 April 2014", } @Article{ONeill:2014:IRT, author = "Patrick K. O'Neill and Robert Forder and Ivan Erill", title = "Informational Requirements for Transcriptional Regulation", journal = j-J-COMPUT-BIOL, volume = "21", number = "5", pages = "373--384", month = may, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0032", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0032; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0032", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2014", } @Article{Wang:2014:FAE, author = "Zhiyong Wang and Jinbo Xu and Xinghua Shi", title = "Finding Alternative Expression Quantitative Trait Loci by Exploring Sparse Model Space", journal = j-J-COMPUT-BIOL, volume = "21", number = "5", pages = "385--393", month = may, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0026", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0026; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0026", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2014", } @Article{Mazza:2014:EII, author = "Arnon Mazza and Irit Gat-Viks and Roded Sharan", title = "Elucidating Influenza Inhibition Pathways via Network Reconstruction", journal = j-J-COMPUT-BIOL, volume = "21", number = "5", pages = "394--404", month = may, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0147", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0147; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0147", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2014", } @Article{Cleary:2014:JVN, author = "John G. Cleary and Ross Braithwaite and Kurt Gaastra and Brian S. Hilbush and Stuart Inglis and Sean A. Irvine and Alan Jackson and Richard Littin and Sahar Nohzadeh-Malakshah and Mehul Rathod and David Ware and Len Trigg and Francisco M. {De La Vega}", title = "Joint Variant and {{\em {De} Novo\/}} Mutation Identification on Pedigrees from High-Throughput Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "21", number = "6", pages = "405--419", month = jun, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0029", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0029; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0029", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2014", } @Article{Hu:2014:PSP, author = "Wei Hu and John Hu", title = "Prediction of {siRNA} Potency Using Sparse Logistic Regression", journal = j-J-COMPUT-BIOL, volume = "21", number = "6", pages = "420--427", month = jun, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0115; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0115", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 November 2010", } @Article{Klie:2014:BCE, author = "Sebastian Klie and Zoran Nikoloski and Joachim Selbig", title = "Biological Cluster Evaluation for Gene Function Prediction", journal = j-J-COMPUT-BIOL, volume = "21", number = "6", pages = "428--445", month = jun, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2009.0129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2009.0129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2009.0129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 January 2010", } @Article{Kundeti:2014:BLM, author = "Vamsi Kundeti and Sanguthevar Rajasekaran and Hieu Dinh", title = "Border Length Minimization Problem on a Square Array", journal = j-J-COMPUT-BIOL, volume = "21", number = "6", pages = "446--455", month = jun, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0127", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0127; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0127", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 February 2014", } @Article{Gill:2014:CDG, author = "Nivit Gill and Shailendra Singh and Trilok C. Aseri", title = "Computational Disease Gene Prioritization: An Appraisal", journal = j-J-COMPUT-BIOL, volume = "21", number = "6", pages = "456--465", month = jun, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0158", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0158; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0158", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 March 2014", } @Article{Khan:2014:SPE, author = "Abdul Arif Khan", title = "{{\em In Silico\/}} Prediction of \bioname{Escherichia coli} Proteins Targeting the Host Cell Nucleus, with Special Reference to Their Role in Colon Cancer Etiology", journal = j-J-COMPUT-BIOL, volume = "21", number = "6", pages = "466--475", month = jun, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0001", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0001; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0001", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2014", } @Article{Anonymous:2014:CJC, author = "Anonymous", title = "Correction: {{\booktitle{Journal of Computational Biology}}}: 2014; {\bf 21}/4:303--319", journal = j-J-COMPUT-BIOL, volume = "21", number = "6", pages = "476--476", month = jun, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.Cor1", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", note = "See \cite{Kannan:2014:ECP}.", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.Cor1", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2014", } @Article{Waldispuhl:2014:SAF, author = "J{\'e}r{\^o}me Waldisp{\"u}hl and Charles W. O'Donnell and Sebastian Will and Srinivas Devadas and Rolf Backofen and Bonnie Berger", title = "Simultaneous Alignment and Folding of Protein Sequences", journal = j-J-COMPUT-BIOL, volume = "21", number = "7", pages = "477--491", month = jul, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 April 2014", } @Article{Haque:2014:ICL, author = "M. Muksitul Haque and Michael K. Skinner and Lawrence B. Holder", title = "Imbalanced Class Learning in Epigenetics", journal = j-J-COMPUT-BIOL, volume = "21", number = "7", pages = "492--507", month = jul, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 May 2014", } @Article{Gamermann:2014:NAP, author = "Daniel Gamermann and Arnaud Montagud and J. Alberto Conejero and Javier F. Urchuegu{\'\i}a and Pedro Fern{\'a}ndez de C{\'o}rdoba", title = "New Approach for Phylogenetic Tree Recovery Based on Genome-Scale Metabolic Networks", journal = j-J-COMPUT-BIOL, volume = "21", number = "7", pages = "508--519", month = jul, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0150", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0150; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0150", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2014", } @Article{deMontgolfier:2014:EIG, author = "Fabien de Montgolfier and Mathieu Raffinot and Irena Rusu", title = "Easy Identification of Generalized Common and Conserved Nested Intervals", journal = j-J-COMPUT-BIOL, volume = "21", number = "7", pages = "520--533", month = jul, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0146", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0146; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0146", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 March 2014", } @Article{Zhukova:2014:KBG, author = "Anna Zhukova and David James Sherman", title = "Knowledge-based Generalization of Metabolic Models", journal = j-J-COMPUT-BIOL, volume = "21", number = "7", pages = "534--547", month = jul, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0143; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 April 2014", } @Article{Tzou:2014:SSN, author = "Wen-Shyong Tzou and Ying-Tsang Lo and Tun-Wen Pai and Chin-Hwa Hu and Chung-Hao Li", title = "Stochastic Simulation of Notch Signaling Reveals Novel Factors That Mediate the Differentiation of Neural Stem Cells", journal = j-J-COMPUT-BIOL, volume = "21", number = "7", pages = "548--567", month = jul, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0022", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0022; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0022", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 May 2014", } @Article{Sharov:2014:CPR, author = "Alexei A. Sharov and Akira Nishiyama and Yong Qian and Dawood B. Dudekula and Dan L. Longo and David Schlessinger and Minoru S. H. Ko", title = "Chromatin Properties of Regulatory {DNA} Probed by Manipulation of Transcription Factors", journal = j-J-COMPUT-BIOL, volume = "21", number = "8", pages = "569--577", month = aug, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0126", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0126; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0126", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2014", } @Article{Zheng:2014:DCR, author = "Yu Zheng and Louxin Zhang", title = "Are the Duplication Cost and {Robinson--Foulds} Distance Equivalent?", journal = j-J-COMPUT-BIOL, volume = "21", number = "8", pages = "578--590", month = aug, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0021", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0021; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0021", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 July 2014", } @Article{Han:2014:CS, author = "Hillary S. W. Han and Thomas J. X. Li and Christian M. Reidys", title = "Combinatorics of $ \gamma $-Structures", journal = j-J-COMPUT-BIOL, volume = "21", number = "8", pages = "591--608", month = aug, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0128", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0128; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0128", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2014", } @Article{Zhong:2014:SFA, author = "Cuncong Zhong and Shaojie Zhang", title = "Simultaneous Folding of Alternative {RNA} Structures with Mutual Constraints: an Application to Next-Generation Sequencing-based {RNA} Structure Probing", journal = j-J-COMPUT-BIOL, volume = "21", number = "8", pages = "609--621", month = aug, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0044", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0044; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0044", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 April 2014", } @Article{Alexeev:2014:RMA, author = "Nikita Alexeev and Peter Zograf", title = "Random Matrix Approach to the Distribution of Genomic Distance", journal = j-J-COMPUT-BIOL, volume = "21", number = "8", pages = "622--631", month = aug, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0066", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0066; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0066", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 March 2014", } @Article{Saravanaraman:2014:NRN, author = "Ponne Saravanaraman and Raj Kumar Chinnadurai and Rathanam Boopathy", title = "A New Role for the Nonpathogenic Nonsynonymous Single-Nucleotide Polymorphisms of Acetylcholinesterase in the Treatment of {Alzheimer}'s Disease: a Computational Study", journal = j-J-COMPUT-BIOL, volume = "21", number = "8", pages = "632--647", month = aug, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0005", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:43 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0005; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0005", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2014", } @Article{Fu:2014:SIR, author = "Benjamin M. M. Fu and Christian M. Reidys", title = "Shapes of Interacting {RNA} Complexes", journal = j-J-COMPUT-BIOL, volume = "21", number = "9", pages = "649--664", month = sep, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0107", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0107; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0107", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2014", } @Article{Ferraro:2014:PRS, author = "Maria Brigida Ferraro and Marco Savarese and Giuseppina {Di Fruscio} and Vincenzo Nigro and Mario Rosario Guarracino", title = "Prediction of Rare Single-Nucleotide Causative Mutations for Muscular Diseases in Pooled Next-Generation Sequencing Experiments", journal = j-J-COMPUT-BIOL, volume = "21", number = "9", pages = "665--675", month = sep, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0037", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0037; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0037", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2014", } @Article{Irvahn:2014:PSM, author = "Jan Irvahn and Vladimir N. Minin", title = "Phylogenetic Stochastic Mapping Without Matrix Exponentiation", journal = j-J-COMPUT-BIOL, volume = "21", number = "9", pages = "676--690", month = sep, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0062", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0062; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0062", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2014", } @Article{Huo:2014:CTM, author = "Yunzhang Huo and Ping Ji", title = "Continuous-Time {Markov} Chain--Based Flux Analysis in Metabolism", journal = j-J-COMPUT-BIOL, volume = "21", number = "9", pages = "691--698", month = sep, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 August 2014", } @Article{Agapie:2014:PCA, author = "Alexandru Agapie and Anca Andreica and Marius Giuclea", title = "Probabilistic Cellular Automata", journal = j-J-COMPUT-BIOL, volume = "21", number = "9", pages = "699--708", month = sep, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0074", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0074; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0074", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2014", } @Article{Vexler:2014:ECT, author = "Albert Vexler and Xiwei Chen and Jihnhee Yu", title = "Evaluations and Comparisons of Treatment Effects Based on Best Combinations of Biomarkers with Applications to Biomedical Studies", journal = j-J-COMPUT-BIOL, volume = "21", number = "9", pages = "709--721", month = sep, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0097", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:45 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0097; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0097", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 July 2014", } @Article{Voorkamp:2014:MAA, author = "Josh Voorkamp", title = "Maximal Acyclic Agreement Forests", journal = j-J-COMPUT-BIOL, volume = "21", number = "10", pages = "723--731", month = oct, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0093", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0093; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0093", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2014", } @Article{Tabb:2014:CED, author = "Loni Philip Tabb and Wei Zhao and Jingyu Huang and Gail L. Rosen", title = "Characterizing the Empirical Distribution of Prokaryotic Genome $n$-mers in the Presence of Nullomers", journal = j-J-COMPUT-BIOL, volume = "21", number = "10", pages = "732--740", month = oct, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0108; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0108", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2014", } @Article{Stepancic:2014:EGS, author = "{\v{Z}}iva Stepan{\v{c}}i{\v{c}}", title = "Enhancing {Gibbs} Sampling Method for Motif Finding in {DNA} with Initial Graph Representation of Sequences", journal = j-J-COMPUT-BIOL, volume = "21", number = "10", pages = "741--752", month = oct, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0106", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0106; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0106", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 August 2014", } @Article{Ram:2014:SAS, author = "Hari Ram and Alok Kumar and Lebin Thomas and Ved Pal Singh", title = "{{\em In silico\/}} Approach to Study Adaptive Divergence in Nucleotide Composition of the 16S {rRNA} Gene Among Bacteria Thriving Under Different Temperature Regimes", journal = j-J-COMPUT-BIOL, volume = "21", number = "10", pages = "753--759", month = oct, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0116", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0116; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0116", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2014", } @Article{Radu:2014:NFE, author = "Alex Radu and Michael Charleston", title = "Node Fingerprinting: an Efficient Heuristic for Aligning Biological Networks", journal = j-J-COMPUT-BIOL, volume = "21", number = "10", pages = "760--770", month = oct, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0114", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0114; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0114", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2014", } @Article{Zhu:2014:ASB, author = "Peican Zhu and Jie Han", title = "Asynchronous Stochastic {Boolean} Networks as Gene Network Models", journal = j-J-COMPUT-BIOL, volume = "21", number = "10", pages = "771--783", month = oct, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0057", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:47 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0057; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0057", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 June 2014", } @Article{Hasegawa:2014:EDA, author = "Takanori Hasegawa and Tomoya Mori and Rui Yamaguchi and Seiya Imoto and Satoru Miyano and Tatsuya Akutsu", title = "An Efficient Data Assimilation Schema for Restoration and Extension of Gene Regulatory Networks Using Time-Course Observation Data", journal = j-J-COMPUT-BIOL, volume = "21", number = "11", pages = "785--798", month = nov, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0171", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0171; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0171", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2014", } @Article{Carmel:2014:WCC, author = "Amir Carmel and Noa Musa-Lempel and Dekel Tsur and Michal Ziv-Ukelson", title = "The Worst Case Complexity of Maximum Parsimony", journal = j-J-COMPUT-BIOL, volume = "21", number = "11", pages = "799--808", month = nov, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0128", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0128; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0128", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 October 2014", } @Article{Konopka:2014:ESP, author = "Bogumil M. Konopka and Tomasz Golda and Ma{\l}gorzata Kotulska", title = "Evaluating the Significance of Protein Functional Similarity Based on Gene Ontology", journal = j-J-COMPUT-BIOL, volume = "21", number = "11", pages = "809--822", month = nov, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0181", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0181; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0181", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 September 2014", } @Article{Santos:2014:EPF, author = "Jos{\'e} Santos and Pablo Villot and Martin Di{\'e}guez", title = "Emergent Protein Folding Modeled with Evolved Neural Cellular Automata Using the {$3$D} {HP} Model", journal = j-J-COMPUT-BIOL, volume = "21", number = "11", pages = "823--845", month = nov, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0077", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0077; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0077", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2014", } @Article{Nguyen:2014:WAD, author = "Nha Nguyen and An Vo and Kyoung-Jae Won", title = "A Wavelet Approach to Detect Enriched Regions and Explore Epigenomic Landscapes", journal = j-J-COMPUT-BIOL, volume = "21", number = "11", pages = "846--854", month = nov, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0095", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0095; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0095", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 July 2014", } @Article{Illner:2014:BBS, author = "Katrin Illner and Christiane Fuchs and Fabian J. Theis", title = "{Bayesian} Blind Source Separation for Data with Network Structure", journal = j-J-COMPUT-BIOL, volume = "21", number = "11", pages = "855--865", month = nov, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0117", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0117; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0117", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 October 2014", } @Article{Yin:2014:NMC, author = "Changchuan Yin and Xuemeng E. Yin and Jiasong Wang", title = "A Novel Method for Comparative Analysis of {DNA} Sequences by {Ramanujan-Fourier} Transform", journal = j-J-COMPUT-BIOL, volume = "21", number = "12", pages = "867--879", month = dec, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0120", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0120; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0120", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 October 2014", } @Article{Badr:2014:ISR, author = "Eman Badr and Lenwood S. Heath", title = "Identifying Splicing Regulatory Elements with {de Bruijn} Graphs", journal = j-J-COMPUT-BIOL, volume = "21", number = "12", pages = "880--897", month = dec, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0183", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0183; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0183", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 November 2014", } @Article{Kakourou:2014:CAI, author = "Alexia Kakourou and Werner Vach and Bart Mertens", title = "Combination Approaches Improve Predictive Performance of Diagnostic Rules for Mass-Spectrometry Proteomic Data", journal = j-J-COMPUT-BIOL, volume = "21", number = "12", pages = "898--914", month = dec, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 October 2014", } @Article{Chen:2014:ZSR, author = "William Y. C. Chen and Qiang-Hui Guo and Lisa H. Sun and Jian Wang", title = "Zigzag Stacks and $m$-Regular Linear Stacks", journal = j-J-COMPUT-BIOL, volume = "21", number = "12", pages = "915--935", month = dec, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0133", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0133; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0133", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 December 2014", } @Article{Maghawry:2014:NPS, author = "Huda A. Maghawry and Mostafa G. M. Mostafa and Tarek F. Gharib", title = "A New Protein Structure Representation for Efficient Protein Function Prediction", journal = j-J-COMPUT-BIOL, volume = "21", number = "12", pages = "936--946", month = dec, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0137", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0137; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0137", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2014", } @Article{Noe:2014:CCS, author = "Laurent No{\'e} and Donald E. K. Martin", title = "A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and $k$-Mer Distances", journal = j-J-COMPUT-BIOL, volume = "21", number = "12", pages = "947--963", month = dec, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 November 2014", } @Article{Liu:2014:WMM, author = "Lizhen Liu and Xuemin Dai and Hanshi Wang and Wei Song and Jingli Lu", title = "A Weighted Multipath Measurement Based on Gene Ontology for Estimating Gene Products Similarity", journal = j-J-COMPUT-BIOL, volume = "21", number = "12", pages = "964--974", month = dec, year = "2014", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0143; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 September 2014", } @Article{Yadav:2015:TPR, author = "Sunita Yadav and D. Swati and Hariharan Chandrasekharan", title = "Thiamine Pyrophosphate Riboswitch in Some Representative Plant Species: a Bioinformatics Study", journal = j-J-COMPUT-BIOL, volume = "22", number = "1", pages = "1--9", month = jan, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0169", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0169; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0169", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2014", } @Article{Persing:2015:SAC, author = "Adam Persing and Ajay Jasra and Alexandros Beskos and David Balding and Maria {De Iorio}", title = "A Simulation Approach for Change-Points on Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "22", number = "1", pages = "10--24", month = jan, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0218", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0218; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0218", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 December 2014", } @Article{Bois:2015:PGR, author = "Frederic Y. Bois and Ghislaine Gayraud", title = "Probabilistic Generation of Random Networks Taking into Account Information on Motifs Occurrence", journal = j-J-COMPUT-BIOL, volume = "22", number = "1", pages = "25--36", month = jan, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0175", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0175; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0175", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 December 2014", } @Article{Chen:2015:PCA, author = "Derek E. Chen and Darryl L. Willick and Joseph B. Ruckel and Wely B. Floriano", title = "Principal Component Analysis of Binding Energies for Single-Point Mutants of {hT2R16} Bound to an Agonist Correlate with Experimental Mutant Cell Response", journal = j-J-COMPUT-BIOL, volume = "22", number = "1", pages = "37--53", month = jan, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0192", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0192; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0192", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 November 2014", } @Article{Amaratunga:2015:RBS, author = "Dhammika Amaratunga and Javier Cabrera and Yung-Seop Lee", title = "Resampling-Based Similarity Measures for High-Dimensional Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "1", pages = "54--62", month = jan, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0195", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0195; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0195", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 December 2014", } @Article{Gui:2015:IHC, author = "Tuantuan Gui and Xiao Dong and Rudong Li and Yixue Li and Zhen Wang", title = "Identification of Hepatocellular Carcinoma--Related Genes with a Machine Learning and Network Analysis", journal = j-J-COMPUT-BIOL, volume = "22", number = "1", pages = "63--71", month = jan, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0122", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0122; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0122", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 September 2014", } @Article{Park:2015:SOG, author = "Heewon Park and Atushi Niida and Satoru Miyano and Seiya Imoto", title = "Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis", journal = j-J-COMPUT-BIOL, volume = "22", number = "2", pages = "73--84", month = feb, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 January 2015", } @Article{Lu:2015:CSI, author = "Wei Lu and Takeyuki Tamura and Jiangning Song and Tatsuya Akutsu", title = "Computing Smallest Intervention Strategies for Multiple Metabolic Networks in a {Boolean} Model", journal = j-J-COMPUT-BIOL, volume = "22", number = "2", pages = "85--110", month = feb, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0274", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0274; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0274", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 February 2015", } @Article{Chen:2015:FGO, author = "Quan Chen and Xianghong J. Zhou and Fengzhu Sun", title = "Finding Genetic Overlaps Among Diseases Based on Ranked Gene Lists", journal = j-J-COMPUT-BIOL, volume = "22", number = "2", pages = "111--123", month = feb, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0149; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0149", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 February 2015", } @Article{Senter:2015:FAK, author = "Evan Senter and Peter Clote", title = "Fast, Approximate Kinetics of {RNA} Folding", journal = j-J-COMPUT-BIOL, volume = "22", number = "2", pages = "124--144", month = feb, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0193", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0193; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0193", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 February 2015", } @Article{Rao:2015:CSM, author = "Aditya Rao and Deepthi P. and C. H. Renumadhavi and M. Girish Chandra and Rajgopal Srinivasan", title = "Compressed Sensing Methods for {DNA} Microarrays, {RNA} Interference, and Metagenomics", journal = j-J-COMPUT-BIOL, volume = "22", number = "2", pages = "145--158", month = feb, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0244; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0244", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 January 2015", } @Article{Guo:2015:DNF, author = "Xuan Guo and Ning Yu and Xiaojun Ding and Jianxin Wang and Yi Pan", title = "{DIME}: a Novel Framework for {{\em {De} Novo\/}} Metagenomic Sequence Assembly", journal = j-J-COMPUT-BIOL, volume = "22", number = "2", pages = "159--177", month = feb, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0251", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0251; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0251", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 February 2015", } @Article{Ghavidel:2015:NHM, author = "Fatemeh Zamanzad Ghavidel and J{\"u}rgen Claesen and Tomasz Burzykowski", title = "A Nonhomogeneous Hidden {Markov} Model for Gene Mapping Based on Next-Generation Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "2", pages = "178--188", month = feb, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0258", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0258; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0258", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2015", } @Article{Jossinet:2015:P, author = "Fabrice Jossinet and Yann Ponty and J{\'e}r{\^o}me Waldisp{\"u}hl", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "22", number = "3", pages = "189--189", month = mar, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.010P", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.010P", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2015", } @Article{Saffarian:2015:MAR, author = "Azadeh Saffarian and Mathieu Giraud and H{\'e}l{\`e}ne Touzet", title = "Modeling Alternate {RNA} Structures in Genomic Sequences", journal = j-J-COMPUT-BIOL, volume = "22", number = "3", pages = "190--204", month = mar, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0272", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0272; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0272", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2015", } @Article{Bourgeade:2015:CSS, author = "Laetitia Bourgeade and C{\'e}dric Chauve and Julien Allali", title = "Chaining Sequence\slash Structure Seeds for Computing {RNA} Similarity", journal = j-J-COMPUT-BIOL, volume = "22", number = "3", pages = "205--217", month = mar, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0283", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0283; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0283", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2015", } @Article{Petroni:2015:SSA, author = "Mattia Petroni and Nikolaj Zimic and Miha Mraz and Miha Mo{\v{s}}kon", title = "Stochastic Simulation Algorithm for Gene Regulatory Networks with Multiple Binding Sites", journal = j-J-COMPUT-BIOL, volume = "22", number = "3", pages = "218--226", month = mar, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0064; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0064", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2014", } @Article{Matur:2015:AAS, author = "Meltem G{\"o}lgeli Matur and Johannes M{\"u}ller and Christina Kuttler and Burkhard A. Hense", title = "An Approximative Approach for Single Cell Spatial Modeling of Quorum Sensing", journal = j-J-COMPUT-BIOL, volume = "22", number = "3", pages = "227--235", month = mar, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0198", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0198; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0198", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 October 2014", } @Article{Nguyen:2015:SWE, author = "Nha Nguyen and An Vo and Inchan Choi and Kyoung-Jae Won", title = "A Stationary Wavelet Entropy-Based Clustering Approach Accurately Predicts Gene Expression", journal = j-J-COMPUT-BIOL, volume = "22", number = "3", pages = "236--249", month = mar, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0221", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0221; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0221", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 November 2014", } @Article{Califano:2015:PRI, author = "AnDrea Califano and Manolis Kellis and Gustavo Stolovitzky", title = "Preface: {RECOMB\slash ISCB Systems Biology, Regulatory Genomics, and DREAM 2014} Special Issue", journal = j-J-COMPUT-BIOL, volume = "22", number = "4", pages = "251--252", month = apr, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.020P", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.020P", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 April 2015", } @Article{Joshi:2015:MSN, author = "Anagha Joshi and Yvonne Beck and Tom Michoel", title = "Multi-Species Network Inference Improves Gene Regulatory Network Reconstruction for Early Embryonic Development in \bioname{Drosophila}", journal = j-J-COMPUT-BIOL, volume = "22", number = "4", pages = "253--265", month = apr, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0290", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0290; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0290", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 April 2015", } @Article{Ong:2015:SMM, author = "Edison Ong and Anthony Szedlak and Yunyi Kang and Peyton Smith and Nicholas Smith and Madison McBride and Darren Finlay and Kristiina Vuori and James Mason and Edward D. Ball and Carlo Piermarocchi and Giovanni Paternostro", title = "A Scalable Method for Molecular Network Reconstruction Identifies Properties of Targets and Mutations in Acute Myeloid Leukemia", journal = j-J-COMPUT-BIOL, volume = "22", number = "4", pages = "266--288", month = apr, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0297", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0297; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0297", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 April 2015", } @Article{Baur:2015:CCA, author = "Brittany Baur and Serdar Bozdag", title = "A Canonical Correlation Analysis-Based Dynamic {Bayesian} Network Prior to Infer Gene Regulatory Networks from Multiple Types of Biological Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "4", pages = "289--299", month = apr, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0296", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0296; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0296", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 April 2015", } @Article{Li:2015:IGW, author = "Xueling Li and Min Zhu and Allan R. Brasier and Andrzej S. Kudlicki", title = "Inferring Genome-Wide Functional Modulatory Network: a Case Study on {NF-$ \kappa $B\slash RelA} Transcription Factor", journal = j-J-COMPUT-BIOL, volume = "22", number = "4", pages = "300--312", month = apr, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0299", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0299; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0299", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 April 2015", } @Article{Xie:2015:DGP, author = "Bingqing Xie and Gady Agam and Sandhya Balasubramanian and Jinbo Xu and T. Conrad Gilliam and Natalia Maltsev and Daniela B{\"o}rnigen", title = "Disease Gene Prioritization Using Network and Feature", journal = j-J-COMPUT-BIOL, volume = "22", number = "4", pages = "313--323", month = apr, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0001", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0001; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0001", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 April 2015", } @Article{Wise:2015:CID, author = "Aaron Wise and Ziv Bar-Joseph", title = "{cDREM}: Inferring Dynamic Combinatorial Gene Regulation", journal = j-J-COMPUT-BIOL, volume = "22", number = "4", pages = "324--333", month = apr, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0010", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:51:59 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0010; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0010", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 April 2015", } @Article{Sharan:2015:P, author = "Roded Sharan", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "335--335", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.030P", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.030P", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 April 2015", } @Article{Chikhi:2015:RBG, author = "Rayan Chikhi and Antoine Limasset and Shaun Jackman and Jared T. Simpson and Paul Medvedev", title = "On the Representation of {de Bruijn} Graphs", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "336--352", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0160", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0160; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0160", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 January 2015", } @Article{Guthals:2015:GFA, author = "Adrian Guthals and Christina Boucher and Nuno Bandeira", title = "The Generating Function Approach for Peptide Identification in Spectral Networks", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "353--366", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 November 2014", } @Article{Leung:2015:IMH, author = "Henry C. M. Leung and Siu-Ming Yiu and Francis Y. L. Chin", title = "{IDBA-MTP}: a Hybrid Metatranscriptomic Assembler Based on Protein Information", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "367--376", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0139", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0139; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0139", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 December 2014", } @Article{Mirarab:2015:PUL, author = "Siavash Mirarab and Nam Nguyen and Sheng Guo and Li-San Wang and Junhyong Kim and Tandy Warnow", title = "{PASTA}: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "377--386", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0156; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0156", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 December 2014", } @Article{Nguyen:2015:BPG, author = "Ngan Nguyen and Glenn Hickey and Daniel R. Zerbino and Brian Raney and Dent Earl and Joel Armstrong and W. James Kent and David Haussler and Benedict Paten", title = "Building a {Pan}-Genome Reference for a Population", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "387--401", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0146", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0146; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0146", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2015", } @Article{Noto:2015:CCS, author = "Keith Noto and Saeed Majidi and Andrea G. Edlow and Heather C. Wick and Diana W. Bianchi and Donna K. Slonim", title = "{CSAX}: Characterizing Systematic Anomalies in {eXpression} Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "402--413", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0155", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0155; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0155", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2015", } @Article{Reimers:2015:FFM, author = "Arne C. Reimers and Frank J. Bruggeman and Brett G. Olivier and Leen Stougie", title = "Fast Flux Module Detection Using Matroid Theory", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "414--424", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0141", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0141; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0141", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2015", } @Article{Shao:2015:EAC, author = "Mingfu Shao and Yu Lin and Bernard M. E. Moret", title = "An Exact Algorithm to Compute the Double-Cut-and-Join Distance for Genomes with Duplicate Genes", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "425--435", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0096; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0096", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 December 2014", } @Article{Xu:2015:GCA, author = "Shutan Xu and Shuxue Zou and Lincong Wang", title = "A Geometric Clustering Algorithm with Applications to Structural Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "436--450", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0162", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0162; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0162", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 December 2014", } @Article{Yang:2015:SHC, author = "Wen-Yun Yang and Farhad Hormozdiari and Eleazar Eskin and Bogdan Pasaniuc", title = "A Spatial Haplotype Copying Model with Applications to Genotype Imputation", journal = j-J-COMPUT-BIOL, volume = "22", number = "5", pages = "451--462", month = may, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 December 2014", } @Article{Chitsaz:2015:ELR, author = "Hamidreza Chitsaz and Mohammad Aminisharifabad", title = "Exact Learning of {RNA} Energy Parameters From Structure", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "463--473", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0164", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0164; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0164", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2015", } @Article{Kamisetty:2015:LSD, author = "Hetunandan Kamisetty and Bornika Ghosh and Christopher James Langmead and Chris Bailey-Kellogg", title = "Learning Sequence Determinants of Protein:Protein Interaction Specificity with Sparse Graphical Models", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "474--486", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0289", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0289; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0289", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 May 2015", } @Article{Konagurthu:2015:SSL, author = "Arun S. Konagurthu and Parthan Kasarapu and Lloyd Allison and James H. Collier and Arthur M. Lesk", title = "On Sufficient Statistics of Least-Squares Superposition of Vector Sets", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "487--497", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0154", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0154; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0154", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2015", } @Article{Patterson:2015:WWH, author = "Murray Patterson and Tobias Marschall and Nadia Pisanti and Leo van Iersel and Leen Stougie and Gunnar W. Klau and Alexander Sch{\"o}nhuth", title = "{WhatsHap}: Weighted Haplotype Assembly for Future-Generation Sequencing Reads", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "498--509", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0157", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0157; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0157", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 February 2015", } @Article{Raphael:2015:SIC, author = "Benjamin J. Raphael and Fabio Vandin", title = "Simultaneous Inference of Cancer Pathways and Tumor Progression from Cross-Sectional Mutation Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "510--527", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0161", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0161; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0161", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 March 2015", } @Article{Safonova:2015:DAH, author = "Yana Safonova and Anton Bankevich and Pavel A. Pevzner", title = "{dipSPAdes}: Assembler for Highly Polymorphic Diploid Genomes", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "528--545", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 March 2015", } @Article{Wang:2015:CPF, author = "Hua Wang and Heng Huang and Chris Ding", title = "Correlated Protein Function Prediction via Maximization of Data-Knowledge Consistency", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "546--562", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0172; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 April 2015", } @Article{Wang:2015:GGI, author = "Zhanyong Wang and Jae Hoon Sul and Sagi Snir and Jose A. Lozano and Eleazar Eskin", title = "Gene--Gene Interactions Detection Using a Two-stage Model", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "563--576", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 April 2015", } @Article{Zakov:2015:RBF, author = "Shay Zakov and Vineet Bafna", title = "Reconstructing Breakage Fusion Bridge Architectures Using Noisy Copy Numbers", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "577--594", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0166", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0166; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0166", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 May 2015", } @Article{Zitnik:2015:DIE, author = "Marinka {\v{Z}}itnik and Bla{\v{z}} Zupan", title = "Data Imputation in Epistatic {MAPs} by Network-Guided Matrix Completion", journal = j-J-COMPUT-BIOL, volume = "22", number = "6", pages = "595--608", month = jun, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0158", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0158; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0158", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 February 2015", } @Article{Guo:2015:NFP, author = "Yuzhen Guo", title = "The Noncompacted Folding of Proteins by Modified Elastic Net Algorithm", journal = j-J-COMPUT-BIOL, volume = "22", number = "7", pages = "609--618", month = jul, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2012.0290", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2012.0290; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2012.0290", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 June 2015", } @Article{Muller:2015:CRS, author = "Robert M{\"u}ller and Markus E. Nebel", title = "Combinatorics of {RNA} Secondary Structures with Base Triples", journal = j-J-COMPUT-BIOL, volume = "22", number = "7", pages = "619--648", month = jul, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0022", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0022; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0022", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 June 2015", } @Article{Costa:2015:ETS, author = "Jose M. J. Costa and Helcio R. B. Orlande and Haroldo F. Campos Velho and Suani T. R. de Pinho and George S. Dulikravich and Renato M. Cotta and Silvio H. da Cunha Neto", title = "Estimation of Tumor Size Evolution Using Particle Filters", journal = j-J-COMPUT-BIOL, volume = "22", number = "7", pages = "649--665", month = jul, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0003", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0003; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0003", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 May 2015", } @Article{Wei:2015:DPA, author = "Zhexue Wei and Daming Zhu and Lusheng Wang", title = "A Dynamic Programming Algorithm For (1,2)-Exemplar Breakpoint Distance", journal = j-J-COMPUT-BIOL, volume = "22", number = "7", pages = "666--676", month = jul, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0200", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0200; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0200", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 June 2015", } @Article{Chang:2015:VCF, author = "Huilan Chang and Yi-Chang Chiu and Yi-Lin Tsai", title = "A Variation of Cover-Free Families and Its Applications", journal = j-J-COMPUT-BIOL, volume = "22", number = "7", pages = "677--686", month = jul, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0222", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0222; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0222", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2015", } @Article{Radu:2015:NHS, author = "Alex Radu and Michael Charleston", title = "Node Handprinting: a Scalable and Accurate Algorithm for Aligning Multiple Biological Networks", journal = j-J-COMPUT-BIOL, volume = "22", number = "7", pages = "687--697", month = jul, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0247", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0247; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0247", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2015", } @Article{Kaiser:2015:NAE, author = "Florian Kaiser and Alexander Eisold and Dirk Labudde", title = "A Novel Algorithm for Enhanced Structural Motif Matching in Proteins", journal = j-J-COMPUT-BIOL, volume = "22", number = "7", pages = "698--713", month = jul, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0263", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:06 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0263; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0263", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2015", } @Article{Simmons:2015:DWD, author = "Sean Simmons and Jian Peng and Jadwiga Bienkowska and Bonnie Berger", title = "Discovering What Dimensionality Reduction Really Tells Us About {RNA-Seq} Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "8", pages = "715--728", month = aug, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0085", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0085; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0085", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 June 2015", } @Article{Zornig:2015:RSI, author = "Peter Z{\"o}rnig", title = "Reduced-Size Integer Linear Programming Models for String Selection Problems: Application to the Farthest String Problem", journal = j-J-COMPUT-BIOL, volume = "22", number = "8", pages = "729--742", month = aug, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0265", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0265; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0265", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 December 2014", } @Article{Koskinen:2015:IDC, author = "Kaisa Koskinen and Petri Auvinen and K. Johanna Bj{\"o}rkroth and Jenni Hultman", title = "Inconsistent Denoising and Clustering Algorithms for Amplicon Sequence Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "8", pages = "743--751", month = aug, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0268", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0268; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0268", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 December 2014", } @Article{Huang:2015:MRR, author = "Chia-Hui Huang", title = "Medical Reasoning with Rough-Set Influence Diagrams", journal = j-J-COMPUT-BIOL, volume = "22", number = "8", pages = "752--764", month = aug, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0293", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0293; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0293", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 April 2015", } @Article{Sun:2015:MSM, author = "Miao Sun and Dejian Lai and Li Zhang and Xuelin Huang", title = "Modified {SuperCurve} Method for Analysis of Reverse-Phase Protein Array Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "8", pages = "765--769", month = aug, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0007", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0007; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0007", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 June 2015", } @Article{Serang:2015:FNM, author = "Oliver Serang", title = "A Fast Numerical Method for Max-Convolution and the Application to Efficient Max-Product Inference in {Bayesian} Networks", journal = j-J-COMPUT-BIOL, volume = "22", number = "8", pages = "770--783", month = aug, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0013", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0013; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0013", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 July 2015", } @Article{He:2015:CSB, author = "Jing He and Amarda Shehu and Nurit Haspel and Brian Chen", title = "The 7th Computational Structural Bioinformatics Workshop", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "785--786", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.28999.jh", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.28999.jh", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 September 2015", } @Article{Dong:2015:CAS, author = "Hui Dong and Jin Seob Kim and Gregory S. Chirikjian", title = "Computational Analysis of {SAXS} Data Acquisition", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "787--805", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0115; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0115", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 August 2015", } @Article{Hashmi:2015:IIM, author = "Irina Hashmi and Amarda Shehu", title = "{idDock+}: Integrating Machine Learning in Probabilistic Search for Protein--Protein Docking", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "806--822", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0108; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0108", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 July 2015", } @Article{Yeh:2015:DDI, author = "Hsin-Yi (Cindy) Yeh and Aaron Lindsey and Chih-Peng Wu and Shawna Thomas and Nancy M. Amato", title = "Decoy Database Improvement for Protein Folding", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "823--836", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0116", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0116; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0116", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2015", } @Article{Biswas:2015:DPA, author = "Abhishek Biswas and Desh Ranjan and Mohammad Zubair and Jing He", title = "A Dynamic Programming Algorithm for Finding the Optimal Placement of a Secondary Structure Topology in {Cryo-EM} Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "837--843", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0120", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0120; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0120", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 August 2015", } @Article{Clausen:2015:DDE, author = "Rudy Clausen and Amarda Shehu", title = "A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "844--860", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0107", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0107; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0107", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 July 2015", } @Article{Guo:2015:CSR, author = "Ziyi Guo and Brian Yuan Chen", title = "Conformational Sampling Reveals Amino Acids with a Steric Influence on Specificity", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "861--875", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0117", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0117; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0117", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 September 2015", } @Article{Zhou:2015:DDA, author = "Ping Zhou and Ning Zhang and Ruth Nussinov and Buyong Ma", title = "Defining the Domain Arrangement of the Mammalian Target of {Rapamycin} Complex Component {Rictor} Protein", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "876--886", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2015", } @Article{Xia:2015:MTS, author = "Kelin Xia and Zhixiong Zhao and Guo-Wei Wei", title = "Multiresolution Topological Simplification", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "887--891", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0104", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0104; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0104", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 July 2015", } @Article{Akbal-Delibas:2015:APD, author = "Bahar Akbal-Delibas and Marc Pomplun and Nurit Haspel", title = "Accurate Prediction of Docked Protein Structure Similarity", journal = j-J-COMPUT-BIOL, volume = "22", number = "9", pages = "892--904", month = sep, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0114", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:10 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0114; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0114", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 September 2015", } @Article{Baran:2015:NRB, author = "Yael Baran and Eran Halperin", title = "A Note on the Relations Between Spatio-Genetic Models", journal = j-J-COMPUT-BIOL, volume = "22", number = "10", pages = "905--917", month = oct, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0080", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0080; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0080", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 June 2015", } @Article{Disanto:2015:CHL, author = "Filippo Disanto and Noah A. Rosenberg", title = "Coalescent Histories for Lodgepole Species Trees", journal = j-J-COMPUT-BIOL, volume = "22", number = "10", pages = "918--929", month = oct, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0015", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0015; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0015", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 May 2015", } @Article{Pragman:2015:MDT, author = "Alexa Pragman and Richard Issacson and Christine Wendt and Cavan Reilly", title = "A Method for Determining Taxonomical Contributions to Group Differences in Microbiomic Investigations", journal = j-J-COMPUT-BIOL, volume = "22", number = "10", pages = "930--939", month = oct, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0021", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0021; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0021", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 May 2015", } @Article{Wallace:2015:ASC, author = "Tim Wallace and Ali Sekmen and Xiaofei Wang", title = "Application of Subspace Clustering in {DNA} Sequence Analysis", journal = j-J-COMPUT-BIOL, volume = "22", number = "10", pages = "940--952", month = oct, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 July 2015", } @Article{Faria:2015:RAP, author = "Alexandre Wagner Chagas Faria and Alisson Marques da Silva and Thiago de Souza Rodrigues and Marcelo Azevedo Costa and Antonio Padua Braga", title = "A Ranking Approach for Probe Selection and Classification of Microarray Data with Artificial Neural Networks", journal = j-J-COMPUT-BIOL, volume = "22", number = "10", pages = "953--961", month = oct, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 September 2015", } @Article{Li:2015:HPG, author = "Bo Li and Xianfang Zheng and Chuancui Hu and Yunxia Cao", title = "Human Papillomavirus Genome-Wide Identification of {T}-Cell Epitopes for Peptide Vaccine Development Against Cervical Cancer: an Integration of Computational Analysis and Experimental Assay", journal = j-J-COMPUT-BIOL, volume = "22", number = "10", pages = "962--974", month = oct, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0287", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:13 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0287; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0287", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 September 2015", } @Article{Lu:2015:EAC, author = "Chin Lung Lu", title = "An Efficient Algorithm for the Contig Ordering Problem under Algebraic Rearrangement Distance", journal = j-J-COMPUT-BIOL, volume = "22", number = "11", pages = "975--987", month = nov, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 August 2015", } @Article{Chen:2015:CAM, author = "Ping Chen and Xuelin Huang", title = "Comparison of Analytic Methods for Quantitative Real-Time Polymerase Chain Reaction Data", journal = j-J-COMPUT-BIOL, volume = "22", number = "11", pages = "988--996", month = nov, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0023; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0023", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 July 2015", } @Article{OHare:2015:IHD, author = "Anthony O'Hare", title = "Inference in High-Dimensional Parameter Space", journal = j-J-COMPUT-BIOL, volume = "22", number = "11", pages = "997--1004", month = nov, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0086", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0086; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0086", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2015", } @Article{Sakhanenko:2015:BDA, author = "Nikita A. Sakhanenko and David J. Galas", title = "Biological Data Analysis as an Information Theory Problem: Multivariable Dependence Measures and the Shadows Algorithm", journal = j-J-COMPUT-BIOL, volume = "22", number = "11", pages = "1005--1024", month = nov, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0051", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0051; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0051", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 September 2015", } @Article{Jasra:2015:BID, author = "Ajay Jasra and Adam Persing and Alexandros Beskos and Kari Heine and Maria {De Iorio}", title = "{Bayesian} Inference for Duplication--Mutation with Complementarity Network Models", journal = j-J-COMPUT-BIOL, volume = "22", number = "11", pages = "1025--1033", month = nov, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0072", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0072; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0072", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 September 2015", } @Article{Kim:2015:SSS, author = "Sera Kim and Kyeongjun Lee and Hokeun Sun", title = "Statistical Selection Strategy for Risk and Protective Rare Variants Associated with Complex Traits", journal = j-J-COMPUT-BIOL, volume = "22", number = "11", pages = "1034--1043", month = nov, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0091", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0091; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0091", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 October 2015", } @Article{Cunha:2015:FAA, author = "Lu{\'\i}s Felipe I. Cunha and Luis Antonio B. Kowada and Rodrigo de A. Hausen and Celina M. H. de Figueiredo", title = "A Faster 1.375-Approximation Algorithm for Sorting by Transpositions*", journal = j-J-COMPUT-BIOL, volume = "22", number = "11", pages = "1044--1056", month = nov, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0298", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:15 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0298; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0298", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 September 2015", } @Article{Frasca:2015:UUA, author = "Marco Frasca and Alberto Bertoni and Giorgio Valentini", title = "{UNIPred}: Unbalance-Aware Network Integration and Prediction of Protein Functions", journal = j-J-COMPUT-BIOL, volume = "22", number = "12", pages = "1057--1074", month = dec, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0110", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0110; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0110", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 September 2015", } @Article{Soliman:2015:DMM, author = "Ahmed T. Soliman and Tao Meng and Shu-Ching Chen and S. S. Iyengar and Puneeth Iyengar and John Yordy and Mei-Ling Shyu", title = "Driver Missense Mutation Identification Using Feature Selection and Model Fusion", journal = j-J-COMPUT-BIOL, volume = "22", number = "12", pages = "1075--1085", month = dec, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0110", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0110; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0110", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 September 2015", } @Article{Tran:2015:NMP, author = "Tuan-Anh Tran and Nam Tri Vo and Hoang Duc Nguyen and Bao The Pham", title = "A Novel Method to Predict Highly Expressed Genes Based on Radius Clustering and Relative Synonymous Codon Usage", journal = j-J-COMPUT-BIOL, volume = "22", number = "12", pages = "1086--1096", month = dec, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0121", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0121; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0121", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 November 2015", } @Article{Kang:2015:PAD, author = "Kyoung-Tak Kang and Sung-Hwan Kim and Juhyun Son and Young Han Lee and Heoung-Jae Chun", title = "Probabilistic Approach for Determining the Material Properties of Meniscal Attachments {{\em In Vivo\/}} Using Magnetic Resonance Imaging and a Finite Element Model", journal = j-J-COMPUT-BIOL, volume = "22", number = "12", pages = "1097--1107", month = dec, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0126", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0126; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0126", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 September 2015", } @Article{Niu:2015:DTI, author = "Shu-Yuan Niu and Ming-Yuan Xin and Jian Luo and Ming-Yao Liu and Zhen-Ran Jiang", title = "{DSEP}: a Tool Implementing Novel Method to Predict Side Effects of Drugs", journal = j-J-COMPUT-BIOL, volume = "22", number = "12", pages = "1108--1117", month = dec, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 October 2015", } @Article{Al-Okaily:2015:ETT, author = "Anas Al-Okaily", title = "Error Tree: a Tree Structure for {Hamming} and Edit Distances and Wildcards Matching", journal = j-J-COMPUT-BIOL, volume = "22", number = "12", pages = "1118--1128", month = dec, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0132", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0132; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0132", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 September 2015", } @Article{Chernomor:2015:CCT, author = "Olga Chernomor and Bui Quang Minh and Arndt von Haeseler", title = "Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference", journal = j-J-COMPUT-BIOL, volume = "22", number = "12", pages = "1129--1142", month = dec, year = "2015", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0146", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:17 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0146; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0146", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 October 2015", } @Article{Deng:2016:DTE, author = "Feilong Deng and Shi-Yi Chen", title = "{dbHT-Trans}: an Efficient Tool for Filtering the Protein-Encoding Transcripts Assembled by {RNA-Seq} According to Search for Homologous Proteins", journal = j-J-COMPUT-BIOL, volume = "23", number = "1", pages = "1--9", month = jan, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0137", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0137; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0137", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 October 2015", } @Article{Aridhi:2016:PIR, author = "Sabeur Aridhi and Ha{\"\i}tham Sghaier and Manel Zoghlami and Mondher Maddouri and Engelbert Mephu Nguifo", title = "Prediction of Ionizing Radiation Resistance in Bacteria Using a Multiple Instance Learning Model", journal = j-J-COMPUT-BIOL, volume = "23", number = "1", pages = "10--20", month = jan, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0134", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0134; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0134", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 October 2015", } @Article{Girdlestone:2016:DWA, author = "Christopher Girdlestone and Steven Hayward", title = "The {DynDom3D Webserver} for the Analysis of Domain Movements in Multimeric Proteins", journal = j-J-COMPUT-BIOL, volume = "23", number = "1", pages = "21--26", month = jan, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0143; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 November 2015", } @Article{Camilo:2016:HOO, author = "Cesar M. Camilo and Gustavo M. A. Lima and Fernando V. Maluf and Rafael V. C. Guido and Igor Polikarpov", title = "{HTP-OligoDesigner}: an Online Primer Design Tool for High-Throughput Gene Cloning and Site-Directed Mutagenesis", journal = j-J-COMPUT-BIOL, volume = "23", number = "1", pages = "27--29", month = jan, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0148", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0148; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0148", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 November 2015", } @Article{Vandin:2016:SCC, author = "Fabio Vandin and Benjamin J. Raphael and Eli Upfal", title = "On the Sample Complexity of Cancer Pathways Identification", journal = j-J-COMPUT-BIOL, volume = "23", number = "1", pages = "30--41", month = jan, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0100; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0100", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 December 2015", } @Article{Hsiao:2016:SAF, author = "Ya-Chun Hsiao and Li-Yu Daisy Liu", title = "A Stepwise Approach of Finding Dependent Variables via Coefficient of Intrinsic Dependence", journal = j-J-COMPUT-BIOL, volume = "23", number = "1", pages = "42--55", month = jan, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0150", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0150; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0150", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 December 2015", } @Article{Hu:2016:CPT, author = "Yucheng Hu and John S. Lowengrub", title = "Collective Properties of a Transcription Initiation Model Under Varying Environment", journal = j-J-COMPUT-BIOL, volume = "23", number = "1", pages = "56--66", month = jan, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0144", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0144; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0144", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 December 2015", } @Article{Orenstein:2016:EDC, author = "Yaron Orenstein and Bonnie Berger", title = "Efficient Design of Compact Unstructured {RNA} Libraries Covering All $k$-mers", journal = j-J-COMPUT-BIOL, volume = "23", number = "2", pages = "67--79", month = feb, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0179", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0179; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0179", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 December 2015", } @Article{Rohani:2016:RSW, author = "Leyla Rohani and Derrick J. Morton and Xiao-Qian Wang and Jaideep Chaudhary", title = "Relative Stability of Wild-Type and Mutant p53 Core Domain: a Molecular Dynamic Study", journal = j-J-COMPUT-BIOL, volume = "23", number = "2", pages = "80--89", month = feb, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 December 2015", } @Article{Pepe:2016:CPP, author = "Daniele Pepe and Jin Hwan Do", title = "Comparison of Perturbed Pathways in Two Different Cell Models for {Parkinson}'s Disease with Structural Equation Model", journal = j-J-COMPUT-BIOL, volume = "23", number = "2", pages = "90--101", month = feb, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0156; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0156", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 December 2015", } @Article{Peng:2016:ZIB, author = "Xiaoling Peng and Gang Li and Zhenqiu Liu", title = "Zero-Inflated Beta Regression for Differential Abundance Analysis with Metagenomics Data", journal = j-J-COMPUT-BIOL, volume = "23", number = "2", pages = "102--110", month = feb, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0157", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0157; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0157", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 December 2015", } @Article{Zhu:2016:MCU, author = "Xiujun (Sylvia) Zhu and Monnie McGee", title = "Metagenomic Classification Using an Abstraction Augmented {Markov} Model", journal = j-J-COMPUT-BIOL, volume = "23", number = "2", pages = "111--122", month = feb, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0141", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0141; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0141", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 November 2015", } @Article{Li:2016:MPL, author = "Haiou Li and Lu Sun and Sheng Luo and Xiaoyan Xia and Qiang Lyu", title = "Modeling Protein Loop Structure by Cyclic Coordinate Descent-based Approach", journal = j-J-COMPUT-BIOL, volume = "23", number = "2", pages = "123--136", month = feb, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0145", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0145; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0145", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 December 2015", } @Article{Bonizzoni:2016:LEM, author = "Paola Bonizzoni and Gianluca Della Vedova and Yuri Pirola and Marco Previtali and Raffaella Rizzi", title = "{LSG}: an External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly", journal = j-J-COMPUT-BIOL, volume = "23", number = "3", pages = "137--149", month = mar, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0172; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2016", } @Article{Avdeyev:2016:RAG, author = "Pavel Avdeyev and Shuai Jiang and Sergey Aganezov and Fei Hu and Max A. Alekseyev", title = "Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss", journal = j-J-COMPUT-BIOL, volume = "23", number = "3", pages = "150--164", month = mar, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0160", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0160; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0160", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 February 2016", } @Article{Smoly:2016:ART, author = "Ilan Smoly and Amir Carmel and Yonat Shemer-Avni and Esti Yeger-Lotem and Michal Ziv-Ukelson", title = "Algorithms for Regular Tree Grammar Network Search and Their Application to Mining Human--viral Infection Patterns", journal = j-J-COMPUT-BIOL, volume = "23", number = "3", pages = "165--179", month = mar, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0168", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0168; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0168", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2016", } @Article{Chakrabarty:2016:DCD, author = "Deeparnab Chakrabarty and Sampath Kannan and Kevin Tian", title = "Detecting Character Dependencies in Stochastic Models of Evolution", journal = j-J-COMPUT-BIOL, volume = "23", number = "3", pages = "180--191", month = mar, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0099", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0099; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0099", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 January 2016", } @Article{Liu:2016:SIC, author = "Zhenqiu Liu and Shili Lin and Nan Deng and Dermot P. B. McGovern and Steven Piantadosi", title = "Sparse Inverse Covariance Estimation with {$L$}$_0$ Penalty for Network Construction with Omics Data", journal = j-J-COMPUT-BIOL, volume = "23", number = "3", pages = "192--202", month = mar, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0102; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0102", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 February 2016", } @Article{Canzar:2016:RCP, author = "Stefan Canzar and Khaled Elbassioni and Mitchell Jones and Juli{\'a}n Mestre", title = "Resolving Conflicting Predictions from Multimapping Reads", journal = j-J-COMPUT-BIOL, volume = "23", number = "3", pages = "203--217", month = mar, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0164", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0164; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0164", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 January 2016", } @Article{Drinkwater:2016:RRA, author = "Benjamin Drinkwater and Michael A. Charleston", title = "{RASCAL}: a Randomized Approach for Coevolutionary Analysis", journal = j-J-COMPUT-BIOL, volume = "23", number = "3", pages = "218--227", month = mar, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0111", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0111; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0111", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 February 2016", } @Article{Chen:2016:BIM, author = "Shi-Yi Chen and Feilong Deng and Ying Huang and Xianbo Jia and Yi-Ping Liu and Song-Jia Lai", title = "{bioOTU}: an Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s {rRNA} Gene Sequences", journal = j-J-COMPUT-BIOL, volume = "23", number = "4", pages = "229--238", month = apr, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0214", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0214; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0214", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 March 2016", } @Article{Anjum:2016:IDE, author = "Arfa Anjum and Seema Jaggi and Eldho Varghese and Shwetank Lall and Arpan Bhowmik and Anil Rai", title = "Identification of Differentially Expressed Genes in {RNA-seq} Data of \bioname{Arabidopsis thaliana}: a Compound Distribution Approach", journal = j-J-COMPUT-BIOL, volume = "23", number = "4", pages = "239--247", month = apr, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0205", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0205; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0205", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 March 2016", } @Article{Perez:2016:CPA, author = "Nelson P{\'e}rez and Miguel Gutierrez and Nelson Vera", title = "Computational Performance Assessment of $k$-mer Counting Algorithms", journal = j-J-COMPUT-BIOL, volume = "23", number = "4", pages = "248--255", month = apr, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0199", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0199; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0199", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 March 2016", } @Article{Sarr:2016:VAR, author = "Abdoulaye Sarr and Anya D{\'e}silles and Alexandra Fronville and Vincent Rodin", title = "A Viability Approach for Robustness Measurement, Organizational Autopoiesis, and Cell Turnover in a Multicellular System", journal = j-J-COMPUT-BIOL, volume = "23", number = "4", pages = "256--269", month = apr, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0187", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0187; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0187", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 March 2016", } @Article{Mier:2016:FFW, author = "Pablo Mier and Miguel A. Andrade-Navarro", title = "{FastaHerder2}: Four Ways to Research Protein Function and Evolution with Clustering and Clustered Databases", journal = j-J-COMPUT-BIOL, volume = "23", number = "4", pages = "270--278", month = apr, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0191", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0191; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0191", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 February 2016", } @Article{Laimighofer:2016:UPF, author = "Michael Laimighofer and Jan Krumsiek and Florian Buettner and Fabian J. Theis", title = "Unbiased Prediction and Feature Selection in High-Dimensional Survival Regression", journal = j-J-COMPUT-BIOL, volume = "23", number = "4", pages = "279--290", month = apr, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0192", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0192; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0192", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2016", } @Article{Lobo:2016:MMC, author = "Daniel Lobo and Jennifer Hammelman and Michael Levin", title = "{MoCha}: Molecular Characterization of Unknown Pathways", journal = j-J-COMPUT-BIOL, volume = "23", number = "4", pages = "291--297", month = apr, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0211", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0211; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0211", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 March 2016", } @Article{Przytycka:2016:P, author = "Teresa Przytycka", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "299--299", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.29001.tp", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.29001.tp", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2016", } @Article{Gong:2016:CSE, author = "Huichao Gong and Sai Zhang and Jiangdian Wang and Haipeng Gong and Jianyang Zeng", title = "Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "300--310", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0184", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0184; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0184", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2016", } @Article{Hallen:2016:CCO, author = "Mark A. Hallen and Bruce R. Donald", title = "comets (Constrained Optimization of Multistate Energies by Tree Search): a Provable and Efficient Protein Design Algorithm to Optimize Binding Affinity and Specificity with Respect to Sequence", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "311--321", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0188", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0188; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0188", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 January 2016", } @Article{Li:2016:DFS, author = "Yifeng Li and Chih-Yu Chen and Wyeth W. Wasserman", title = "Deep Feature Selection: Theory and Application to Identify Enhancers and Promoters", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "322--336", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0189; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 January 2016", } @Article{Shao:2016:FEA, author = "Mingfu Shao and Bernard M. E. Moret", title = "A Fast and Exact Algorithm for the Exemplar Breakpoint Distance", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "337--346", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0193", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0193; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0193", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 March 2016", } @Article{Salmela:2016:GFE, author = "Leena Salmela and Kristoffer Sahlin and Veli M{\"a}kinen and Alexandru I. Tomescu", title = "Gap Filling as Exact Path Length Problem", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "347--361", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 March 2016", } @Article{Fonseca:2016:PRN, author = "Rasmus Fonseca and Henry van den Bedem and Julie Bernauer", title = "Probing {RNA} Native Conformational Ensembles with Structural Constraints", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "362--371", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0201", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0201; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0201", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 March 2016", } @Article{Lee:2016:ENR, author = "Seunghak Lee and Aur{\'e}lie Lozano and Prabhanjan Kambadur and Eric P. Xing", title = "An Efficient Nonlinear Regression Approach for Genome-wide Detection of Marginal and Interacting Genetic Variations", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "372--389", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0202", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0202; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0202", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2016", } @Article{Mazza:2016:FAM, author = "Arnon Mazza and Allon Wagner and Eytan Ruppin and Roded Sharan", title = "Functional Alignment of Metabolic Networks", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "390--399", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0203", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0203; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0203", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 January 2016", } @Article{Leelananda:2016:PDS, author = "Sumudu P. Leelananda and Robert L. Jernigan and Andrzej Kloczkowski", title = "Predicting Designability of Small Proteins from Graph Features of Contact Maps", journal = j-J-COMPUT-BIOL, volume = "23", number = "5", pages = "400--411", month = may, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0209", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0209; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0209", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2016", } @Article{Jou:2016:BNP, author = "Jonathan D. Jou and Swati Jain and Ivelin S. Georgiev and Bruce R. Donald", title = "{BWM*}: a Novel, Provable, Ensemble-based Dynamic Programming Algorithm for Sparse Approximations of Computational Protein Design", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "413--424", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0194", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0194; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0194", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 January 2016", } @Article{Sefer:2016:DEC, author = "Emre Sefer and Geet Duggal and Carl Kingsford", title = "Deconvolution of Ensemble Chromatin Interaction Data Reveals the Latent Mixing Structures in Cell Subpopulations", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "425--438", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0210", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0210; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0210", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 June 2016", } @Article{Zhou:2016:CPD, author = "Yichao Zhou and Yuexin Wu and Jianyang Zeng", title = "Computational Protein Design Using {AND/OR} Branch-and-Bound Search", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "439--451", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0212", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0212; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0212", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2016", } @Article{Thankachan:2016:APM, author = "Sharma V. Thankachan and Sriram P. Chockalingam and Yongchao Liu and Alberto Apostolico and Srinivas Aluru", title = "{ALFRED}: a Practical Method for Alignment-Free Distance Computation", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "452--460", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0217", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0217; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0217", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 May 2016", } @Article{Ben-Bassat:2016:CDS, author = "Ilan Ben-Bassat and Benny Chor", title = "{CRISPR} Detection From Short Reads Using Partial Overlap Graphs", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "461--471", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0226", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0226; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0226", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2016", } @Article{Thankachan:2016:PEA, author = "Sharma V. Thankachan and Alberto Apostolico and Srinivas Aluru", title = "A Provably Efficient Algorithm for the $k$-Mismatch Average Common Substring Problem", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "472--482", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0235", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0235; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0235", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2016", } @Article{Bonissone:2016:ICU, author = "Stefano R. Bonissone and Pavel A. Pevzner", title = "Immunoglobulin Classification Using the Colored Antibody Graph", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "483--494", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0010", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0010; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0010", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 May 2016", } @Article{Yang:2016:RRI, author = "Shuo Yang and Shai Carmi and Itsik Pe'er", title = "Rapidly Registering Identity-by-Descent Across Ancestral Recombination Graphs", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "495--507", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0016", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0016; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0016", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2016", } @Article{Manescu:2016:SLA, author = "David Manescu and Uri Keich", title = "A Symmetric Length-Aware Enrichment Test", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "508--525", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0038", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0038; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0038", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 May 2016", } @Article{Biswas:2016:LMI, author = "Surojit Biswas and Meredith Mcdonald and Derek S. Lundberg and Jeffery L. Dangl and Vladimir Jojic", title = "Learning Microbial Interaction Networks from Metagenomic Count Data", journal = j-J-COMPUT-BIOL, volume = "23", number = "6", pages = "526--535", month = jun, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0061", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0061; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0061", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 June 2016", } @Article{Chen:2016:BIB, author = "Zhi-Zhong Chen and Fei Deng and Chao Shen and Yiji Wang and Lusheng Wang", title = "Better {ILP-Based} Approaches to Haplotype Assembly", journal = j-J-COMPUT-BIOL, volume = "23", number = "7", pages = "537--552", month = jul, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0035", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0035; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0035", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 June 2016", } @Article{Zhang:2016:TBP, author = "Louxin Zhang", title = "On Tree-Based Phylogenetic Networks", journal = j-J-COMPUT-BIOL, volume = "23", number = "7", pages = "553--565", month = jul, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0228", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0228; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0228", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 May 2016", } @Article{Chen:2016:EFR, author = "Jiawen Chen and Zhong-Ru Xie and Yinghao Wu", title = "Elucidating the Functional Roles of Spatial Organization in Cross-Membrane Signal Transduction by a Hybrid Simulation Method", journal = j-J-COMPUT-BIOL, volume = "23", number = "7", pages = "566--584", month = jul, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0227", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0227; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0227", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 March 2016", } @Article{Guan:2016:EPE, author = "Boxin Guan and Changsheng Zhang and Jiaxu Ning", title = "{EDGA}: a Population Evolution Direction-Guided Genetic Algorithm for Protein--Ligand Docking", journal = j-J-COMPUT-BIOL, volume = "23", number = "7", pages = "585--596", month = jul, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0190", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0190; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0190", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2016", } @Article{Wang:2016:CWB, author = "Yi Wang and Shuangshuang Wang and Dongjie Zhou and Shuai Yang and Yongchao Xu and Chao Yang and Long Yang", title = "{CsSNP}: a {Web}-Based Tool for the Detecting of Comparative Segments {SNPs}", journal = j-J-COMPUT-BIOL, volume = "23", number = "7", pages = "597--602", month = jul, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0215", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0215; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0215", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 June 2016", } @Article{Serra:2016:SMB, author = "Fabrizio Serra and Chiara Romualdi and Federico Fogolari", title = "Similarity Measures Based on the Overlap of Ranked Genes Are Effective for Comparison and Classification of Microarray Data", journal = j-J-COMPUT-BIOL, volume = "23", number = "7", pages = "603--614", month = jul, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0057", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0057; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0057", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2016", } @Article{Al-Okaily:2016:MSE, author = "Anas Al-Okaily and Chun-Hsi Huang", title = "{ET-Motif}: Solving the Exact $ (l, d)$-Planted Motif Problem Using Error Tree Structure", journal = j-J-COMPUT-BIOL, volume = "23", number = "7", pages = "615--623", month = jul, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0238", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0238; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0238", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2016", } @Article{Jindalertudomdee:2016:EMS, author = "Jira Jindalertudomdee and Morihiro Hayashida and Tatsuya Akutsu", title = "Enumeration Method for Structural Isomers Containing User-Defined Structures Based on Breadth-First Search Approach", journal = j-J-COMPUT-BIOL, volume = "23", number = "8", pages = "625--640", month = aug, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0056", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0056; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0056", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 June 2016", } @Article{Goz:2016:EDE, author = "Eli Goz and Tamir Tuller", title = "Evidence of a Direct Evolutionary Selection for Strong Folding and Mutational Robustness Within {HIV} Coding Regions", journal = j-J-COMPUT-BIOL, volume = "23", number = "8", pages = "641--650", month = aug, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0052", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0052; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0052", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 June 2016", } @Article{More:2016:IDP, author = "Ravi P. More and Hemant J. Purohit", title = "The Identification of Discriminating Patterns from 16S {rRNA} Gene to Generate Signature for Bacillus Genus", journal = j-J-COMPUT-BIOL, volume = "23", number = "8", pages = "651--661", month = aug, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0002; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0002", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2016", } @Article{Traykov:2016:NHA, author = "Metodi Traykov and Slav Angelov and Nicola Yanev", title = "A New Heuristic Algorithm for Protein Folding in the {HP} Model", journal = j-J-COMPUT-BIOL, volume = "23", number = "8", pages = "662--668", month = aug, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0015", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0015; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0015", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2016", } @Article{Chen:2016:CPN, author = "Duo Chen and Jiasong Wang and Ming Yan and Forrest Sheng Bao", title = "A Complex Prime Numerical Representation of Amino Acids for Protein Function Comparison", journal = j-J-COMPUT-BIOL, volume = "23", number = "8", pages = "669--677", month = aug, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0178", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0178; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0178", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 June 2016", } @Article{deAndres-Galiana:2016:DBR, author = "Enrique J. deAndr{\'e}s-Galiana and Juan Luis Fern{\'a}ndez-Mart{\'\i}nez and Stephen T. Sonis", title = "Design of Biomedical Robots for Phenotype Prediction Problems", journal = j-J-COMPUT-BIOL, volume = "23", number = "8", pages = "678--692", month = aug, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 June 2016", } @Article{Wang:2016:IMN, author = "Yuandi Wang and Jinyu Cong", title = "An Improved Model of Nonuniform Coleochaete Cell Division", journal = j-J-COMPUT-BIOL, volume = "23", number = "8", pages = "693--709", month = aug, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0021", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:34 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0021; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0021", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 June 2016", } @Article{Pirogov:2016:RPN, author = "Sergey Pirogov and Alexander Rybko and Anastasia Kalinina and Mikhail Gelfand", title = "Recombination Processes and Nonlinear {Markov} Chains", journal = j-J-COMPUT-BIOL, volume = "23", number = "9", pages = "711--717", month = sep, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0051", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0051; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0051", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2016", } @Article{Bonizzoni:2016:MEC, author = "Paola Bonizzoni and Riccardo Dondi and Gunnar W. Klau and Yuri Pirola and Nadia Pisanti and Simone Zaccaria", title = "On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes", journal = j-J-COMPUT-BIOL, volume = "23", number = "9", pages = "718--736", month = sep, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0220", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0220; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0220", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 June 2016", } @Article{Pan:2016:CCB, author = "Yuchao Pan and Yuxi Dong and Jingtian Zhou and Mark Hallen and Bruce R. Donald and Jianyang Zeng and Wei Xu", title = "{cOSPREY}: a Cloud-Based Distributed Algorithm for Large-Scale Computational Protein Design", journal = j-J-COMPUT-BIOL, volume = "23", number = "9", pages = "737--749", month = sep, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0234", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0234; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0234", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2016", } @Article{Alic:2016:MHB, author = "Andy S. Alic and Ignacio Blanquer", title = "{MuffinInfo}: {HTML5-Based} Statistics Extractor from Next-Generation Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "23", number = "9", pages = "750--755", month = sep, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0031", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0031; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0031", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 September 2016", } @Article{Gartner:2016:IVC, author = "Kerstin G{\"a}rtner and Andreas Futschik", title = "Improved Versions of Common Estimators of the Recombination Rate", journal = j-J-COMPUT-BIOL, volume = "23", number = "9", pages = "756--768", month = sep, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0039", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0039; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0039", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 July 2016", } @Article{Fomin:2016:SARa, author = "Eduard Fomin", title = "A Simple Approach to the Reconstruction of a Set of Points from the Multiset of $ n^2 $ Pairwise Distances in $ n^2 $ Steps for the Sequencing Problem: {I}. {Theory}", journal = j-J-COMPUT-BIOL, volume = "23", number = "9", pages = "769--775", month = sep, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0044", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0044; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0044", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 June 2016", } @Article{McGrane:2016:BNE, author = "Martin McGrane and Michael A. Charleston", title = "Biological Network Edit Distance", journal = j-J-COMPUT-BIOL, volume = "23", number = "9", pages = "776--788", month = sep, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0062", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:36 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0062; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0062", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 June 2016", } @Article{OReilly:2016:EEO, author = "Eliza O'Reilly and Fran{\c{c}}ois Baccelli and Gustavo {De Veciana} and Haris Vikalo", title = "End-to-End Optimization of High-Throughput {DNA} Sequencing", journal = j-J-COMPUT-BIOL, volume = "23", number = "10", pages = "789--800", month = oct, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2016", } @Article{Galvez:2016:SBA, author = "Sergio G{\'a}lvez and Adis Ferusic and Francisco J. Esteban and Pilar Hern{\'a}ndez and Juan A. Caballero and Gabriel Dorado", title = "Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous {Smith-Waterman} {(HHeterSW)}", journal = j-J-COMPUT-BIOL, volume = "23", number = "10", pages = "801--809", month = oct, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0237", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0237; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0237", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2016", } @Article{Hernandez:2016:DSG, author = "Troy Hernandez and Jie Yang", title = "Descriptive Statistics of the Genome: Phylogenetic Classification of Viruses", journal = j-J-COMPUT-BIOL, volume = "23", number = "10", pages = "810--820", month = oct, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2013.0132", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2013.0132; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2013.0132", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 July 2016", } @Article{Zhao:2016:GTM, author = "Shufang Zhao and Yichao He and Xinlu Zhang and Wen Xu and Weili Wu and Suogang Gao", title = "Group Testing with Multiple Inhibitor Sets and Error-Tolerant and Its Decoding Algorithms", journal = j-J-COMPUT-BIOL, volume = "23", number = "10", pages = "821--829", month = oct, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2014.0202", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2014.0202; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2014.0202", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2016", } @Article{Hu:2016:SEU, author = "Yucheng Hu and Gongrong Yang", title = "Sequence Evolution Under Constraints: Lessons Learned from {Sudoku}", journal = j-J-COMPUT-BIOL, volume = "23", number = "10", pages = "830--840", month = oct, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0218", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0218; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0218", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 March 2016", } @Article{Madec:2016:GOS, author = "Morgan Madec and Fran{\c{c}}ois Pecheux and Yves Gendrault and Elise Rosati and Christophe Lallement and Jacques Haiech", title = "{GeNeDA}: an Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics", journal = j-J-COMPUT-BIOL, volume = "23", number = "10", pages = "841--855", month = oct, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0229", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:38 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/gnu.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0229; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0229", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2016", } @Article{Barrett:2016:RSS, author = "Christopher L. Barrett and Thomas J. X. Li and Christian M. Reidys", title = "{RNA} Secondary Structures Having a Compatible Sequence of Certain Nucleotide Ratios", journal = j-J-COMPUT-BIOL, volume = "23", number = "11", pages = "857--873", month = nov, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0049", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:40 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0049; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0049", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2016", } @Article{Ristov:2016:FSP, author = "Strahil Ristov", title = "A Fast and Simple Pattern Matching with {Hamming} Distance on Large Alphabets", journal = j-J-COMPUT-BIOL, volume = "23", number = "11", pages = "874--876", month = nov, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0020", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:40 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0020; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0020", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 June 2016", } @Article{Guo:2016:NRR, author = "Wenchuan Guo and Zhenqiu Liu and Shujie Ma", title = "Nonparametric Regularized Regression for Phenotype-Associated Taxa Selection and Network Construction with Metagenomic Count Data", journal = j-J-COMPUT-BIOL, volume = "23", number = "11", pages = "877--890", month = nov, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:40 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0023; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0023", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 July 2016", } @Article{Pereira:2016:HFA, author = "Mariana Buongermino Pereira and Mikael Wallroth and Erik Kristiansson and Marina Axelson-Fisk", title = "{HattCI}: Fast and Accurate \bioname{attC} site Identification Using Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "23", number = "11", pages = "891--902", month = nov, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0024", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:40 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0024; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0024", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 July 2016", } @Article{Hashemifar:2016:JAM, author = "Somaye Hashemifar and Qixing Huang and Jinbo Xu", title = "Joint Alignment of Multiple Protein--Protein Interaction Networks via Convex Optimization", journal = j-J-COMPUT-BIOL, volume = "23", number = "11", pages = "903--911", month = nov, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0025", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:40 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0025; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0025", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 July 2016", } @Article{Amar:2016:CUP, author = "Lamiaa A. Amar and Nahla A. Belal and Shaheera Rashwan", title = "Comparing Unlabeled Pedigree Graphs via Covering with Bipartite and Path", journal = j-J-COMPUT-BIOL, volume = "23", number = "11", pages = "912--922", month = nov, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0040", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:40 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0040; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0040", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 July 2016", } @Article{Bizjak:2016:CFM, author = "Manca Bizjak and Nikolaj Zimic and Miha Mraz and Miha Mo{\v{s}}kon", title = "Computational Framework for Modeling Multiple Noncooperative Transcription Factor Binding and Its Application to the Analysis of Nuclear Factor Kappa {B} Oscillatory Response", journal = j-J-COMPUT-BIOL, volume = "23", number = "12", pages = "923--933", month = dec, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0065", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0065; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0065", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2016", } @Article{Fomin:2016:SARb, author = "Eduard Fomin", title = "A Simple Approach to the Reconstruction of a Set of Points from the Multiset of $ n^2 $ Pairwise Distances in $ n^2 $ Steps for the Sequencing Problem: {II.} Algorithm", journal = j-J-COMPUT-BIOL, volume = "23", number = "12", pages = "934--942", month = dec, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0046", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0046; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0046", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 June 2016", } @Article{Guo:2016:EER, author = "Qiang-Hui Guo and Lisa H. Sun and Jian Wang", title = "Enumeration of Extended $m$-Regular Linear Stacks", journal = j-J-COMPUT-BIOL, volume = "23", number = "12", pages = "943--956", month = dec, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0041", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0041; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0041", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 June 2016", } @Article{Deandres-Galiana:2016:IMP, author = "Enrique J. Deandr{\'e}s-Galiana and Juan Luis Fern{\'a}ndez-Mart{\'\i}nez and Leorey N. Saligan and Stephen T. Sonis", title = "Impact of Microarray Preprocessing Techniques in Unraveling Biological Pathways", journal = j-J-COMPUT-BIOL, volume = "23", number = "12", pages = "957--968", month = dec, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0042", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0042; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0042", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 August 2016", } @Article{Johnston:2016:PDP, author = "Sean B. Johnston and Ronald T. Raines", title = "{PTENpred}: a Designer Protein Impact Predictor for {PTEN-related} Disorders", journal = j-J-COMPUT-BIOL, volume = "23", number = "12", pages = "969--975", month = dec, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0058", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0058; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0058", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 June 2016", } @Article{Pirro:2016:BPE, author = "Stefano Pirr{\`o} and Antonella Minutolo and Andrea Galgani and Marina Potest{\`a} and Vittorio Colizzi and Carla Montesano", title = "Bioinformatics Prediction and Experimental Validation of {MicroRNAs} Involved in Cross-Kingdom Interaction", journal = j-J-COMPUT-BIOL, volume = "23", number = "12", pages = "976--989", month = dec, year = "2016", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0059", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:42 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0059; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0059", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 July 2016", } @Article{He:2017:PSA, author = "Jing He and Nurit Haspel and Brian Chen", title = "Preface: Selected Articles from {2015 Computational Structural Bioinformatics Workshop}", journal = j-J-COMPUT-BIOL, volume = "24", number = "1", pages = "1--1", month = jan, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.29004.jh", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.29004.jh", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 January 2017", } @Article{Cao:2017:UVL, author = "Hu Cao and Yonggang Lu", title = "Using Variable-Length Aligned Fragment Pairs and an Improved Transition Function for Flexible Protein Structure Alignment", journal = j-J-COMPUT-BIOL, volume = "24", number = "1", pages = "2--12", month = jan, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0135", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0135; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0135", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 October 2016", } @Article{Kim:2017:CVD, author = "Jin Seob Kim and Bijan Afsari and Gregory S. Chirikjian", title = "Cross-Validation of Data Compatibility Between Small Angle {X}-ray Scattering and Cryo-Electron Microscopy", journal = j-J-COMPUT-BIOL, volume = "24", number = "1", pages = "13--30", month = jan, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0139", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0139; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0139", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 October 2016", } @Article{Cheng:2017:GAM, author = "Wen Cheng and Changhui Yan", title = "A Graph Approach to Mining Biological Patterns in the Binding Interfaces", journal = j-J-COMPUT-BIOL, volume = "24", number = "1", pages = "31--39", month = jan, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0128", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0128; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0128", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 November 2016", } @Article{Farhoodi:2017:MLA, author = "Roshanak Farhoodi and Bahar Akbal-Delibas and Nurit Haspel", title = "Machine Learning Approaches for Predicting Protein Complex Similarity", journal = j-J-COMPUT-BIOL, volume = "24", number = "1", pages = "40--51", month = jan, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0137", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0137; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0137", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2016", } @Article{Zeil:2017:CAM, author = "Stephanie Zeil and Julio Kovacs and Willy Wriggers and Jing He", title = "Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix", journal = j-J-COMPUT-BIOL, volume = "24", number = "1", pages = "52--67", month = jan, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0145", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0145; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0145", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 December 2016", } @Article{Nolan:2017:IMS, author = "Bridget E. Nolan and Emily Levenson and Brian Y. Chen", title = "Influential Mutations in the {SMAD4} Trimer Complex Can Be Detected from Disruptions of Electrostatic Complementarity", journal = j-J-COMPUT-BIOL, volume = "24", number = "1", pages = "68--78", month = jan, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0162", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0162; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0162", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 January 2017", } @Article{Novinskaya:2017:DLD, author = "Anastasia Novinskaya and Didier Devaurs and Mark Moll and Lydia E. Kavraki", title = "Defining Low-Dimensional Projections to Guide Protein Conformational Sampling", journal = j-J-COMPUT-BIOL, volume = "24", number = "1", pages = "79--89", month = jan, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0144", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0144; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0144", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 November 2016", } @Article{Dediu:2017:PSA, author = "Adrian-Horia Dediu and Carlos Mart{\'\i}n-Vide", title = "Preface: Selected Articles of the {Second International Conference on Algorithms for Computational Biology (AlCoB 2015)}", journal = j-J-COMPUT-BIOL, volume = "24", number = "2", pages = "91--92", month = feb, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.29005.ahd", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.29005.ahd", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 February 2017", } @Article{Alexeev:2017:GHN, author = "Nikita Alexeev and Anna Pologova and Max A. Alekseyev", title = "Generalized {Hultman} Numbers and Cycle Structures of Breakpoint Graphs", journal = j-J-COMPUT-BIOL, volume = "24", number = "2", pages = "93--105", month = feb, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0190", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0190; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0190", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2017", } @Article{Jansson:2017:MPA, author = "Jesper Jansson and Ramesh Rajaby", title = "A More Practical Algorithm for the Rooted Triplet Distance", journal = j-J-COMPUT-BIOL, volume = "24", number = "2", pages = "106--126", month = feb, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 December 2016", } @Article{Zeira:2017:SCJ, author = "Ron Zeira and Ron Shamir", title = "Sorting by Cuts, Joins, and Whole Chromosome Duplications", journal = j-J-COMPUT-BIOL, volume = "24", number = "2", pages = "127--137", month = feb, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0045", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0045; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0045", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 October 2016", } @Article{Park:2017:IBF, author = "Heewon Park and Atsushi Niida and Seiya Imoto and Satoru Miyano", title = "Interaction-Based Feature Selection for Uncovering Cancer Driver Genes Through Copy Number-Driven Expression Level", journal = j-J-COMPUT-BIOL, volume = "24", number = "2", pages = "138--152", month = feb, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0140", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0140; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0140", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 October 2016", } @Article{Allman:2017:SCM, author = "Elizabeth S. Allman and John A. Rhodes and Seth Sullivant", title = "Statistically Consistent $k$-mer Methods for Phylogenetic Tree Reconstruction", journal = j-J-COMPUT-BIOL, volume = "24", number = "2", pages = "153--171", month = feb, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0216", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0216; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0216", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2016", } @Article{Tian:2017:IGI, author = "Xin Tian and Mingyuan Xin and Jian Luo and Mingyao Liu and Zhenran Jiang", title = "Identification of Genes Involved in Breast Cancer Metastasis by Integrating Protein--Protein Interaction Information with Expression Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "2", pages = "172--182", month = feb, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0206", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0206; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0206", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2016", } @Article{Zhou:2017:EPR, author = "Jie Zhou", title = "Effect of Protein Repetitiveness on Protein--Protein Interaction Prediction Results Using Support Vector Machines", journal = j-J-COMPUT-BIOL, volume = "24", number = "2", pages = "183--192", month = feb, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0233", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0233; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0233", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 August 2016", } @Article{Wilczynski:2017:FIT, author = "Bartek Wilczynski and Jerzy Tiuryn", title = "{FastBill}: an Improved Tool for Prediction of {{\em Cis\/}}-Regulatory Modules", journal = j-J-COMPUT-BIOL, volume = "24", number = "3", pages = "193--199", month = mar, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0108; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0108", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 October 2016", } @Article{Prakash:2017:ECM, author = "Celine Prakash and Arndt {Von Haeseler}", title = "An Enumerative Combinatorics Model for Fragmentation Patterns in {RNA} Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile", journal = j-J-COMPUT-BIOL, volume = "24", number = "3", pages = "200--212", month = mar, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0096; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0096", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 September 2016", } @Article{Budden:2017:CTI, author = "David Budden and Mitchell Jones", title = "Cautionary Tales of Inapproximability", journal = j-J-COMPUT-BIOL, volume = "24", number = "3", pages = "213--216", month = mar, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0097", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0097; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0097", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 September 2016", } @Article{Zhang:2017:OOM, author = "Li Zhang and Han Wang and Lun Yan and Lingtao Su and Dong Xu", title = "{OMPcontact}: an Outer Membrane Protein Inter-Barrel Residue Contact Prediction Method", journal = j-J-COMPUT-BIOL, volume = "24", number = "3", pages = "217--228", month = mar, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2015.0236", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2015.0236; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2015.0236", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 August 2016", } @Article{Cole:2017:NMS, author = "Marc Cole and Steffen Eikenberry and Takahide Kato and Roman A. Sandler and Stanley M. Yamashiro and Vasilis Z. Marmarelis", title = "Nonparametric Model of Smooth Muscle Force Production During Electrical Stimulation", journal = j-J-COMPUT-BIOL, volume = "24", number = "3", pages = "229--237", month = mar, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0070", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0070; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0070", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 August 2016", } @Article{Gigrich:2017:NAA, author = "James Gigrich and Shahryar Sarkani and Thomas Holzer", title = "A New Approach in Applying Systems Engineering Tools and Analysis to Determine Hepatocyte Toxicogenomics Risk Levels to Human Health", journal = j-J-COMPUT-BIOL, volume = "24", number = "3", pages = "238--254", month = mar, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2016", } @Article{Borguesan:2017:NSN, author = "Bruno Borguesan and Mario Inostroza-Ponta and M{\'a}rcio Dorn", title = "{NIAS-Server}: Neighbors Influence of Amino acids and Secondary Structures in Proteins", journal = j-J-COMPUT-BIOL, volume = "24", number = "3", pages = "255--265", month = mar, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0074", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:49 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0074; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0074", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 August 2016", } @Article{Sverdlov:2017:CME, author = "Serge Sverdlov and Elizabeth Thompson", title = "Combinatorial Methods for Epistasis and Dominance", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "267--279", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0112", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0112; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0112", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 November 2016", } @Article{Al-Okaily:2017:TBC, author = "Anas Al-Okaily and Badar Almarri and Sultan {Al Yami} and Chun-Hsi Huang", title = "Toward a Better Compression for {DNA} Sequences Using {Huffman} Encoding", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "280--288", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/datacompression.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 December 2016", } @Article{Yang:2017:DHH, author = "Doo Yang and Ilya Ioshikhes", title = "\bioname{Drosophila} {H2A} and {H2A.Z} Nucleosome Sequences Reveal Different Nucleosome Positioning Sequence Patterns", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "289--298", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 December 2016", } @Article{Yang:2017:MGR, author = "Lianping Yang and Weilin Zhang", title = "A Multiresolution Graphical Representation for Similarity Relationship and Multiresolution Clustering for Biological Sequences", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "299--310", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0030", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0030; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0030", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 December 2016", } @Article{Jonsson:2017:VMC, author = "Viktor Jonsson and Tobias {\"O}sterlund and Olle Nerman and Erik Kristiansson", title = "Variability in Metagenomic Count Data and Its Influence on the Identification of Differentially Abundant Genes", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "311--326", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0180", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0180; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0180", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 November 2016", } @Article{Venkat:2017:BNB, author = "Priya S. Venkat and Krishna R. Narayanan and Aniruddha Datta", title = "A {Bayesian} Network-Based Approach to Selection of Intervention Points in the Mitogen-Activated Protein Kinase Plant Defense Response Pathway", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "327--339", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0089", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0089; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0089", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 September 2016", } @Article{Gogoshin:2017:NAS, author = "Grigoriy Gogoshin and Eric Boerwinkle and Andrei S. Rodin", title = "New Algorithm and Software {(BNOmics)} for Inferring and Visualizing {Bayesian} Networks from Heterogeneous Big Biological and Genetic Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "340--356", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0100; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0100", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2016", } @Article{Jakaitiene:2017:BBM, author = "Audrone Jakaitiene and Mariano Avino and Mario Rosario Guarracino", title = "Beta-Binomial Model for the Detection of Rare Mutations in Pooled Next-Generation Sequencing Experiments", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "357--367", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0106", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0106; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0106", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 September 2016", } @Article{Wang:2017:RFA, author = "Ying Wang and Haiyan Hu and Xiaoman Li", title = "{rRNAFilter}: a Fast Approach for Ribosomal {RNA} Read Removal Without a Reference Database", journal = j-J-COMPUT-BIOL, volume = "24", number = "4", pages = "368--375", month = apr, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:51 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2016", } @Article{Dhar:2017:CHO, author = "Amrit Dhar and Vladimir N. Minin", title = "Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time", journal = j-J-COMPUT-BIOL, volume = "24", number = "5", pages = "377--399", month = may, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0172; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 February 2017", } @Article{Lee:2017:SPR, author = "Gira Lee and Hokeun Sun", title = "Selection Probability for Rare Variant Association Studies", journal = j-J-COMPUT-BIOL, volume = "24", number = "5", pages = "400--411", month = may, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0222", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0222; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0222", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2017", } @Article{Yanev:2017:PFP, author = "Nicola Yanev and Metodi Traykov and Peter Milanov and Borislav Yurukov", title = "Protein Folding Prediction in a Cubic Lattice in Hydrophobic-Polar Model", journal = j-J-COMPUT-BIOL, volume = "24", number = "5", pages = "412--421", month = may, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0181", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0181; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0181", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 November 2016", } @Article{Bogdanowicz:2017:CPT, author = "Damian Bogdanowicz and Krzysztof Giaro", title = "Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions", journal = j-J-COMPUT-BIOL, volume = "24", number = "5", pages = "422--435", month = may, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0204", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0204; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0204", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 February 2017", } @Article{Yang:2017:PAM, author = "Sihai Yang and Xianhua Han and Yukako Tohsato and Koji Kyoda and Shuichi Onami and Ikuko Nishikawa and Yenwei Chen", title = "Phenotype Analysis Method for Identification of Gene Functions Involved in Asymmetric Division of \bioname{Caenorhabditis elegans}", journal = j-J-COMPUT-BIOL, volume = "24", number = "5", pages = "436--446", month = may, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0210", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0210; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0210", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 February 2017", } @Article{Barrios:2017:DIG, author = "David Barrios and Carlos Prieto", title = "{D3GB}: an Interactive Genome Browser for {R}, {Python}, and {WordPress}", journal = j-J-COMPUT-BIOL, volume = "24", number = "5", pages = "447--449", month = may, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0213", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/python.bib; https://www.math.utah.edu/pub/tex/bib/s-plus.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0213; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0213", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 February 2017", } @Article{Tran:2017:CBM, author = "Ngoc Tam L. Tran and Chun-Hsi Huang", title = "Cloud-based {MOTIFSIM}: Detecting Similarity in Large {DNA} Motif Data Sets", journal = j-J-COMPUT-BIOL, volume = "24", number = "5", pages = "450--459", month = may, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0080", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0080; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0080", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 September 2016", } @Article{Anand:2017:EGI, author = "Rajat Anand and Samrat Chatterjee", title = "Extracting Genes Involved in Disease from a Connected Network of Perturbed Biological Processes", journal = j-J-COMPUT-BIOL, volume = "24", number = "5", pages = "460--469", month = may, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0090", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:53 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0090; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0090", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 March 2017", } @Article{Anonymous:2017:PSP, author = "Anonymous", title = "Preface: Selected Papers from {RECOMB 2016}", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "471--471", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.29006.ms", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.29006.ms", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 June 2017", } @Article{Zuo:2017:MBA, author = "Chandler Zuo and Kailei Chen and S{\"u}nd{\"u}z Kele{\c{s}}", title = "A {MAD-Bayes} Algorithm for State-Space Inference and Clustering with Application to Querying Large Collections of {ChIP-Seq} Data Sets", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "472--485", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0138", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0138; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0138", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 November 2016", } @Article{Wang:2017:ARR, author = "Hao Wang and Joel McManus and Carl Kingsford", title = "Accurate Recovery of Ribosome Positions Reveals Slow Translation of Wobble-Pairing Codons in Yeast", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "486--500", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0147", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0147; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0147", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 October 2016", } @Article{Kshirsagar:2017:MMC, author = "Meghana Kshirsagar and Keerthiram Murugesan and Jaime G. Carbonell and Judith Klein-Seetharaman", title = "Multitask Matrix Completion for Learning Protein Interactions Across Diseases", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "501--514", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0201", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0201; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0201", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 January 2017", } @Article{Donmez:2017:CIS, author = "Nilgun Donmez and Salem Malikic and Alexander W. Wyatt and Martin E. Gleave and Colin C. Collins and S. Cenk Sahinalp", title = "Clonality Inference from Single Tumor Samples Using Low-Coverage Sequence Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "515--523", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0148", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0148; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0148", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 January 2017", } @Article{Fusi:2017:FMG, author = "Nicolo Fusi and Jennifer Listgarten", title = "Flexible Modeling of Genetic Effects on Function-Valued Traits", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "524--535", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0174", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0174; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0174", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 January 2017", } @Article{Hallen:2017:LLU, author = "Mark A. Hallen and Jonathan D. Jou and Bruce R. Donald", title = "{LUTE} (Local Unpruned Tuple Expansion): Accurate Continuously Flexible Protein Design with General Energy Functions and Rigid Rotamer-Like Efficiency", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "536--546", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0136", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0136; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0136", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2016", } @Article{Pellow:2017:IBF, author = "David Pellow and Darya Filippova and Carl Kingsford", title = "Improving {Bloom} Filter Performance on Sequence Data Using $k$-mer {Bloom} Filters", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "547--557", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0155", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0155; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0155", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 November 2016", } @Article{Artyomenko:2017:LSM, author = "Alexander Artyomenko and Nicholas C. Wu and Serghei Mangul and Eleazar Eskin and Ren Sun and Alex Zelikovsky", title = "Long Single-Molecule Reads Can Resolve the Complexity of the Influenza Virus Composed of Rare, Closely Related Mutant Variants", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "558--570", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0146", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0146; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0146", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 November 2016", } @Article{Shao:2017:CBD, author = "Mingfu Shao and Bernard M. E. Moret", title = "On Computing Breakpoint Distances for Genomes with Duplicate Genes", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "571--580", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0149; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0149", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 October 2016", } @Article{Sahlin:2017:SVD, author = "Kristoffer Sahlin and Mattias Fr{\aa}nberg and Lars Arvestad", title = "Structural Variation Detection with Read Pair Information: an Improved Null Hypothesis Reduces Bias", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "581--589", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0124", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0124; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0124", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2016", } @Article{Tomescu:2017:SCC, author = "Alexandru I. Tomescu and Paul Medvedev", title = "Safe and Complete Contig Assembly Through Omnitigs", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "590--602", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0141", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0141; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0141", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2016", } @Article{Cristea:2017:PJI, author = "Simona Cristea and Jack Kuipers and Niko Beerenwinkel", title = "{pathTiMEx}: Joint Inference of Mutually Exclusive Cancer Pathways and Their Progression Dynamics", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "603--615", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0171", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0171; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0171", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 December 2016", } @Article{Doerr:2017:NGS, author = "Daniel Doerr and Luis Antonio B. Kowada and Eloi Araujo and Shachi Deshpande and Simone Dantas and Bernard M. E. Moret and Jens Stoye", title = "New Genome Similarity Measures based on Conserved Gene Adjacencies", journal = j-J-COMPUT-BIOL, volume = "24", number = "6", pages = "616--634", month = jun, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0065", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0065; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0065", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 June 2017", } @Article{Huang:2017:SIS, author = "Haiyan Huang and Hua Tang and Jing Huang and Bin Chen and Ruixiao Liu and Rui (Sammi) Tang and Ying Lu and Peng Yang", title = "Special Issue: Selected Papers of the {Inaugural DahShu Data Science Symposium: Computational Precision Health (CPH 2017)}", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "635--636", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.29007.hh", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.29007.hh", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2017", } @Article{Hao:2017:RFD, author = "Yangyang Hao and Xiaoling Xuei and Lang Li and Harikrishna Nakshatri and Howard J. Edenberg and Yunlong Liu", title = "{RareVar}: a Framework for Detecting Low-Frequency Single-Nucleotide Variants", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "637--646", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0057", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0057; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0057", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2017", } @Article{Ma:2017:JBM, author = "Tianzhou Ma and Faming Liang and Steffi Oesterreich and George C. Tseng", title = "A Joint {Bayesian} Model for Integrating Microarray and {RNA} Sequencing Transcriptomic Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "647--662", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0056", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0056; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0056", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2017", } @Article{Shi:2017:ICS, author = "Funan Shi and Haiyan Huang", title = "Identifying Cell Subpopulations and Their Genetic Drivers from Single-Cell {RNA-Seq} Data Using a Biclustering Approach", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "663--674", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0049", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0049; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0049", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2017", } @Article{Clifton:2017:HSM, author = "Sara M. Clifton and Chaeryon Kang and Jingyi Jessica Li and Qi Long and Nirmish Shah and Daniel M. Abrams", title = "Hybrid Statistical and Mechanistic Mathematical Model Guides Mobile Health Intervention for Chronic Pain", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "675--688", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0059", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0059; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0059", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 June 2017", } @Article{Yang:2017:SCA, author = "Hu Yang and Xiaoqin Liu", title = "Studies on the Clustering Algorithm for Analyzing Gene Expression Data with a Bidirectional Penalty", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "689--698", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0051", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0051; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0051", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 May 2017", } @Article{Fang:2017:GCD, author = "Huaying Fang and Chengcheng Huang and Hongyu Zhao and Minghua Deng", title = "{gCoda}: Conditional Dependence Network Inference for Compositional Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "699--708", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0054", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0054; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0054", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 May 2017", } @Article{Lee:2017:CTS, author = "Minhyeok Lee and Junhee Seok and Donghyun Tae and Hua Zhong and Sung Won Han", title = "A Comparison of Two-Stage Approaches Based on Penalized Regression for Estimating Gene Networks", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "709--720", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0052", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0052; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0052", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 May 2017", } @Article{Choi:2017:PLN, author = "Yoonha Choi and Marc Coram and Jie Peng and Hua Tang", title = "A {Poisson} Log-Normal Model for Constructing Gene Covariation Network Using {RNA-seq} Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "7", pages = "721--731", month = jul, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0053", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:52:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0053; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0053", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 May 2017", } @Article{Diallo:2017:PSP, author = "Abdoulaye Banir{\'e} Diallo and Engelbert Mephu Nguifo and Mohammed J. Zaki", title = "Preface: Selected Papers from the {Workshop Bioinformatics and Artificial Intelligence Joined with the International Joint Conference on Artificial Intelligence}", journal = j-J-COMPUT-BIOL, volume = "24", number = "8", pages = "733--733", month = aug, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.29008.abd", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.29008.abd", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2017", } @Article{Picard:2017:LCP, author = "Vincent Picard and Anne Siegel and J{\'e}r{\'e}mie Bourdon", title = "A Logic for Checking the Probabilistic Steady-State Properties of Reaction Networks", journal = j-J-COMPUT-BIOL, volume = "24", number = "8", pages = "734--745", month = aug, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0099", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0099; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0099", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2017", } @Article{Alkhateeb:2017:ZAP, author = "Abedalrhman Alkhateeb and Luis Rueda", title = "Zseq: an Approach for Preprocessing Next-Generation Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "8", pages = "746--755", month = aug, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0021", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0021; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0021", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2017", } @Article{Firoozbakht:2017:IAI, author = "Forough Firoozbakht and Iman Rezaeian and Michele D'agnillo and Lisa Porter and Luis Rueda and Alioune Ngom", title = "An Integrative Approach for Identifying Network Biomarkers of Breast Cancer Subtypes Using Genomic, Interactomic, and Transcriptomic Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "8", pages = "756--766", month = aug, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0010", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0010; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0010", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 June 2017", } @Article{Vasiljeva:2017:DPE, author = "Ieva Vasiljeva and Ognjen Arandjelovi{\'c}", title = "Diagnosis Prediction from Electronic Health Records Using the Binary Diagnosis History Vector Representation", journal = j-J-COMPUT-BIOL, volume = "24", number = "8", pages = "767--786", month = aug, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0023; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0023", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2017", } @Article{Lam:2017:EVI, author = "Ham Ching Lam and Xuan Bi and Srinand Sreevatsan and Daniel Boley", title = "Evolution and Vaccination of Influenza Virus", journal = j-J-COMPUT-BIOL, volume = "24", number = "8", pages = "787--798", month = aug, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0025", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0025; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0025", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2017", } @Article{Halioui:2017:GDG, author = "Ahmed Halioui and Petko Valtchev and Abdoulaye Banir{\'e} Diallo", title = "{T-GOWler}: Discovering Generalized Process Models Within Texts", journal = j-J-COMPUT-BIOL, volume = "24", number = "8", pages = "799--808", month = aug, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0085", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0085; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0085", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2017", } @Article{DeSouzaJacomini:2017:GNF, author = "Ricardo {De Souza Jacomini} and David Correa {Martins, Jr.} and Felipe Leno {Da Silva} and Anna Helena {Reali Costa}", title = "{GeNICE}: a Novel Framework for Gene Network Inference by Clustering, Exhaustive Search, and Multivariate Analysis", journal = j-J-COMPUT-BIOL, volume = "24", number = "8", pages = "809--830", month = aug, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0022", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:00 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0022; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0022", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2017", } @Article{Disanto:2017:EAC, author = "Filippo Disanto and Noah A. Rosenberg", title = "Enumeration of Ancestral Configurations for Matching Gene Trees and Species Trees", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "831--850", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0159", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0159; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0159", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 April 2017", } @Article{Dai:2017:SST, author = "Zheng Dai and David Becerra and J{\'e}r{\^o}me Waldisp{\"u}hl", title = "On Stable States in a Topologically Driven Protein Folding Model", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "851--862", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0034", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0034; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0034", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2017", } @Article{Altarawy:2017:PIC, author = "Doaa Altarawy and Fatma-Elzahraa Eid and Lenwood S. Heath", title = "{PEAK}: Integrating Curated and Noisy Prior Knowledge in Gene Regulatory Network Inference", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "863--873", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0199", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0199; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0199", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 March 2017", } @Article{White:2017:AIA, author = "Daniel J. White and Jing Wang and Richard J. Hall", title = "Assessing the Impact of Assemblers on Virus Detection in a {De} {Novo} Metagenomic Analysis Pipeline", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "874--881", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2017", } @Article{Khanna:2017:DCA, author = "Radhika Khanna and Sangeeta Mittal and Sujata Mohanty", title = "Development of Computer Algorithm for Editing of Next Generation Sequencing Metagenome Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "882--894", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0179", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0179; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0179", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2017", } @Article{Tran:2017:MES, author = "Ngoc Tam L. Tran and Chun-Hsi Huang", title = "{MOTIFSIM 2.1}: an Enhanced Software Platform for Detecting Similarity in Multiple {DNA} Motif Data Sets", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "895--905", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0005", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0005; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0005", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2017", } @Article{Godin:2017:MPA, author = "Noa Godin and Jerry Eichler", title = "The Mitochondrial Protein Atlas: a Database of Experimentally Verified Information on the Human Mitochondrial Proteome", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "906--916", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0011", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0011; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0011", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2017", } @Article{Park:2017:PCA, author = "Byeonghyeok Park and Min-Jeong Baek and Byoungnam Min and In-Geol Choi", title = "Prokaryotic Contig Annotation Pipeline Server: {Web} Application for a Prokaryotic Genome Annotation Pipeline Based on the \pkg{Shiny App} Package", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "917--922", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0066", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0066; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0066", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2017", } @Article{Ma:2017:DCB, author = "Xiuli Ma and Guangyu Zhou and Jingbo Shang and Jingjing Wang and Jian Peng and Jiawei Han", title = "Detection of Complexes in Biological Networks Through Diversified Dense Subgraph Mining", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "923--941", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0037", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0037; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0037", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 June 2017", } @Article{Zheng:2017:ICA, author = "Yu Zheng and Xiaoyang Li and Lydia C. Manor and Hongbao Cao and Qiusheng Chen", title = "An Integrative Computational Approach to Evaluate Genetic Markers for Chronic Lymphocytic Leukemia", journal = j-J-COMPUT-BIOL, volume = "24", number = "9", pages = "942--952", month = sep, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0041", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:02 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0041; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0041", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 June 2017", } @Article{Bonizzoni:2017:FFS, author = "Paola Bonizzoni and Gianluca Della Vedova and Yuri Pirola and Marco Previtali and Raffaella Rizzi", title = "{FSG}: Fast String Graph Construction for {De} {Novo} Assembly", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "953--968", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0089", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0089; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0089", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 July 2017", } @Article{Balaur:2017:EGD, author = "Irina Balaur and Mansoor Saqi and Ana Barat and Artem Lysenko and Alexander Mazein and Christopher J. Rawlings and Heather J. Ruskin and Charles Auffray", title = "{EpiGeNet}: a Graph Database of Interdependencies Between Genetic and Epigenetic Events in Colorectal Cancer", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "969--980", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0095", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0095; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0095", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 September 2016", } @Article{Yang:2017:PSO, author = "Cheng-Hong Yang and Yu-Shiun Lin and Li-Yeh Chuang and Hsueh-Wei Chang", title = "A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "981--994", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0104", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0104; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0104", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2017", } @Article{Gonzalez-Perez:2017:CAS, author = "Pedro P. Gonz{\'a}lez-P{\'e}rez and Daniel J. Orta and Irving Pe{\~n}a and Eduardo C. Flores and Jos{\'e} U. Ram{\'\i}rez and Hiram I. Beltr{\'a}n and Salom{\'o}n J. Alas", title = "A Computational Approach to Studying Protein Folding Problems Considering the Crucial Role of the Intracellular Environment", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "995--1013", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0115; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0115", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 February 2017", } @Article{Milewski:2017:ENS, author = "Marek C. Milewski and Karol Kamel and Anna Kurzynska-Kokorniak and Marcin K. Chmielewski and Marek Figlerowicz", title = "{EvOligo}: a Novel Software to Design and Group Libraries of Oligonucleotides Applicable for Nucleic Acid-Based Experiments", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "1014--1028", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0154", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0154; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0154", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 March 2017", } @Article{Thomas:2017:ERT, author = "Lebin Thomas and Hari Ram and Ved Pal Singh", title = "Evolutionary Relationships and Taxa-Specific Conserved Signature Indels Among Cellulases of Archaea, Bacteria, and Eukarya", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "1029--1042", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0161", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0161; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0161", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 February 2017", } @Article{Kadumuri:2017:LGU, author = "Rajashekar Varma Kadumuri and Ramakrishna Vadrevu", title = "{LoopX}: a Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "1043--1049", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 April 2017", } @Article{Ai:2017:PPP, author = "Haixin Ai and Runlin Wu and Li Zhang and Xuewei Wu and Junchao Ma and Huan Hu and Liangchao Huang and Wen Chen and Jian Zhao and Hongsheng Liu", title = "{pSuc-PseRat}: Predicting {Lysine} Succinylation in Proteins by Exploiting the Ratios of Sequence Coupling and Properties", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "1050--1059", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0206", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0206; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0206", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2017", } @Article{Deng:2017:GWS, author = "Feilong Deng and Shi-Yi Chen and Zhou-Lin Wu and Yongsong Hu and Xianbo Jia and Song-Jia Lai", title = "{GFFview}: a {Web} Server for Parsing and Visualizing Annotation Information of Eukaryotic Genome", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "1060--1064", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0216", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0216; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0216", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 March 2017", } @Article{Krupska:2017:IOE, author = "Aldona Krupska", title = "Influence of Oscillatory Enzyme Activity on the Reaction Kinetics: Mathematical Model", journal = j-J-COMPUT-BIOL, volume = "24", number = "10", pages = "1065--1070", month = oct, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0001", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:04 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0001; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0001", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2017", } @Article{Castro:2017:UNM, author = "Christina J. Castro and Terry Fei Fan Ng", title = "{U$_{50}$}: a New Metric for Measuring Assembly Output Based on Non-Overlapping, Target-Specific Contigs", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1071--1080", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0013", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0013; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0013", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 April 2017", } @Article{Sagiroglu:2017:SAE, author = "Mahmut {\c{S}}am{\.i}l Sa{\u{g}}iro{\u{g}}lu and M. O{\u{g}}uzhan K{\"u}lekc{\.i}", title = "A System Architecture for Efficient Transmission of Massive {DNA} Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1081--1088", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0016", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0016; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0016", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2017", } @Article{Blazej:2017:RSS, author = "Pawe{\l} B{\l}a{\.z}ej and Ma{\l}gorzata Wn{\k{e}}trzak and Ma{\l}gorzata Grabi{\'n}ska and Pawe{\l} Mackiewicz", title = "Representations of Search Spaces in the Problem of Mutational Pressure Optimization According to Protein-Coding Sequences", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1089--1098", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0017", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0017; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0017", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2017", } @Article{Zhou:2017:GRN, author = "Yan Zhou and Baoxue Zhang and Gaorong Li and Tiejun Tong and Xiang Wan", title = "{GD-RDA}: a New Regularized Discriminant Analysis for High-Dimensional Data", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1099--1111", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0029", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0029; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0029", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2017", } @Article{Lv:2017:ATF, author = "Shengqing Lv and Yimin Chen and Zeyu Li and Jiahui Lu and Mingke Gao and Rongrong Lu", title = "Application of Time-Frequency Domain Transform to Three-Dimensional Interpolation of Medical Images", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1112--1124", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0038", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0038; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0038", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2017", } @Article{Barros-Carvalho:2017:EAE, author = "Gesiele Almeida Barros-Carvalho and Marie-Anne {Van Sluys} and Fabricio Martins Lopes", title = "An Efficient Approach to Explore and Discriminate Anomalous Regions in Bacterial Genomes Based on Maximum Entropy", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1125--1133", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0042", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0042; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0042", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 June 2017", } @Article{Cerisier:2017:CVL, author = "Natacha Cerisier and Leslie Regad and Dhoha Triki and Anne-Claude Camproux and Michel Petitjean", title = "Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1134--1137", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0061", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0061; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0061", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 June 2017", } @Article{Kechin:2017:CNT, author = "Andrey Kechin and Uljana Boyarskikh and Alexander Kel and Maxim Filipenko", title = "{cutPrimers}: a New Tool for Accurate Cutting of Primers from Reads of Targeted Next Generation Sequencing", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1138--1143", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0096; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0096", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 July 2017", } @Article{Rubio-Largo:2017:RAT, author = "{\'A}lvaro Rubio-Largo and Leonardo Vanneschi and Mauro Castelli and Miguel A. Vega-Rodr{\'\i}guez", title = "Reducing Alignment Time Complexity of Ultra-Large Sets of Sequences", journal = j-J-COMPUT-BIOL, volume = "24", number = "11", pages = "1144--1152", month = nov, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0097", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:07 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0097; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0097", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 July 2017", } @Article{Sakhanenko:2017:ICD, author = "Nikita A. Sakhanenko and James Kunert-Graf and David J. Galas", title = "The Information Content of Discrete Functions and Their Application in Genetic Data Analysis", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1153--1178", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0143; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 October 2017", } @Article{Zeira:2017:LTA, author = "Ron Zeira and Meirav Zehavi and Ron Shamir", title = "A Linear-Time Algorithm for the Copy Number Transformation Problem", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1179--1194", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0060", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0060; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0060", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 August 2017", } @Article{Chen:2017:AWP, author = "Wenbin Chen and William Hendrix and Nagiza F. Samatova", title = "The Application of the Weighted $k$-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1195--1211", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0064; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0064", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 September 2017", } @Article{Yang:2017:JAS, author = "Cheng-Hong Yang and Yu-Da Lin and Li-Yeh Chuang and Jin-Bor Chen and Hsueh-Wei Chang", title = "Joint Analysis of {SNP--SNP-Environment} Interactions for Chronic Dialysis by an Improved Branch and Bound Algorithm", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1212--1225", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0090", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0090; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0090", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 September 2017", } @Article{Elmarakeby:2017:BEC, author = "Haitham Elmarakeby and Mostafa Arefiyan and Elijah Myers and Song Li and Ruth Grene and Lenwood S. Heath", title = "{Beacon Editor}: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1226--1229", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0095", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0095; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0095", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 August 2017", } @Article{Su:2017:MSA, author = "Wenhe Su and Xiangke Liao and Yutong Lu and Quan Zou and Shaoliang Peng", title = "Multiple Sequence Alignment Based on a Suffix Tree and Center-Star Strategy: a Linear Method for Multiple Nucleotide Sequence Alignment on {Spark} Parallel Framework", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1230--1242", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0040", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0040; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0040", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2017", } @Article{Pei:2017:GCP, author = "Chao Pei and Shu-Lin Wang and Jianwen Fang and Wei Zhang", title = "{GSMC}: Combining Parallel {Gibbs} Sampling with Maximal Cliques for Hunting {DNA} Motif", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1243--1253", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0100; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0100", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2017", } @Article{Tsai:2017:ESM, author = "Shin-Fu Tsai and Chih-Wei Tung and Chen-An Tsai and Chen-Tuo Liao", title = "An Exhaustive Scan Method for {SNP} Main Effects and {SNP $ \times $ SNP} Interactions Over Highly Homozygous Genomes", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1254--1264", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0140", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0140; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0140", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 November 2017", } @Article{Shrestha:2017:GED, author = "Samana Shrestha and Adam Vanasse and Leon N. Cooper and Michael P. Antosh", title = "Gene Expression as a Dosimeter in Irradiated \bioname{Drosophila melanogaster}", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1265--1274", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0170", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0170; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0170", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 October 2017", } @Article{Shahinuzzaman:2017:MAS, author = "Md Shahinuzzaman and Dipak Barua", title = "A Multiscale Algorithm for Spatiotemporal Modeling of Multivalent Protein--Protein Interaction", journal = j-J-COMPUT-BIOL, volume = "24", number = "12", pages = "1275--1283", month = dec, year = "2017", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0178", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:09 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0178; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0178", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 November 2017", } @Article{He:2018:SIP, author = "Jing He and Kamal {Al Nasr} and Weitao Sun and Yonggang Lu", title = "{{\em Special Issue\/}} Preface: The {9th Computational Structural Bioinformatics Workshop}", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "1--2", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.29010.jh", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.29010.jh", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 January 2018", } @Article{Abella:2018:MED, author = "Jayvee R. Abella and Mark Moll and Lydia E. Kavraki", title = "Maintaining and Enhancing Diversity of Sampled Protein Conformations in Robotics-Inspired Methods", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "3--20", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0164", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0164; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0164", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 October 2017", } @Article{AlNasr:2018:PFC, author = "Kamal {Al Nasr} and Christopher Jones and Feras Yousef and Ruba Jebril", title = "{\em {{PEM-fitter}}\/}: a Coarse-Grained Method to Validate Protein Candidate Models", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "21--32", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0191", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0191; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0191", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 November 2017", } @Article{Maximova:2018:SBM, author = "Tatiana Maximova and Zijing Zhang and Daniel B. Carr and Erion Plaku and Amarda Shehu", title = "Sample-Based Models of Protein Energy Landscapes and Slow Structural Rearrangements", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "33--50", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0158", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0158; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0158", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 November 2017", } @Article{Clement:2018:VCA, author = "Nathan Clement and Muhibur Rasheed and Chandrajit Lal Bajaj", title = "Viral Capsid Assembly: a Quantified Uncertainty Approach", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "51--71", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0218", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0218; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0218", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 January 2018", } @Article{Kim:2018:SPR, author = "Jin Seob Kim and Gregory S. Chirikjian", title = "Symmetrical Parameterization of Rigid Body Transformations for Biomolecular Structures", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "72--88", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0166", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0166; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0166", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 November 2017", } @Article{Siderius:2018:MSM, author = "Michael Siderius and Filip Jagodzinski", title = "Mutation Sensitivity Maps: Identifying Residue Substitutions That Impact Protein Structure Via a Rigidity Analysis In Silico Mutation Approach", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "89--102", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 October 2017", } @Article{Sun:2018:RBL, author = "Weitao Sun", title = "The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "103--113", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0171", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0171; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0171", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 September 2017", } @Article{Islam:2018:QTC, author = "Tunazzina Islam and Michael Poteat and Jing He", title = "Quantification of Twist from the Central Lines of $ \beta $-Strands", journal = j-J-COMPUT-BIOL, volume = "25", number = "1", pages = "114--120", month = jan, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0174", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:12 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0174; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0174", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 January 2018", } @Article{Altschul:2018:ICA, author = "Stephen F. Altschul and Andrew F. Neuwald", title = "Initial Cluster Analysis", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "121--129", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0050", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0050; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0050", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 August 2017", } @Article{Park:2018:ANI, author = "Heewon Park and Teppei Shimamura and Seiya Imoto and Satoru Miyano", title = "Adaptive {NetworkProfiler} for Identifying Cancer Characteristic-Specific Gene Regulatory Networks", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "130--145", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0120", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0120; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0120", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 October 2017", } @Article{He:2018:ALM, author = "Jin-Hua He and Ze-Ping Han and Mao-Xian Zou and Li Wang and Yu Bing Lv and Jia Bin Zhou and Ming-Rong Cao and Yu-Guang Li", title = "Analyzing the {LncRNA}, {miRNA}, and {mRNA} Regulatory Network in Prostate Cancer with Bioinformatics Software", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "146--157", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0093", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0093; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0093", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 August 2017", } @Article{Yang:2018:CTL, author = "Cheng-Hong Yang and Yi-Cheng Chiang and Li-Yeh Chuang and Yu-Da Lin", title = "A {CpGCluster-Teaching--Learning-Based} Optimization for Prediction of {CpG} Islands in the Human Genome", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "158--169", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2016.0178", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2016.0178; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2016.0178", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 October 2017", } @Article{Morad:2018:SAI, author = "Fatima A. Morad and Omran M. Rashidi and Saida S. Sadath and Faisal A. Al-Allaf and Mohammad Athar and Mohamed N. Alama and Sherif E. Edris and Nabeel S. Bondagji and Noor A. Shaik and Babajan Banaganapalli and Zuhier Awan", title = "In Silico Approach to Investigate the Structural and Functional Attributes of Familial Hypercholesterolemia Variants Reported in the {Saudi} Population", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "170--181", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0018", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0018; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0018", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 November 2017", } @Article{Rahman:2018:HNA, author = "Mohammad S. Rahman and Ann E. Nicholson and Gholamreza Haffari", title = "{HetFHMM}: a Novel Approach to Infer Tumor Heterogeneity Using Factorial Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "182--193", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0101; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0101", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 October 2017", } @Article{Costa:2018:MGF, author = "Evaldo Bezerra Costa", title = "{MELC} Genomics: a Framework for {De} {Novo} Genome Assembly", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "194--199", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0102; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0102", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2017", } @Article{Vilaplana:2018:MED, author = "Jordi Vilaplana and Rui Alves and Francesc Solsona and Jordi Mateo and Ivan Teixid{\'o} and Marc Pifarr{\'e}", title = "{MetReS}, an Efficient Database for Genomic Applications", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "200--213", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2017", } @Article{Benshahar:2018:BAR, author = "Arnon Benshahar and Vered Chalifa-Caspi and Danny Hermelin and Michal Ziv-Ukelson", title = "A Biclique Approach to Reference-Anchored Gene Blocks and Its Applications to Genomic Islands", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "214--235", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0108; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0108", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 October 2017", } @Article{Kanj:2018:SNN, author = "Sawsan Kanj and Thomas Br{\"u}ls and St{\'e}phane Gazut", title = "Shared Nearest Neighbor Clustering in a Locality Sensitive Hashing Framework", journal = j-J-COMPUT-BIOL, volume = "25", number = "2", pages = "236--250", month = feb, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:14 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/hash.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 September 2017", } @Article{Cai:2018:SIP, author = "Zhipeng Cai and Pavel Skums and Alexander Zelikovsky", title = "{{\em Special Issue\/}} Preface: {13th International Symposium on Bioinformatics Research and Applications (ISBRA 2017)}", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "251--252", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.29012.zc", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.29012.zc", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 March 2018", } @Article{Chang:2018:ROA, author = "Kuang-Yu Chang and Yun Cui and Siu-Ming Yiu and Wing-Kai Hon", title = "Reconstructing One-Articulated Networks with Distance Matrices", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "253--269", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0148", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0148; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0148", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 October 2017", } @Article{Wang:2018:IMI, author = "Zihao Wang and Yu Chen and Jingrong Zhang and Lun Li and Xiaohua Wan and Zhiyong Liu and Fei Sun and Fa Zhang", title = "{ICON-MIC}: Implementing a {CPU\slash MIC} Collaboration Parallel Framework for {ICON} on {Tianhe-2} Supercomputer", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "270--281", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/super.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2017", } @Article{Ciach:2018:ERR, author = "Micha{\l} Aleksander Ciach and Mateusz Krzysztof {\L}{\k{a}}cki and B{\l}a{\.z}ej Miasojedow and Frederik Lermyte and Dirk Valkenborg and Frank Sobott and Anna Gambin", title = "Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "282--301", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0156; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0156", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 September 2017", } @Article{Xia:2018:MSP, author = "Ruofan Xia and Yu Lin and Jun Zhou and Bing Feng and Jijun Tang", title = "A Median Solver and Phylogenetic Inference Based on Double-Cut-and-Join Sorting", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "302--312", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0157", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0157; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0157", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 October 2017", } @Article{Mishra:2018:CNN, author = "Rashika Mishra and Ovidiu Daescu and Patrick Leavey and Dinesh Rakheja and Anita Sengupta", title = "Convolutional Neural Network for Histopathological Analysis of Osteosarcoma", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "313--325", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0153", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0153; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0153", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2017", } @Article{Ng:2018:BBD, author = "Albert Ng and Dong Si", title = "Beta-Barrel Detection for Medium Resolution Cryo-Electron Microscopy Density Maps Using Genetic Algorithms and Ray Tracing", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "326--336", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0155", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0155; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0155", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 October 2017", } @Article{Xiao:2018:OMB, author = "Xiuchun Xiao and Bing Liu and Jing Zhang and Xueli Xiao and Yi Pan", title = "An Optimized Method for {Bayesian} Connectivity Change Point Model", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "337--347", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0154", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0154; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0154", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2017", } @Article{Fosso:2018:UTA, author = "Bruno Fosso and Graziano Pesole and Francesc Rossell{\'o} and Gabriel Valiente", title = "Unbiased Taxonomic Annotation of Metagenomic Samples", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "348--360", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0144", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0144; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0144", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 October 2017", } @Article{Wang:2018:CBM, author = "Lei Wang and Zhu-Hong You and Xing Chen and Shi-Xiong Xia and Feng Liu and Xin Yan and Yong Zhou and Ke-Jian Song", title = "A Computational-Based Method for Predicting Drug-Target Interactions by Using Stacked Autoencoder Deep Neural Network", journal = j-J-COMPUT-BIOL, volume = "25", number = "3", pages = "361--373", month = mar, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0135", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:16 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0135; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0135", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 September 2017", } @Article{Jelovic:2018:FSS, author = "Ana M. Jelovic and Nenad S. Mitic and Samira Eshafah and Milos V. Beljanski", title = "Finding Statistically Significant Repeats in Nucleic Acids and Proteins", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "375--387", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0046", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0046; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0046", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 December 2017", } @Article{Wang:2018:SFS, author = "Hong Wang and Xiaolin Chen and Gang Li", title = "Survival Forests with {$R$}-Squared Splitting Rules", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "388--395", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0107", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0107; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0107", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 December 2017", } @Article{Li:2018:MMH, author = "Lingling Li and Tianhai Tian and Xinan Zhang", title = "Mutation Mechanisms of Human Breast Cancer", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "396--404", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0111", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0111; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0111", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 December 2017", } @Article{Huang:2018:NRT, author = "Hsin-Hsiung Huang and Senthil B. Girimurugan", title = "A Novel Real-Time Genome Comparison Method Using Discrete Wavelet Transform", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "405--416", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0115; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0115", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 December 2017", } @Article{Ahn:2018:PIA, author = "Jaeil Ahn and Brian Conkright and Simina M. Boca and Subha Madhavan", title = "{POPSTR}: Inference of Admixed Population Structure Based on Single-Nucleotide Polymorphisms and Copy Number Variations", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "417--429", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0127", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0127; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0127", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 January 2018", } @Article{Kist:2018:DMP, author = "Andreas M. Kist and Angelika Lampert and Andrias O. O'Reilly", title = "{DIsulfide} Mapping {PLanner} Software Tool", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "430--434", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2017", } @Article{Fan:2018:PCN, author = "Jun Fan and Jing Yang and Zhenran Jiang", title = "Prediction of Central Nervous System Side Effects Through Drug Permeability to Blood--Brain Barrier and Recommendation Algorithm", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "435--443", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0149; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0149", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2017", } @Article{Minarsky:2018:TM, author = "Andrey Minarsky and Nadya Morozova and Robert Penner and Christophe Soul{\'e}", title = "Theory of Morphogenesis", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "444--450", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0150", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0150; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0150", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2017", } @Article{Ligabue-Braun:2018:EPR, author = "Rodrigo Ligabue-Braun and Bruno Borguesan and Hugo Verli and Mathias J. Krause and M{\'a}rcio Dorn", title = "Everyone Is a Protagonist: Residue Conformational Preferences in High-Resolution Protein Structures", journal = j-J-COMPUT-BIOL, volume = "25", number = "4", pages = "451--465", month = apr, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0182", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:19 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0182; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0182", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 December 2017", } @Article{Sun:2018:ASB, author = "Chen Sun and Robert S. Harris and Rayan Chikhi and Paul Medvedev", title = "{AllSome} Sequence {Bloom} Trees", journal = j-J-COMPUT-BIOL, volume = "25", number = "5", pages = "467--479", month = may, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0258", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0258; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0258", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2018", } @Article{Fonseca-Junior:2018:PNB, author = "N{\'e}li J. Fonseca-J{\'u}nior and Marcelo Q. L. Afonso and Lucas C. Oliveira and Lucas Bleicher", title = "{PFstats}: a Network-Based Open Tool for Protein Family Analysis", journal = j-J-COMPUT-BIOL, volume = "25", number = "5", pages = "480--486", month = may, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0181", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0181; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0181", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 February 2018", } @Article{Guo:2018:AAP, author = "Qianghui Guo and Jian Wang and Zhao Xu", title = "Approximation Algorithms for Protein Folding in the Hydrophobic-Polar Model on {$3$D} Hexagonal Prism Lattice", journal = j-J-COMPUT-BIOL, volume = "25", number = "5", pages = "487--498", month = may, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 April 2018", } @Article{Xu:2018:PPP, author = "Yang Xu and Xiao-Chun Luo", title = "{PyPathway}: {Python} Package for Biological Network Analysis and Visualization", journal = j-J-COMPUT-BIOL, volume = "25", number = "5", pages = "499--504", month = may, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0199", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/python.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0199; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0199", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2018", } @Article{Moskon:2018:GAV, author = "Miha Mo{\v{s}}kon and Nikolaj Zimic and Miha Mraz", title = "Grohar: Automated Visualization of Genome-Scale Metabolic Models and Their Pathways", journal = j-J-COMPUT-BIOL, volume = "25", number = "5", pages = "505--508", month = may, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0209", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0209; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0209", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 February 2018", } @Article{Wu:2018:RRE, author = "Shuangyang Wu and Wanfei Liu and Hasan Awad Aljohi and Sarah A. Alromaih and Ibrahim O. Alanazi and Qiang Lin and Jun Yu and Songnian Hu", title = "{REDO}: {RNA} Editing Detection in Plant Organelles Based on Variant Calling Results", journal = j-J-COMPUT-BIOL, volume = "25", number = "5", pages = "509--516", month = may, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0214", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0214; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0214", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2018", } @Article{Fischer:2018:SRA, author = "Carlos N. Fischer and Victor {De A.Campos} and Victor H. Barella", title = "On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden {Markov} Models", journal = j-J-COMPUT-BIOL, volume = "25", number = "5", pages = "517--527", month = may, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0219", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:21 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0219; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0219", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2018", } @Article{Zhao:2018:SAA, author = "Yongan Zhao and Xiaofeng Wang and Haixu Tang", title = "A Secure Alignment Algorithm for Mapping Short Reads to Human Genome", journal = j-J-COMPUT-BIOL, volume = "25", number = "6", pages = "529--540", month = jun, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0094", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0094; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0094", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2018", } @Article{Vexler:2018:TTV, author = "Albert Vexler and Jihnhee Yu", title = "To $t$-Test or Not to $t$-Test? {A} $p$-Values-Based Point of View in the Receiver Operating Characteristic Curve Framework", journal = j-J-COMPUT-BIOL, volume = "25", number = "6", pages = "541--550", month = jun, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0216", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0216; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0216", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 April 2018", } @Article{Zeng:2018:GWA, author = "Lu Zeng and Stephen M. Pederson and Danfeng Cao and Zhipeng Qu and Zhiqiang Hu and David L. Adelson and Chaochun Wei", title = "Genome-Wide Analysis of the Association of Transposable Elements with Gene Regulation Suggests that \bioname{Alu} Elements Have the Largest Overall Regulatory Impact", journal = j-J-COMPUT-BIOL, volume = "25", number = "6", pages = "551--562", month = jun, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0228", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0228; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0228", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 April 2018", } @Article{Wang:2018:SLS, author = "Xiaodong Wang and Lei Wang", title = "A Simple Linear Space Algorithm for Computing Nonoverlapping Inversion and Transposition Distance in Quadratic Average Time", journal = j-J-COMPUT-BIOL, volume = "25", number = "6", pages = "563--575", month = jun, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0257", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0257; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0257", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2018", } @Article{Dong:2018:CTG, author = "Yan Dong and Hongbao Cao and Zhigang Liang", title = "A Curated Target Gene Pool Assisting Early Disease Prediction and Patient-Specific Treatment for Small Cell Lung Cancer", journal = j-J-COMPUT-BIOL, volume = "25", number = "6", pages = "576--585", month = jun, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0071", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0071; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0071", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2018", } @Article{Liu:2018:MPP, author = "Lizhen Liu and Xiaowu Sun and Wei Song and Chao Du", title = "A Method for Predicting Protein Complexes from Dynamic Weighted Protein--Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "25", number = "6", pages = "586--605", month = jun, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0114", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0114; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0114", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 April 2018", } @Article{Lawhorn:2018:SCA, author = "Chelsea M. Lawhorn and Rachel Schomaker and Jonathan T. Rowell and Olav Rueppell", title = "Simple Comparative Analyses of Differentially Expressed Gene Lists {May} Overestimate Gene Overlap", journal = j-J-COMPUT-BIOL, volume = "25", number = "6", pages = "606--612", month = jun, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0262", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0262; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0262", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2018", } @Article{Boenn:2018:SSS, author = "Markus Boenn", title = "{ShRangeSim}: Simulation of Single Nucleotide Polymorphism Clusters in Next-Generation Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "25", number = "6", pages = "613--622", month = jun, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0007", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:23 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0007; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0007", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2018", } @Article{Sahinalp:2018:PSA, author = "Cenk Sahinalp", title = "Preface: Selected Articles from {RECOMB 2017}", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "623--623", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.29017.cs", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.29017.cs", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2018", } @Article{Rajaraman:2018:TRA, author = "Ashok Rajaraman and Jian Ma", title = "Toward Recovering Allele-specific Cancer Genome Graphs", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "624--636", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0022", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0022; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0022", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2018", } @Article{Ahn:2018:ABM, author = "Soyeon Ahn and Haris Vikalo", title = "{aBayesQR}: a {Bayesian} Method for Reconstruction of Viral Populations Characterized by Low Diversity", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "637--648", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0249", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0249; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0249", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 February 2018", } @Article{Paten:2018:SUC, author = "Benedict Paten and Jordan M. Eizenga and Yohei M. Rosen and Adam M. Novak and Erik Garrison and Glenn Hickey", title = "Superbubbles, Ultrabubbles, and Cacti", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "649--663", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0251", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0251; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0251", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 February 2018", } @Article{Haussler:2018:FPL, author = "David Haussler and Maciej Smuga-Otto and Jordan M. Eizenga and Benedict Paten and Adam M. Novak and Sergei Nikitin and Maria Zueva and Dmitrii Miagkov", title = "A Flow Procedure for Linearization of Genome Sequence Graphs", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "664--676", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0248", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0248; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0248", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 May 2018", } @Article{Popic:2018:FMB, author = "Victoria Popic and Volodymyr Kuleshov and Michael Snyder and Serafim Batzoglou", title = "Fast Metagenomic Binning via Hashing and {Bayesian} Clustering", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "677--688", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0250", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/hash.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0250; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0250", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2018", } @Article{Zaccaria:2018:PCN, author = "Simone Zaccaria and Mohammed El-Kebir and Gunnar W. Klau and Benjamin J. Raphael", title = "Phylogenetic Copy-Number Factorization of Multiple Tumor Samples", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "689--708", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0253", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0253; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0253", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2018", } @Article{Ness:2018:BAL, author = "Robert O. Ness and Karen Sachs and Parag Mallick and Olga Vitek", title = "A {Bayesian} Active Learning Experimental Design for Inferring Signaling Networks", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "709--725", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0247", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0247; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0247", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2018", } @Article{Ojewole:2018:BBB, author = "Adegoke A. Ojewole and Jonathan D. Jou and Vance G. Fowler and Bruce R. Donald", title = "{{\em BBK* (Branch and Bound Over K*)\/}}: a Provable and Efficient Ensemble-Based Protein Design Algorithm to Optimize Stability and Binding Affinity Over Large Sequence Spaces", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "726--739", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0267", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0267; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0267", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 March 2018", } @Article{Jansson:2018:DCR, author = "Jesper Jansson and Andrzej Lingas and Ramesh Rajaby and Wing-Kin Sung", title = "Determining the Consistency of Resolved Triplets and Fan Triplets", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "740--754", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0256", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0256; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0256", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 February 2018", } @Article{Solomon:2018:ISL, author = "Brad Solomon and Carl Kingsford", title = "Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence {Bloom} Trees", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "755--765", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0265", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0265; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0265", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 March 2018", } @Article{Jain:2018:FAA, author = "Chirag Jain and Alexander Dilthey and Sergey Koren and Srinivas Aluru and Adam M. Phillippy", title = "A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "766--779", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0036", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0036; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0036", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 April 2018", } @Article{DeBlasio:2018:ALR, author = "Dan DeBlasio and John Kececioglu", title = "Adaptive Local Realignment of Protein Sequences", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "780--793", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0045", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0045; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0045", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2018", } @Article{Schweiger:2018:USA, author = "Regev Schweiger and Eyal Fisher and Elior Rahmani and Liat Shenhav and Saharon Rosset and Eran Halperin", title = "Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "794--808", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0047", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0047; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0047", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 June 2018", } @Article{Wang:2018:LGP, author = "Xiaoqian Wang and Jingwen Yan and Xiaohui Yao and Sungeun Kim and Kwangsik Nho and Shannon L. Risacher and Andrew J. Saykin and Li Shen and Heng Huang", title = "Longitudinal Genotype--Phenotype Association Study through Temporal Structure Auto-Learning Predictive Model", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "809--824", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2018", } @Article{Holley:2018:DAF, author = "Guillaume Holley and Roland Wittler and Jens Stoye and Faraz Hach", title = "Dynamic Alignment-Free and Reference-Free Read Compression", journal = j-J-COMPUT-BIOL, volume = "25", number = "7", pages = "825--836", month = jul, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0068", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:25 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0068; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0068", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2018", } @Article{Vega-Rodriguez:2018:PSI, author = "Miguel A. Vega-Rodr{\'\i}guez and Jos{\'e} M. Granado-Criado", title = "{{\em Preface to the Special Issue\/}}: Parallel Computing in Computational Biology: a Technological Point of View", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "837--840", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.29018.mavr", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.29018.mavr; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.29018.mavr", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2018", } @Article{Perez-Wohlfeil:2018:PPP, author = "Esteban P{\'e}rez-Wohlfeil and Oswaldo Trelles", title = "Precise and Parallel Pairwise Metagenomic Comparisons", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "841--849", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0081", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0081; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0081", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2018", } @Article{Teixeira:2018:LSS, author = "Andreia Sofia Teixeira and Pedro T. Monteiro and Jo{\~a}o A. Carri{\c{c}}o and Francisco C. Santos and Alexandre P. Francisco", title = "Large-Scale Simulations of Bacterial Populations Over Complex Networks", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "850--861", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0083", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0083; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0083", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 July 2018", } @Article{Martinez:2018:FLT, author = "H{\'e}ctor Mart{\'\i}nez and Sergio Barrachina and Maribel Castillo and Enrique S. Quintana-Ort{\'i} and Jordi Rambla de Argila and Xavier Farr{\'e} and Arcadi Navarro", title = "{FaST-LMM} for Two-Way Epistasis Tests on High-Performance Clusters", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "862--870", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0087", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0087; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0087", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 July 2018", } @Article{Nowicki:2018:MPI, author = "Marek Nowicki and Davit Bzhalava and Piotr Ba{\l}a", title = "Massively Parallel Implementation of Sequence Alignment with Basic Local Alignment Search Tool Using Parallel Computing in {Java} Library", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "871--881", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0079", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/java2010.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0079; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0079", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 July 2018", } @Article{Escobar:2018:PPP, author = "Juan Jos{\'e} Escobar and Julio Ortega and Antonio Francisco D{\'\i}az and Jes{\'u}s Gonz{\'a}lez and Miguel Damas", title = "A Power--Performance Perspective to Multiobjective Electroencephalogram Feature Selection on Heterogeneous Parallel Platforms", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "882--893", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0080", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0080; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0080", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 June 2018", } @Article{Llados:2018:SCC, author = "Jordi Llad{\'o}s and Fernando Cores and Fernando Guirado", title = "Scalable Consistency in {T}-Coffee Through {Apache Spark} and {Cassandra} Database", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "894--906", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0084; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0084", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 July 2018", } @Article{Wen:2018:SGI, author = "Jian-Xin Wen and Xiao-Qin Li and Yu Chang", title = "Signature Gene Identification of Cancer Occurrence and Pattern Recognition", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "907--916", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0261", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0261; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0261", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 June 2018", } @Article{Rosati:2018:EMS, author = "Elise Rosati and Morgan Madec and Jean-Baptiste Kammerer and Luc H{\'e}brard and Christophe Lallement and Jacques Haiech", title = "Efficient Modeling and Simulation of Space-Dependent Biological Systems", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "917--933", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0012", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0012; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0012", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 May 2018", } @Article{Pang:2018:CAC, author = "Fengqian Pang and Heng Li and Yonggang Shi and Zhiwen Liu", title = "Computational Analysis of Cell Dynamics in Videos with Hierarchical-Pooled Deep-Convolutional Features", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "934--953", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0023; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0023", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 April 2018", } @Article{Naito:2018:HSS, author = "Tatsuhiko Naito", title = "Human Splice-Site Prediction with Deep Neural Networks", journal = j-J-COMPUT-BIOL, volume = "25", number = "8", pages = "954--961", month = aug, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0041", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:28 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0041; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0041", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 April 2018", } @Article{Zhao:2018:DPE, author = "Jian Zhao and Jiasong Wang and Hongmei Jiang", title = "Detecting Periodicities in Eukaryotic Genomes by {Ramanujan} {Fourier} Transform", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "963--975", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0252", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0252; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0252", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 July 2018", } @Article{Fukunaga:2018:NMA, author = "Tsukasa Fukunaga and Michiaki Hamada", title = "A Novel Method for Assessing the Statistical Significance of {RNA-RNA} Interactions Between Two Long {RNAs}", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "976--986", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0260", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0260; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0260", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 July 2018", } @Article{Kim:2018:EDS, author = "Yoonji Kim and Jaejik Kim", title = "Estimation of Dynamic Systems for Gene Regulatory Networks from Dependent Time-Course Data", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "987--996", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0062", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0062; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0062", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2018", } @Article{Kumari:2018:PRP, author = "Bandana Kumari and Ravindra Kumar and Manish Kumar", title = "Prediction of Rare Palmitoylation Events in Proteins", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "997--1008", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0069", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0069; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0069", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 July 2018", } @Article{Rubio-Largo:2018:PMM, author = "{\'A}lvaro Rubio-Largo and Mauro Castelli and Leonardo Vanneschi and Miguel A. Vega-Rodr{\'\i}guez", title = "A Parallel Multiobjective Metaheuristic for Multiple Sequence Alignment", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "1009--1022", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0031", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0031; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0031", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 April 2018", } @Article{Atitey:2018:DTR, author = "Komlan Atitey and Pavel Loskot and Paul Rees", title = "Determining the Transcription Rates Yielding Steady-State Production of {mRNA} in the \bioname{Lac} Genetic Switch of \bioname{Escherichia coli}", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "1023--1039", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0055", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0055; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0055", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 June 2018", } @Article{Larson:2018:ISN, author = "Nicholas B. Larson and Chen Wang and Jie Na and Ross A. Rowsey and William Edward Highsmith and Nicole L. Hoppman and Jean-Pierre Kocher and Eric W. Klee", title = "Improving Single-Nucleotide Polymorphism-Based Fetal Fraction Estimation of Maternal Plasma Circulating Cell-Free {DNA} Using {Bayesian} Hierarchical Models", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "1040--1049", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0056", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0056; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0056", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 June 2018", } @Article{Huang:2018:AMW, author = "Xinrui Huang and Sha Li and Song Gao", title = "Applying a Modified Wavelet Shrinkage Filter to Improve Cryo-Electron Microscopy Imaging", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "1050--1058", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0060", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0060; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0060", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2018", } @Article{Park:2018:SMB, author = "Joonyeon Park and Myeongji Cho and Hyeon S. Son", title = "Simulation Model of Bacterial Resistance to Antibiotics Using Individual-Based Modeling", journal = j-J-COMPUT-BIOL, volume = "25", number = "9", pages = "1059--1070", month = sep, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:30 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0064; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0064", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2018", } @Article{Bao:2018:ACR, author = "Yu Bao and Morihiro Hayashida and Pengyu Liu and Masayuki Ishitsuka and Jose C. Nacher and Tatsuya Akutsu", title = "Analysis of Critical and Redundant Vertices in Controlling Directed Complex Networks Using Feedback Vertex Sets", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1071--1090", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0019", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0019; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0019", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 August 2018", } @Article{Beretta:2018:IEA, author = "Stefano Beretta and Mauro Castelli and Ivo Gon{\c{c}}alves and Ivan Kel and Valentina Giansanti and Ivan Merelli", title = "Improving {eQTL} Analysis Using a Machine Learning Approach for Data Integration: a Logistic Model Tree Solution", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1091--1105", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0167", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0167; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0167", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 July 2018", } @Article{Palkowski:2018:PTC, author = "Marek Palkowski and Wlodzimierz Bielecki", title = "Parallel Tiled Codes Implementing the {Smith--Waterman} Alignment Algorithm for Two and Three Sequences", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1106--1119", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0006", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0006; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0006", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 July 2018", } @Article{Kosesoy:2018:PWS, author = "{\.I}rfan K{\"o}sesoy and Murat G{\"o}k and Cemil {\"O}z", title = "{PROSES}: a {Web} Server for Sequence-Based Protein Encoding", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1120--1122", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0049", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0049; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0049", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 July 2018", } @Article{Wang:2018:MPC, author = "Shisheng Wang and Wen Zheng and Liqiang Hu and Meng Gong and Hao Yang", title = "{MixProTool}: a Powerful and Comprehensive {Web} Tool for Analyzing and Visualizing Multigroup Proteomics Data", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1123--1127", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0050", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0050; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0050", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 July 2018", } @Article{Chen:2018:DCN, author = "Jie Chen and Shirong Deng", title = "Detection of Copy Number Variation Regions Using the {DNA-Sequencing} Data from Multiple Profiles with Correlated Structure", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1128--1140", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0053", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0053; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0053", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 July 2018", } @Article{Voges:2018:TLS, author = "Jan Voges and Ali Fotouhi and J{\"o}rn Ostermann and Muhammed O{\u{g}}uzhan K{\"u}lekci", title = "A Two-Level Scheme for Quality Score Compression", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1141--1151", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0065", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0065; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0065", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2018", } @Article{Liu:2018:SWF, author = "Qie Liu and Min Liu and Wenfa Wu", title = "Strong/Weak Feature Recognition of Promoters Based on Position Weight Matrix and Ensemble Set-Valued Models", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1152--1160", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0067", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0067; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0067", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 July 2018", } @Article{Wang:2018:MSG, author = "Xuedong Wang and Wenhui Shang and Yu Chang and Xiaoqin Li", title = "Methylation Signature Genes Identification of the Lung Squamous Cell Carcinoma Occurrence and Recognition Research", journal = j-J-COMPUT-BIOL, volume = "25", number = "10", pages = "1161--1169", month = oct, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0069", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:32 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0069; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0069", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2018", } @Article{Orenstein:2018:JBC, author = "Yaron Orenstein and Yun William Yu and Bonnie Berger", title = "{Joker de Bruijn}: Covering $k$-Mers Using Joker Characters", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1171--1178", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0032", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0032; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0032", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2018", } @Article{Barrett:2018:EDS, author = "Christopher Barrett and Qijun He and Fenix W. Huang and Christian M. Reidys", title = "An Efficient Dual Sampling Algorithm with {Hamming} Distance Filtration", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1179--1192", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0075", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0075; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0075", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2018", } @Article{Zhou:2018:EDB, author = "Xinrui Zhou and Amihood Amir and Concettina Guerra and Gadi Landau and Jarek Rossignac", title = "{EDoP} Distance Between Sets of Incomplete Permutations: Application to Bacteria Classification Based on Gene Order", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1193--1202", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0063", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0063; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0063", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 August 2018", } @Article{Alexeev:2018:CSP, author = "Nikita Alexeev and Max A. Alekseyev", title = "Combinatorial Scoring of Phylogenetic Trees and Networks Based on Homoplasy-Free Characters", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1203--1219", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0082", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0082; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0082", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2018", } @Article{Alexandrov:2018:TEM, author = "Theodore Alexandrov and Nina Golyandina and David Holloway and Alex Shlemov and Alexander Spirov", title = "Two-Exponential Models of Gene Expression Patterns for Noisy Experimental Data", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1220--1230", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0063", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0063; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0063", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2018", } @Article{Sorooshyari:2018:PMP, author = "Siamak K. Sorooshyari and Matthew P. Taylor and H. Vincent Poor", title = "Probabilistic Modeling of Pseudorabies Virus Infection in a Neural Circuit", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1231--1246", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0131", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0131; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0131", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2018", } @Article{Yousefian-Jazi:2018:SIF, author = "Ali Yousefian-Jazi and Jinwook Choi", title = "Sequential Integration of Fuzzy Clustering and Expectation Maximization for Transcription Factor Binding Site Identification", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1247--1256", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0230", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0230; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0230", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2018", } @Article{Tambonis:2018:DEA, author = "Tiago Tambonis and Marcelo Boareto and Vitor B. P. Leite", title = "Differential Expression Analysis in {RNA-seq} Data Using a Geometric Approach", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1257--1265", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0244; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0244", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2018", } @Article{Yang:2018:ISB, author = "Hui Yang and Hao Lv and Hui Ding and Wei Chen and Hao Lin", title = "{iRNA-2OM}: a Sequence-Based Predictor for Identifying {2'-O}-Methylation Sites in \bioname{Homo sapiens}", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1266--1277", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0004", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0004; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0004", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 August 2018", } @Article{Osmankovic:2018:NAD, author = "Dinko Osmankovic and Semir Doric and Naris Pojskic and Lada Lukic Bilela", title = "New Approach to Detect Coiled Coil and Leucine Zipper Motifs in Protein Sequences", journal = j-J-COMPUT-BIOL, volume = "25", number = "11", pages = "1278--1283", month = nov, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0104", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:35 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0104; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0104", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 August 2018", } @Article{Costa:2018:SMS, author = "Jos{\'e} M. J. Costa and Helcio R. B. Orlande and Viviane O. F. Lione and Antonio G. F. Lima and Tayn{\'a} C. S. Cardoso and Leonardo A. B. Var{\'o}n", title = "Simultaneous Model Selection and Model Calibration for the Proliferation of Tumor and Normal Cells During In Vitro Chemotherapy Experiments", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1285--1300", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0130", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0130; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0130", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 September 2018", } @Article{Rangamaran:2018:ETI, author = "Vijaya Raghavan Rangamaran and Bharathram Uppili and Dharani Gopal and Kirubagaran Ramalingam", title = "{EasyQC}: Tool with Interactive User Interface for Efficient Next-Generation Sequencing Data Quality Control", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1301--1311", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0186", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0186; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0186", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 September 2018", } @Article{Yan:2018:ICT, author = "Xiaoping Yan and Yu Huang and Jiabin Wu", title = "Identify Cross Talk Between Circadian Rhythm and Coronary Heart Disease by Multiple Correlation Analysis", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1312--1327", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0254", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0254; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0254", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 September 2018", } @Article{Santiago:2018:HDU, author = "Caio Santiago and Vivian Pereira and Luciano Digiampietri", title = "Homology Detection Using Multilayer Maximum Clustering Coefficient", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1328--1338", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0266", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0266; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0266", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 August 2018", } @Article{Werner:2018:LDP, author = "Matthias Werner and Pascal Fieth and Alexander Hartmann", title = "Large-Deviation Properties of Sequence Alignment of Correlated Sequences", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1339--1346", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0269", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0269; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0269", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 September 2018", } @Article{Wang:2018:MLB, author = "Hsin-Yao Wang and Shih-Cheng Chang and Wan-Ying Lin and Chun-Hsien Chen and Szu-Hsien Chiang and Kai-Yao Huang and Bo-Yu Chu and Jang-Jih Lu and Tzong-Yi Lee", title = "Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1347--1360", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0002; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0002", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 September 2018", } @Article{Yang:2018:DRR, author = "Ming Yang and Louis Z. Yang", title = "Determining a Reasonable Range of Relative Numerical Tolerance Values for Simulating Deterministic Models of Biochemical Reactions", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1361--1364", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0026", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0026; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0026", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 August 2018", } @Article{Lall:2018:SAP, author = "Snehalika Lall and Debajyoti Sinha and Sanghamitra Bandyopadhyay and Debarka Sengupta", title = "Structure-Aware Principal Component Analysis for Single-Cell {RNA-seq} Data", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1365--1373", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0027", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0027; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0027", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2018", } @Article{Garren:2018:BTC, author = "Jeonifer M. Garren and Jaejik Kim", title = "Bootstrapping Time-Course Gene Expression Data for Gene Networks: Application to Gene Relevance Networks", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1374--1384", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0029", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0029; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0029", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2018", } @Article{Liu:2018:PMD, author = "Yue Liu and Shu-Lin Wang and Jun-Feng Zhang", title = "Prediction of Microbe--Disease Associations by Graph Regularized Non-Negative Matrix Factorization", journal = j-J-COMPUT-BIOL, volume = "25", number = "12", pages = "1385--1394", month = dec, year = "2018", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0072", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:37 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0072; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0072", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 August 2018", } @Article{Yang:2019:MMC, author = "Yanshen Yang and Jeffrey A. Robertson and Zhen Guo and Jake Martinez and Christy Coghlan and Lenwood S. Heath", title = "{MCAT}: Motif Combining and Association Tool", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "1--15", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0113; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0113", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 November 2018", } @Article{Surujon:2019:SWN, author = "Defne Surujon and Yann Ponty and Peter Clote", title = "Small-World Networks and {RNA} Secondary Structures", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "16--26", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 October 2018", } @Article{Avni:2019:NQB, author = "Eliran Avni and Sagi Snir", title = "A New Quartet-Based Statistical Method for Comparing Sets of Gene Trees Is Developed Using a Generalized {Hoeffding} Inequality", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "27--37", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 November 2018", } @Article{Duong:2019:WSE, author = "Dat Duong and Wasi Uddin Ahmad and Eleazar Eskin and Kai-Wei Chang and Jingyi Jessica Li", title = "Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "38--52", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0093", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0093; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0093", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 October 2018", } @Article{Kavya:2019:SAD, author = "Vaddadi Naga Sai Kavya and Kshitij Tayal and Rajgopal Srinivasan and Naveen Sivadasan", title = "Sequence Alignment on Directed Graphs", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "53--67", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2017.0264", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2017.0264; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2017.0264", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 September 2018", } @Article{Fomin:2019:SAR, author = "Eduard Fomin", title = "A Simple Approach to the Reconstruction of a Set of Points from the Multiset of Pairwise Distances in $ n^2 $ Steps for the Sequencing Problem: {III.} Noise Inputs for the {Beltway} Case", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "68--75", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2018", } @Article{Mellem:2019:MMD, author = "Daniel Mellem and Frank Fischer and S{\"o}ren Jaspers and Horst Wenck and Michael R{\"u}bhausen", title = "Mitochondrial Morphologies Driven by Energy-Consuming Cell Sites in a Spatially and Time-Resolved Quality Model", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "76--85", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0086", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0086; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0086", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 September 2018", } @Article{Lo:2019:IPL, author = "Shih-Chiang Lo and Feng-You Liu and Wun-Sin Jhang and Che-Chi Shu", title = "The Insight into Protein-Ligand Interactions, a Novel Way of Buffering Protein Noise in Gene Expression", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "86--95", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 September 2018", } @Article{Ta:2019:WIV, author = "Michael Ta and Changchuan Yin and Gary Lee Smith and Wenbo Xu", title = "A Workflow to Improve Variant Calling Accuracy in Molecular Barcoded Sequencing Reads", journal = j-J-COMPUT-BIOL, volume = "26", number = "1", pages = "96--103", month = jan, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0110", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:39 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0110; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0110", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 August 2018", } @Article{Samykannu:2019:SCB, author = "Gopinath Samykannu and Princy Vijayababu and Christian Bharathi Antonyraj and Perumal Perumal and Sundarabaalaji Narayanan and Syed Ibrahim Basheer Ahamed and Jeyakumar Natarajan", title = "In Silico Characterization of {B} Cell and {T} Cell Epitopes for Subunit Vaccine Design of \bioname{Salmonella typhi} {PgtE}: a Molecular Dynamics Simulation Approach", journal = j-J-COMPUT-BIOL, volume = "26", number = "2", pages = "105--116", month = feb, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0010", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0010; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0010", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 December 2018", } @Article{Kokas:2019:SNF, author = "Filip Zavadil Kok{\'a}{\v{s}} and V{\'e}ronique Bergougnoux and M{\'a}ria Majesk{\'a} {\v{C}}udejkov{\'a}", title = "{SATrans}: New Free Available Software for Annotation of Transcriptome and Functional Analysis of Differentially Expressed Genes", journal = j-J-COMPUT-BIOL, volume = "26", number = "2", pages = "117--123", month = feb, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0149; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0149", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 October 2018", } @Article{Ershov:2019:IHS, author = "Vasily Ershov and Artem Tarasov and Alla Lapidus and Anton Korobeynikov", title = "{IonHammer}: Homopolymer-Space {Hamming} Clustering for {IonTorrent} Read Error Correction", journal = j-J-COMPUT-BIOL, volume = "26", number = "2", pages = "124--127", month = feb, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0152", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0152; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0152", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 October 2018", } @Article{Yang:2019:TDE, author = "Sihai Yang and Xianhua Han and Yenwei Chen", title = "Three-Dimensional Embryonic Image Segmentation and Registration Based on Shape Index and Ellipsoid-Fitting Method", journal = j-J-COMPUT-BIOL, volume = "26", number = "2", pages = "128--142", month = feb, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2018", } @Article{Yin:2019:EDD, author = "Changchuan Yin", title = "Encoding and Decoding {DNA} Sequences by Integer Chaos Game Representation", journal = j-J-COMPUT-BIOL, volume = "26", number = "2", pages = "143--151", month = feb, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0173", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0173; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0173", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2018", } @Article{Uechi:2019:MAD, author = "Lisa Uechi and David J. Galas and Nikita A. Sakhanenko", title = "Multivariate Analysis of Data Sets with Missing Values: an Information Theory-Based Reliability Function", journal = j-J-COMPUT-BIOL, volume = "26", number = "2", pages = "152--171", month = feb, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0179", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:41 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0179; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0179", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2018", } @Article{Barrett:2019:BSP, author = "Christopher Barrett and Qijun He and Fenix W. Huang and Christian M. Reidys", title = "A {Boltzmann} Sampler for $1$-Pairs with Double Filtration", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "173--192", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0095", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0095; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0095", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 January 2019", } @Article{Wang:2019:CNI, author = "Xiaodong Wang and Lei Wang", title = "Computing Nonoverlapping Inversion Distance Between Two Strings in Linear Average Time", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "193--201", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0136", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0136; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0136", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 January 2019", } @Article{Park:2019:RSS, author = "Heewon Park and Makoto Yamada and Seiya Imoto and Satoru Miyano", title = "Robust Sample-Specific Stability Selection with Effective Error Control", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "202--217", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0180", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0180; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0180", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 January 2019", } @Article{Mao:2019:HDH, author = "Xiaodan Mao and Yichen Xu and Zhenran Jiang", title = "{HColonDB}: a Database for Human Colon Cancer Research", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "218--224", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0193", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0193; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0193", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2019", } @Article{Viswanath:2019:IDI, author = "bBiju Viswanath and Naren P. Rao and Janardhanan C. Narayanaswamy and Palanimuthu T. Sivakumar and Arunkandaswamy and Muralidharankesavan and Urvakhsh-Meherwan Mehta and Ganesanvenkatasubramanian and John P. John and Odity Mukherjee and Meerapurushottam and Ramakrishnankannan and Bhupesh Mehta and Thennarasukandavel and B. Binukumar and Jitendersaini and Deepak Jayarajan and A. Shyamsundar and Sydney Moirangthem and Kumar G. Vijay and Jagadishathirthalli and Prabha S. Chandra and Bangalore N. Gangadhar and Pratima Murthy and Mitradas M. Panicker and Upinder S. Bhalla and Sumantrachattarji and Vivekbenegal and Mathew Varghese and Janardhan Y. C. Reddy and Padinjat Raghu and Mahendrarao and Sanjeev Jain", title = "{INDEX-db}: The {Indian Exome Reference Database (Phase I)}", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "225--234", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0199", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0199; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0199", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 January 2019", } @Article{Piwowar:2019:DAM, author = "Monika Piwowar and Tomasz Ku{\l}aga", title = "Directional Association Measurement in Contingency Tables: Genomic Case", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "235--240", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0202", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0202; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0202", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 December 2018", } @Article{Wang:2019:CMB, author = "Yuandi Wang and Qingmei Wen and Zhigang Zhou and Nanjun Yan", title = "Cell Modeling Based on Bubbles with Weighted Membranes", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "241--265", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0205", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0205; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0205", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 January 2019", } @Article{Solar:2019:SOP, author = "Roberto Solar and Victor Sepulveda and Alonso Inostrosa-Psijas and Oscar Rojas and Veronica Gil-Costa and Mauricio Marin", title = "A Service-Oriented Platform for Approximate {Bayesian} Computation in Population Genetics", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "266--279", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0217", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0217; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0217", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 January 2019", } @Article{Kim:2019:MPP, author = "Baekdoo Kim and Thahmina Ali and Changsu Dong and Carlos Lijeron and Raja Mazumder and Claudia Wultsch and Konstantinos Krampis", title = "{{\em miCloud\/}}: a Plug-n-Play, Extensible, On-Premises Bioinformatics Cloud for Seamless Execution of Complex Next-Generation Sequencing Data Analysis Pipelines", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "280--284", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0218", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0218; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0218", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 January 2019", } @Article{Gunawan:2019:CPN, author = "Andreas D. M. Gunawan and Hongwei Yan and Louxin Zhang", title = "Compression of Phylogenetic Networks and Algorithm for the Tree Containment Problem", journal = j-J-COMPUT-BIOL, volume = "26", number = "3", pages = "285--294", month = mar, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0220", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:44 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0220; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0220", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 January 2019", } @Article{Cho:2019:MDC, author = "Soonweng Cho and Hyun-Seok Kim and Martha A. Zeiger and Christopher B. Umbricht and Leslie M. Cope", title = "Measuring {DNA} Copy Number Variation Using High-Density Methylation Microarrays", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "295--304", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0143", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0143; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0143", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2019", } @Article{Zaborowski:2019:BEM, author = "Rafa{\l} Zaborowski and Bartek Wilczy{\'n}ski", title = "{BPscore}: an Effective Metric for Meaningful Comparisons of Structural Chromosome Segmentations", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "305--314", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0162", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0162; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0162", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 February 2019", } @Article{Wang:2019:PSC, author = "Yi Wang and Kun Tian and Stephen S.-T. Yau", title = "Protein Sequence Classification Using Natural Vector and Convex Hull Method", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "315--321", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0216", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0216; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0216", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 February 2019", } @Article{Urban:2019:DST, author = "Paulina Urban and Vahid Rezaei and Grzegorz Bokota and Micha{\l} Denkiewicz and Subhadip Basu and Dariusz Plewczy{\'n}ski", title = "Dendritic Spines Taxonomy: The Functional and Structural Classification $ \bullet $ Time-Dependent Probabilistic Model of Neuronal Activation", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "322--335", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0155", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0155; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0155", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 February 2019", } @Article{Lee:2019:RBN, author = "Kyu Min Lee and Minhyeok Lee and Junhee Seok and Sung Won Han", title = "Regression-Based Network Estimation for High-Dimensional Genetic Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "336--349", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0225", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0225; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0225", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 January 2019", } @Article{Ye:2019:STS, author = "Yusong Ye and Zhuoqin Yang and Jinzhi Lei", title = "Stochastic Telomere Shortening and the Route to Limitless Replicative Potential", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "350--363", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0234", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0234; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0234", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 February 2019", } @Article{Qi:2019:BAK, author = "Yuewen Qi and Haowen Qi and Zeyuan Liu and Peiyuan He and Bingqing Li", title = "Bioinformatics Analysis of Key Genes and Pathways in Colorectal Cancer", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "364--375", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0237", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0237; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0237", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 February 2019", } @Article{Feltes:2019:CEC, author = "Bruno C{\'e}sar Feltes and Eduardo Bassani Chandelier and Bruno Iochins Grisci and M{\'a}rcio Dorn", title = "{CuMiDa}: an Extensively Curated Microarray Database for Benchmarking and Testing of Machine Learning Approaches in Cancer Research", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "376--386", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0238", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0238; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0238", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2019", } @Article{Liu:2019:RSD, author = "Huan Liu and Li Liu and Hong Zhu", title = "The Role of Significantly Deregulated {MicroRNAs} in Recurrent Cervical Cancer Based on Bioinformatic Analysis of the Cancer Genome Atlas Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "387--395", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0241", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0241; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0241", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 February 2019", } @Article{Marongiu:2019:MCL, author = "Luigi Marongiu and Heike Allgayer", title = "{Mingle}: a Command Line Utility for Merging Multi-fasta Files", journal = j-J-COMPUT-BIOL, volume = "26", number = "4", pages = "396--404", month = apr, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:46 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0243; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0243", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 February 2019", } @Article{Kothiyal:2019:MIS, author = "Prachi Kothiyal and Wendy S. W. Wong and Dale L. Bodian and John E. Niederhuber", title = "{Mendelian} Inconsistent Signatures from 1314 Ancestrally Diverse Family Trios Distinguish Biological Variation from Sequencing Error", journal = j-J-COMPUT-BIOL, volume = "26", number = "5", pages = "405--419", month = may, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0253", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0253; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0253", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 April 2019", } @Article{Oliveira:2019:SWR, author = "Andre Rodrigues Oliveira and Klairton Lima Brito and Zanoni Dias and Ulisses Dias", title = "Sorting by Weighted Reversals and Transpositions", journal = j-J-COMPUT-BIOL, volume = "26", number = "5", pages = "420--431", month = may, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0257", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0257; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0257", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2019", } @Article{Ahn:2019:RNB, author = "Jaegyoon Ahn and Junhyeok Choi and Harrim Kim and Jibum Kim", title = "{RN$^+$}: a Novel Biclustering Algorithm for Analysis of Gene Expression Data Using Protein--Protein Interaction Network", journal = j-J-COMPUT-BIOL, volume = "26", number = "5", pages = "432--441", month = may, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0003", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0003; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0003", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 February 2019", } @Article{Castro:2019:FPM, author = "Guilherme Torres Castro and Luis Enrique Z{\'a}rate and Cristiane Neri Nobre and Henrique Cota Freitas", title = "A Fast Parallel {$K$}-Modes Algorithm for Clustering Nucleotide Sequences to Predict Translation Initiation Sites", journal = j-J-COMPUT-BIOL, volume = "26", number = "5", pages = "442--456", month = may, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0245", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0245; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0245", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2019", } @Article{Ravi:2019:ENC, author = "Guru Raj Rao Ravi and Jayashree Biswal and Sureka Kanagarajan and Jeyaraman Jeyakanthan", title = "Exploration of {N5-CAIR} Mutase Novel Inhibitors from \bioname{Pyrococcus horikoshii} {OT3}: a Computational Study", journal = j-J-COMPUT-BIOL, volume = "26", number = "5", pages = "457--472", month = may, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0248", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0248; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0248", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2019", } @Article{Hu:2019:CMC, author = "Xi Hu and Wenling Yi and Ling Jiang and Sijia Wu and Yan Zhang and Jianqiang Du and Tianyou Ma and Tong Wang and Xiaoming Wu", title = "Classification of Metaphase Chromosomes Using Deep Convolutional Neural Network", journal = j-J-COMPUT-BIOL, volume = "26", number = "5", pages = "473--484", month = may, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0212", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0212; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0212", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 April 2019", } @Article{Chen:2019:IPK, author = "Zide Chen and Jiehua Chen and Xuan Huang and Yi Wu and Kuiyuan Huang and Weikang Xu and Linqing Xie and Xiaoyong Zhang and Hongyan Liu", title = "Identification of Potential Key Genes for Hepatitis {B} Virus-Associated Hepatocellular Carcinoma by Bioinformatics Analysis", journal = j-J-COMPUT-BIOL, volume = "26", number = "5", pages = "485--494", month = may, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0244; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0244", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 March 2019", } @Article{Liang:2019:BDA, author = "Wei Liang and Yuxiao Yang and Yusi Fang and Zhongying Zhao and Jie Hu", title = "{Bayesian} Detection of Abnormal Asynchrony of Division Between Sister Cells in Mutant \bioname{Caenorhabditis elegans} Embryos", journal = j-J-COMPUT-BIOL, volume = "26", number = "5", pages = "495--505", month = may, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0246", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Jun 1 09:53:48 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0246; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0246", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 April 2019", } @Article{Diallo:2019:SPW, author = "Abdoulaye Banir{\'e} Diallo and Engelbert Mephu Nguifo and Wajdi Dhifli and Elham Azizi and Sandhya Prabhakaran and Wesley Tansey", title = "Selected Papers from the {Workshop on Computational Biology: Joint with the International Joint Conference on Artificial Intelligence and the International Conference on Machine Learning, 2018}", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "507--508", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.29020.abd", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.29020.abd", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 June 2019", } @Article{Menegaux:2019:CED, author = "Romain Menegaux and Jean-Philippe Vert", title = "Continuous Embeddings of {DNA} Sequencing Reads and Application to Metagenomics", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "509--518", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0174", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0174; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0174", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2019", } @Article{Lebatteux:2019:TAF, author = "Dylan Lebatteux and Amine M. Remita and Abdoulaye Banir{\'e} Diallo", title = "Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "519--535", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0239", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0239; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0239", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 May 2019", } @Article{Deac:2019:ACM, author = "Andreea Deac and Petar Veli{\v{c}}kovi{\'c} and Pietro Sormanni", title = "Attentive Cross-Modal Paratope Prediction", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "536--545", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0175", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0175; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0175", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 December 2018", } @Article{Moretti:2019:ATF, author = "Antonio Moretti and Andrew Stirn and Gabriel Marks and Itsik Pe'er", title = "Autoencoding Topographic Factors", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "546--560", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0176", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0176; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0176", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 December 2018", } @Article{Saidi:2019:EMR, author = "Rabie Saidi and Wajdi Dhifli and Mondher Maddouri and Engelbert Mephu Nguifo", title = "Efficiently Mining Recurrent Substructures from Protein Three-Dimensional Structure Graphs", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "561--571", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0171", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0171; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0171", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2018", } @Article{Eghbal-Zadeh:2019:DEE, author = "Hamid Eghbal-Zadeh and Lukas Fischer and Niko Popitsch and Florian Kromp and Sabine Taschner-Mandl and Teresa Gerber and Eva Bozsaky and Peter F. Ambros and Inge M. Ambros and Gerhard Widmer and Bernhard A. Moser", title = "{DeepSNP}: an End-to-End Deep Neural Network with Attention-Based Localization for Breakpoint Detection in Single-Nucleotide Polymorphism Array Genomic Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "572--596", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0172; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 December 2018", } @Article{Petersen:2019:DRL, author = "Brenden K. Petersen and Jiachen Yang and Will S. Grathwohl and Chase Cockrell and Claudio Santiago and Gary An and Daniel M. Faissol", title = "Deep Reinforcement Learning and Simulation as a Path Toward Precision Medicine", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "597--604", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0168", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0168; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0168", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 January 2019", } @Article{Chen:2019:SEN, author = "Qingyu Chen and Xiuzhen Zhang and Yu Wan and Justin Zobel and Karin Verspoor", title = "Search Effectiveness in Nonredundant Sequence Databases: Assessments and Solutions", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "605--617", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0198", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0198; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0198", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 December 2018", } @Article{Bazin:2019:NRC, author = "Alexandre Bazin and Didier Debroas and Engelbert Mephu Nguifo", title = "A De Novo Robust Clustering Approach for Amplicon-Based Sequence Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "6", pages = "618--624", month = jun, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0170", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 26 08:04:05 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0170; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0170", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 December 2018", } @Article{Deichmann:2019:SIG, author = "Guest Editor Ute Deichmann", title = "{{\em Special Issue\/}}: Genomic Regulation: Experiments, Computational Modeling, and Philosophy", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "625--628", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.29021.ud", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.29021.ud; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.29021.ud", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2019", } @Article{Morange:2019:TMT, author = "Michel Morange", title = "A Time to Model and a Time to Experiment", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "629--636", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0133", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0133; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0133", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 June 2019", } @Article{Deichmann:2019:GME, author = "Ute Deichmann", title = "From {Gregor Mendel} to {Eric Davidson}: Mathematical Models and Basic Principles in Biology", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "637--652", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0087", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0087; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0087", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 May 2019", } @Article{Istrail:2019:EDR, author = "Sorin Istrail", title = "{Eric Davidson}'s Regulatory Genome for Computer Science: Causality, Logic, and Proof Principles of the Genomic {\em cis\/}-Regulatory Code", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "653--684", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0144", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0144; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0144", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2019", } @Article{Istrail:2019:HDR, author = "Sorin Istrail and Isabelle S. Peter", title = "How Does the Regulatory Genome Work?", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "685--695", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0097", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0097; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0097", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 June 2019", } @Article{Briscoe:2019:UPF, author = "James Briscoe", title = "Understanding Pattern Formation in Embryos: Experiment, Theory, and Simulation", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "696--702", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0090", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0090; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0090", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2019", } @Article{Rothenberg:2019:CGR, author = "Ellen V. Rothenberg", title = "Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "703--718", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0098", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0098; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0098", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2019", } @Article{Ciau-Uitz:2019:GRN, author = "Aldo Ciau-Uitz and Roger Patient", title = "Gene Regulatory Networks Governing the Generation and Regeneration of Blood", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "719--725", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0114", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0114; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0114", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2019", } @Article{Travis:2019:CMP, author = "Anthony S. Travis", title = "Chemical Modeling: From {Paul Ehrlich}'s Dyes to $ \beta $-Blockers --- A Brief History", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "726--734", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0092", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0092; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0092", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2019", } @Article{Erwin:2019:PGT, author = "Douglas H. Erwin", title = "Prospects for a General Theory of Evolutionary Novelty", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "735--744", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0089", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0089; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0089", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2019", } @Article{Engel:2019:CGB, author = "Jonathan Engel and Isana Veksler-Lublinsky and Michal Ziv-Ukelson", title = "Constrained Gene Block Discovery and Its Application to Prokaryotic Genomes", journal = j-J-COMPUT-BIOL, volume = "26", number = "7", pages = "745--766", month = jul, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:55 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0096; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0096", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2019", } @Article{Cai:2019:PIS, author = "Zhipeng Cai and Pavel Skums and Alexander Zelikovsky", title = "Preface: {14th International Symposium on Bioinformatics Research and Applications (ISBRA 2018)}", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "767--768", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.29022.zc", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.29022.zc", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2019", } @Article{Li:2019:DSF, author = "Huiyu Li and Sheng-Jun Li and Junliang Shang and Jin-Xing Liu and Chun-Hou Zheng", title = "A Dynamic Scale-Free Network Particle Swarm Optimization for Extracting Features on Multi-Omics Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "769--781", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0185; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0185", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2018", } @Article{Gogolewski:2019:TRP, author = "Krzysztof Gogolewski and Maciej Sykulski and Neo Christopher Chung and Anna Gambin", title = "Truncated Robust Principal Component Analysis and Noise Reduction for Single Cell {RNA} Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "782--793", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0255", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0255; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0255", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 May 2019", } @Article{Yohay:2019:EEM, author = "Ben Yohay and Sagi Snir", title = "Extending the Evolvability Model to the Prokaryotic World: Simulations and Results on Real Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "794--805", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0189; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 November 2018", } @Article{Snir:2019:BIG, author = "Sagi Snir", title = "Bounds on Identification of Genome Evolution Pacemakers", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "806--821", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0178", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0178; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0178", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 January 2019", } @Article{Moussa:2019:LSI, author = "Marmar Moussa and Ion I. M{\u{a}}ndoiu", title = "Locality Sensitive Imputation for Single Cell {RNA-Seq} Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "822--835", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0236", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0236; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0236", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2019", } @Article{Chen:2019:IIB, author = "Qingfeng Chen and Canshang Deng and Wei Lan and Zhixian Liu and Ruiqing Zheng and Jin Liu and Jianxin Wang", title = "Identifying Interactions Between Kinases and Substrates Based on Protein--Protein Interaction Network", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "836--845", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0048", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0048; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0048", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2019", } @Article{Kopp:2019:DMM, author = "Wolfgang Kopp and Martin Vingron", title = "{DNA} Motif Match Statistics Without {Poisson} Approximation", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "846--865", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0144", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0144; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0144", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2019", } @Article{Acosta:2019:MMI, author = "Juan Pablo Acosta and Silvia Restrepo and Juan David Henao and Liliana L{\'o}pez-Kleine", title = "Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "866--874", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0013", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0013; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0013", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 May 2019", } @Article{Chung:2019:MIC, author = "Dahye Chung and Kaiyuan Zhang and Jihoon Yang", title = "Method for Identifying Cancer-Related Genes Using Gene Similarity-Based Collaborative Filtering", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "875--881", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0115; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0115", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 May 2019", } @Article{Hussain:2019:PDT, author = "Shahid Hussain and Javed Ferzund and Raza Ul-Haq", title = "Prediction of Drug Target Sensitivity in Cancer Cell Lines Using {Apache Spark}", journal = j-J-COMPUT-BIOL, volume = "26", number = "8", pages = "882--889", month = aug, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:57 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0102; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0102", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 May 2019", } @Article{Martin-Vide:2019:P, author = "Carlos Mart{\'\i}n-Vide and Miguel A. Vega-Rodr{\'\i}guez", title = "Preface", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "891--892", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.29023.cmv", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.29023.cmv", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2019", } @Article{Jansson:2019:EAR, author = "Jesper Jansson and Ramesh Rajaby and Wing-Kin Sung", title = "An Efficient Algorithm for the Rooted Triplet Distance Between Galled Trees", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "893--907", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0033", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0033; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0033", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2019", } @Article{Silva:2019:UMF, author = "Gabriel H. G. Silva and Edans F. O. Sandes and George Teodoro and Alba C. M. A. Melo", title = "Using Multiple {Fickett} Bands to Accelerate Biological Sequence Comparisons", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "908--922", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0031", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0031; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0031", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2019", } @Article{Hayashi:2019:ANB, author = "Shuto Hayashi and Takuya Moriyama and Rui Yamaguchi and Shinichi Mizuno and Mitsuhiro Komura and Satoru Miyano and Hidewaki Nakagawa and Seiya Imoto", title = "{ALPHLARD-NT}: {Bayesian} Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "923--937", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0224", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0224; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0224", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 April 2019", } @Article{Wang:2019:ECL, author = "Xiaodong Wang and Lei Wang and Daxin Zhu", title = "Efficient Computation of Longest Common Subsequences with Multiple Substring Inclusive Constraints", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "938--947", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0008; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0008", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2019", } @Article{Bonizzoni:2019:MMB, author = "Paola Bonizzoni and Gianluca Della Vedova and Yuri Pirola and Marco Previtali and Raffaella Rizzi", title = "Multithread Multistring {Burrows--Wheeler} Transform and Longest Common Prefix Array", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "948--961", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0230", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/multithreading.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0230; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0230", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2019", } @Article{Yildiz:2019:MDS, author = "Muslum Yildiz and Abdulkadir Kocak", title = "Molecular Dynamics Studies of Histo-Blood Group Antigen Blocking Human Immunoglobulin {A} Antibody and Escape Mechanism in Noroviruses Upon Mutation", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "962--974", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0163", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0163; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0163", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2018", } @Article{Yang:2019:RLN, author = "Yushuang Yang and Wei Yang and Ling Jin", title = "The Role of Long Non-coding {RNA} Prostate Cancer-Associated Transcript 1 in Prostate Cancer", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "975--984", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0240", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0240; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0240", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 May 2019", } @Article{Rahman:2019:ATH, author = "Mohammad S. Rahman and Gholamreza Haffari", title = "Analyzing Tumor Heterogeneity by Incorporating Long-Range Mutational Influences and Multiple Sample Data into Heterogeneity Factorial Hidden {Markov} Model", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "985--1002", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0242", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0242; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0242", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 May 2019", } @Article{Demongeot:2019:BDC, author = "Jacques Demongeot and Herv{\'e} Seligmann", title = "Bias for 3$^\prime $-Dominant Codon Directional Asymmetry in Theoretical Minimal {RNA} Rings", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "1003--1012", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0256", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0256; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0256", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 May 2019", } @Article{Ge:2019:PGI, author = "Fangfang Ge and Yi Wang and Huayang Li and Rui Zhang and Xiaotong Wang and Qingyun Li and Zhenchang Liang and Long Yang", title = "{Plant-GQ}: an Integrative Database of {G}-Quadruplex in Plant", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "1013--1019", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0010", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0010; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0010", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2019", } @Article{Li:2019:SAS, author = "Zhicheng Li and Shijian Li and Xian Wei and Qing Zhao", title = "Scaled Alternating Steepest Descent Algorithm Applied for Protein Structure Determination from Nuclear Magnetic Resonance Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "1020--1029", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0013", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0013; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0013", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2019", } @Article{Mao:2019:PPA, author = "Guo Mao and Shu-Lin Wang and Wei Zhang", title = "Prediction of Potential Associations Between {MicroRNA} and Disease Based on {Bayesian} Probabilistic Matrix Factorization Model", journal = j-J-COMPUT-BIOL, volume = "26", number = "9", pages = "1030--1039", month = sep, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0012", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Oct 8 06:02:58 MDT 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0012; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0012", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 June 2019", } @Article{Solodskikh:2019:PER, author = "Sergey A. Solodskikh and Alexey S. Velikorondy and Vasily N. Popov", title = "Predictive Estimates of Risks Associated with Type 2 Diabetes Mellitus on the Basis of Biochemical Biomarkers and Derived Time-Dependent Parameters", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1041--1049", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0028", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0028; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0028", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2019", } @Article{Yang:2019:MBO, author = "Louis Z. Yang and Ming Yang", title = "Modeling Biological Oscillations: Integration of Short Reaction Pauses into a Stationary Model of a Negative Feedback Loop Generates Sustained Long Oscillations", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1050--1066", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0017", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0017; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0017", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2019", } @Article{Ye:2019:OMM, author = "Yan Ye and Chunde Bao and Wei Fan", title = "Overexpression of {miR-101} {May} Target {DUSP1} to Promote the Cartilage Degradation in Rheumatoid Arthritis", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1067--1079", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0021", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0021; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0021", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 June 2019", } @Article{Li:2019:ICG, author = "Qi Li and Zhengqiang Luo", title = "Identification of Candidate Genes for Skeletal Muscle Injury Prevention in Two Different Types", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1080--1089", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0022", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0022; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0022", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 May 2019", } @Article{Li:2019:TRN, author = "Qi Li and Zhengqiang Luo", title = "Transcriptional Regulatory Network Analysis to Reveal the Key Genes Involved in Skeletal Muscle Injury", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1090--1099", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0025", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0025; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0025", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 May 2019", } @Article{Budhlakoti:2019:CSS, author = "Neeraj Budhlakoti and Dwijesh Chandra Mishra and Anil Rai and S. B. Lal and Krishna Kumar Chaturvedi and Rajeev Ranjan Kumar", title = "A Comparative Study of Single-Trait and Multi-Trait Genomic Selection", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1100--1112", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0032", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0032; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0032", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2019", } @Article{Liang:2019:IMD, author = "Xiao Liang and William Chad Young and Ling-Hong Hung and Adrian E. Raftery and Ka Yee Yeung", title = "Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1113--1129", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0036", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0036; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0036", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2019", } @Article{Sun:2019:BAS, author = "Chao Sun and Yifan Gu and Guoqing Chen and Yibao Du", title = "Bioinformatics Analysis of Stromal Molecular Signatures Associated with Breast and Prostate Cancer", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1130--1139", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0045", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0045; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0045", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2019", } @Article{Wang:2019:DMM, author = "Liang Wang and Yuquan Pei and Shaolei Li and Shanyuan Zhang and Yue Yang", title = "Distinct Molecular Mechanisms Analysis of Three Lung Cancer Subtypes Based on Gene Expression Profiles", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1140--1155", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0046", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0046; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0046", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2019", } @Article{Ghrifi:2019:CSA, author = "Fatima Ghrifi and Loubna Allam and Lakhlili Wiame and Azeddine Ibrahimi", title = "Curcumin-Synthetic Analogs Library Screening by Docking and Quantitative Structure--Activity Relationship Studies for {AXL} Tyrosine Kinase Inhibition in Cancers", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1156--1167", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0052", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0052; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0052", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2019", } @Article{Zhang:2019:IAG, author = "Yudong Zhang and Wenxiang Wu and Hao Qu", title = "Integrated Analysis of the Gene Expression Changes During Colorectal Cancer Progression by Bioinformatic Methods", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1168--1176", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0056", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0056; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0056", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 June 2019", } @Article{Urrutia-Baca:2019:IAD, author = "Victor Hugo Urrutia-Baca and Ricardo Gomez-Flores and Myriam Ang{\'e}lica {De La Garza-Ramos} and Patricia Tamez-Guerra and Daniela Guadalupe Lucio-Sauceda and Mar{\'\i}a Cristina Rodr{\'\i}guez-Padilla", title = "Immunoinformatics Approach to Design a Novel Epitope-Based Oral Vaccine Against \bioname{Helicobacter pylori}", journal = j-J-COMPUT-BIOL, volume = "26", number = "10", pages = "1177--1190", month = oct, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0062", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:52 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0062; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0062", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 May 2019", } @Article{Rosenthal:2019:BET, author = "Michael Rosenthal and Darshan Bryner and Fred Huffer and Shane Evans and Anuj Srivastava and Nicola Neretti", title = "{Bayesian} Estimation of Three-Dimensional Chromosomal Structure from Single-Cell {Hi-C} Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1191--1202", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0100; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0100", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 June 2019", } @Article{Wu:2019:IIA, author = "Yue Wu and Farhad Hormozdiari and Jong Wha J. Joo and Eleazar Eskin", title = "Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1203--1213", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0139", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0139; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0139", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 October 2018", } @Article{Cunha:2019:GRM, author = "Lu{\'\i}s Felipe I. Cunha and F{\'a}bio Protti", title = "Genome Rearrangements on Multigenomic Models: Applications of Graph Convexity Problems", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1214--1222", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0091", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0091; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0091", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 May 2019", } @Article{Oliveira:2019:CSR, author = "Andre Rodrigues Oliveira and Klairton Lima Brito and Ulisses Dias and Zanoni Dias", title = "On the Complexity of Sorting by Reversals and Transpositions Problems", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1223--1229", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0078; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0078", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 May 2019", } @Article{Yan:2019:BND, author = "Chao-Kun Yan and Wen-Xiu Wang and Ge Zhang and Jian-Lin Wang and Ashutosh Patel", title = "{BiRWDDA}: a Novel Drug Repositioning Method Based on Multisimilarity Fusion", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1230--1242", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0063", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0063; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0063", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2019", } @Article{Dong:2019:DFC, author = "Chaoxuan Dong and Xiao-Yan Chen and Chao-Yi Dong", title = "Discerning Functional Connections in the Pulsed Neural Networks with the Dynamic {Bayesian} Network Structure Search Method Based on a Genetic Algorithm", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1243--1252", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0147", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0147; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0147", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 June 2019", } @Article{Suvorova:2019:NMP, author = "Yulia M. Suvorova and Eugene V. Korotkov", title = "New Method for Potential Fusions Detection in Protein-Coding Sequences", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1253--1261", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0122", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0122; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0122", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 June 2019", } @Article{Liu:2019:CAC, author = "Bao-Xinzi Liu and Guan-Jiang Huang and Hai-Bo Cheng", title = "Comprehensive Analysis of Core Genes and Potential Mechanisms in Rectal Cancer", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1262--1277", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0073", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0073; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0073", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 June 2019", } @Article{Li:2019:IKB, author = "Feng Li and Peiyuan Guo and Keqin Dong and Peng Guo and Haoyuan Wang and Xianqiang Lv", title = "Identification of Key Biomarkers and Potential Molecular Mechanisms in Renal Cell Carcinoma by Bioinformatics Analysis", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1278--1295", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0145", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0145; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0145", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2019", } @Article{Ai:2019:QCB, author = "Shangjie Ai and Guanfei Lin and Yong Bai and Xiande Liu and Linghua Piao", title = "{QSAR} Classification-Based Virtual Screening Followed by Molecular Docking Identification of Potential {COX-2} Inhibitors in a Natural Product Library", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1296--1315", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0142", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0142; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0142", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2019", } @Article{Zheng:2019:SSA, author = "Shunxin Zheng and Liuhong Yang and Yisong Dai and Lifang Jiang and Yi Wei and Hongwei Wen and Yingfang Xu", title = "Screening and Survival Analysis of Hub Genes in Gastric Cancer Based on Bioinformatics", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1316--1325", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0119", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0119; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0119", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2019", } @Article{Li:2019:RMQ, author = "Yufang Li and Aoshen Wu and Gang Liu and Lei Liu", title = "A Review of Methods to Quantify the Genomic Similarity of Topological Associating Domains", journal = j-J-COMPUT-BIOL, volume = "26", number = "11", pages = "1326--1338", month = nov, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0129", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Nov 30 06:32:54 MST 2019", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0129; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0129", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2019", } @Article{Kazakiewicz:2019:MNB, author = "Denis Kazakiewicz and J{\"u}rgen Claesen and Katarzyna G{\'o}rczak and Dariusz Plewczynski and Tomasz Burzykowski", title = "A Multivariate Negative-Binomial Model with Random Effects for Differential Gene-Expression Analysis of Correlated {mRNA} Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1339--1348", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0168", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0168; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0168", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 July 2019", } @Article{Toubiana:2019:GAO, author = "David Toubiana and Rami Puzis and Avi Sadka and Eduardo Blumwald", title = "A Genetic Algorithm to Optimize Weighted Gene Co-Expression Network Analysis", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1349--1366", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0221", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0221; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0221", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2019", } @Article{Shen:2019:MMD, author = "Kexin Shen and Shujuan Zhang and Shurong Ma and Haishan Zhang", title = "Molecular Markers and Diagnostic Model Specific for {Barrett}'s Esophagus", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1367--1378", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0064; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0064", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2019", } @Article{Qiu:2019:EDE, author = "Yong Qiu and Ling-bing Meng and Chen-yi Di and Yu-hu Huo and Bo-chen Yao and Teng-jiao Zhang and Zhen Hua", title = "Exploration of the Differentially Expressed Long Noncoding {RNAs} and Genes of Morphine Tolerance via Bioinformatic Analysis", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1379--1393", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0188", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0188; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0188", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 July 2019", } @Article{Wu:2019:IMM, author = "Jie Wu and Yijian Zhang and Maolan Li", title = "Identification of Methylation Markers and Differentially Expressed Genes with Prognostic Value in Breast Cancer", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1394--1408", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0179", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0179; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0179", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 July 2019", } @Article{Jia:2019:IFC, author = "Xi Jia and Qian Zhao and Yuanyuan Zhang and Yiping Dong and Li Lei and Ramone A. Williamson and Yutiantian Lei and Xinyue Tan and Dan Zhang and Jinsong Hu", title = "Identification of a Five-{CpG} Signature with Diagnostic Value in Thyroid Cancer", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1409--1417", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0165", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0165; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0165", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 July 2019", } @Article{Chen:2019:BAD, author = "Hengxi Chen and Shuting Cheng and Chang Liu and Jing Fu and Wei Huang", title = "Bioinformatics Analysis of Differentially Expressed Genes, Methylated Genes, and {miRNAs} in Unexplained Recurrent Spontaneous Abortion", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1418--1426", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0158", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0158; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0158", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2019", } @Article{Sharma:2019:SBA, author = "B. Sharan Sharma and Prabodha K. Swain and Ramtej J. Verma", title = "A Systematic Bioinformatics Approach to {Motif}-Based Analysis of Human Locus Control Regions", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1427--1437", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0155", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0155; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0155", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 July 2019", } @Article{Liu:2019:KGI, author = "Xinxin Liu and Xinqiang Li", title = "Key Genes Involved in Diabetic Nephropathy Investigated by Microarray Analysis", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1438--1447", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0182", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0182; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0182", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2019", } @Article{Wen:2019:ENB, author = "Mingxiang Wen and Xiang Qu and Yanyan Zhu and Lingfang Tian and Zhongqin Shen and Xiulin Yang and Xianqing Shi", title = "Exploration of Novel Biomarkers in Vasculitis by Integrated Bioinfomatic Approaches", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1448--1457", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0176", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0176; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0176", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2019", } @Article{Tarraga:2019:PIA, author = "Wilson Alberto T{\'a}rraga and Horacio Alberto Garda and Juan Domingo Toledo and Marina Cecilia Gonzalez", title = "Potential Inhibitors of the Activity of the Cholesterol-Ester Transfer Protein", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1458--1469", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0227", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0227; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0227", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 July 2019", } @Article{Mishra:2019:INS, author = "Avinash Mishra and Megan Cross and Andreas Hofmann and Mark J. Coster and Abdul Karim and Abdul Sattar", title = "Identification of a Novel Scaffold for Inhibition of Dipeptidyl Peptidase-4", journal = j-J-COMPUT-BIOL, volume = "26", number = "12", pages = "1470--1486", month = dec, year = "2019", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0201", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:44 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0201; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0201", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2019", } @Article{Zhang:2020:IHG, author = "Rupeng Zhang and Leifeng Lv and Wenrui Ban and Xiaoqian Dang and Chen Zhang", title = "Identification of Hub Genes in {Duchenne} Muscular Dystrophy: Evidence from Bioinformatic Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "1--8", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0167", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0167; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0167", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2019", } @Article{Xu:2020:DAM, author = "Yangchun Xu and Yan Mu and Ling Wang and Xuan Zhang", title = "Detailed Analysis of Molecular Mechanisms in Primary and Metastatic Melanoma", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "9--19", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0197; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0197", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 August 2019", } @Article{Ilan:2020:ATR, author = "Yaron Ilan", title = "Advanced Tailored Randomness: a Novel Approach for Improving the Efficacy of Biological Systems", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "20--29", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0231", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0231; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0231", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 August 2019", } @Article{Zhao:2020:MLP, author = "Jing Zhao and Linlin Yin and Ling He", title = "The {MicroRNA} Landscapes Profiling Reveals Potential Signatures of Necrotizing Enterocolitis in Infants", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "30--39", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0183", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0183; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0183", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2019", } @Article{Yang:2020:IKB, author = "Bao Yang and Keqin Dong and Peiyuan Guo and Peng Guo and Guo Jie and Guanhua Zhang and Tianke Li", title = "Identification of Key Biomarkers and Potential Molecular Mechanisms in Oral Squamous Cell Carcinoma by Bioinformatics Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "40--54", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0211", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0211; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0211", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 August 2019", } @Article{Zou:2020:IFE, author = "Yang-fan Zou and Ling-bing Meng and Qing-qing Wang and Zhao-kai He and Chen-hao Hu and Meng-jie Shan and Deng-yuan Wang and Xin Yu", title = "Identification and Functional Enrichment Analysis of Potential Diagnostic and Therapeutic Targets in Adamantinomatous Craniopharyngioma", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "55--68", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0184", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0184; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0184", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 August 2019", } @Article{Chen:2020:IBA, author = "Mengwei Chen and Chengqi Kong and Zhiyuan Zheng and Yin Li", title = "Identification of Biomarkers Associated with Septic Cardiomyopathy Based on Bioinformatics Analyses", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "69--80", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0181", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0181; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0181", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 August 2019", } @Article{Hu:2020:PMI, author = "Guozhang Hu and Rui Wang and Bo Wei and Le Wang and Qi Yang and Daliang Kong and Chao Du", title = "Prognostic Markers Identification in Glioma by Gene Expression Profile Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "81--90", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0217", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0217; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0217", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2019", } @Article{Mohanty:2020:IMT, author = "Partha Sarathi Mohanty and Sandeep Sharma and Farah Naaz and Dilip Kumar and Archana Raikwar and Shripad A. Patil", title = "Inhibition of \bioname{Mycobacterium tuberculosis} {tRNA}-Ligases Using {siRNA}-Based Gene Silencing Method: a Computational Approach", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "91--99", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0156; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0156", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 August 2019", } @Article{Liu:2020:IBA, author = "Shanshan Liu and Wenjuan Tian and Burong Li", title = "Integrative Bioinformatics Analysis Identifies {NEK2} as a Potential Biomarker in Head and Neck Squamous Cell Carcinoma", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "100--108", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0208", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0208; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0208", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 August 2019", } @Article{Shi:2020:CDM, author = "Ke Shi and Meng-na Ge and Xiao-qiao Chen", title = "Coordinated {DNA} Methylation and Gene Expression Data for Identification of the Critical Genes Associated with Childhood Atopic Asthma", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "109--120", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0194", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0194; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0194", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 August 2019", } @Article{Zhang:2020:IDE, author = "Zhenan Zhang and Yuqin Liu and Wei Wang and Yue Xing and Nanyang Jiang and Hongrui Zhang and Hanwen Zhang and Lei He and Wei Yue and Lianju Jiang and Kaili Wang", title = "Identification of Differentially Expressed Genes Associated with Lymph Node Tuberculosis by the Bioinformatic Analysis Based on a Microarray", journal = j-J-COMPUT-BIOL, volume = "27", number = "1", pages = "121--130", month = jan, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0161", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:46 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0161; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0161", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 August 2019", } @Article{Cai:2020:PSI, author = "Zhipeng Cai and Pavel Skums and Alexander Zelikovsky", title = "Preface Special Issue: {15th International Symposium on Bioinformatics Research and Applications (ISBRA 2019)}", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "131--132", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.29024.zc", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.29024.zc", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 February 2020", } @Article{Bruner:2020:RAD, author = "Ariel Bruner and Roded Sharan", title = "A Robustness Analysis of Dynamic {Boolean} Models of Cellular Circuits", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "133--143", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0290", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0290; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0290", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 November 2019", } @Article{Gouveia:2020:RBM, author = "Filipe Gouveia and In{\^e}s Lynce and Pedro T. Monteiro", title = "Revision of {Boolean} Models of Regulatory Networks Using Stable State Observations", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "144--155", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0289", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0289; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0289", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2019", } @Article{Brito:2020:SGR, author = "Klairton Lima Brito and G{\'e}raldine Jean and Guillaume Fertin and Andre Rodrigues Oliveira and Ulisses Dias and Zanoni Dias", title = "Sorting by Genome Rearrangements on Both Gene Order and Intergenic Sizes", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "156--174", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0293", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0293; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0293", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 December 2019", } @Article{Chen:2020:CCP, author = "Zhi-zhong Chen and Shohei Ueta and Jingyu Li and Lusheng Wang", title = "Computing a Consensus Phylogeny via Leaf Removal", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "175--188", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0269", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0269; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0269", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2019", } @Article{Delfino:2020:ESS, author = "Francesco Delfino and Yuri Porozov and Eugene Stepanov and Gaik Tamazian and Valentina Tozzini", title = "Evolutionary Switches Structural Transitions via Coarse-Grained Models", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "189--199", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0338", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0338; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0338", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 November 2019", } @Article{Liu:2020:MSB, author = "Lixin Liu and Haitao Jiang and Peiqiang Liu and Binhai Zhu and Daming Zhu", title = "Maximum Stacking Base Pairs: Hardness and Approximation by Nonlinear Linear Programming-Rounding", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "200--211", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0288", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0288; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0288", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2020", } @Article{Wang:2020:CFD, author = "Zihao Wang and Jingrong Zhang and Weifang Gao and Zhiyong Liu and Xiaohua Wan and Fa Zhang", title = "A Consensus Framework of Distributed Multiple-Tilt Reconstruction in Electron Tomography", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "212--222", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0287", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0287; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0287", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 December 2019", } @Article{Petrucci:2020:ISS, author = "Enrico Petrucci and Laurent No{\'e} and Cinzia Pizzi and Matteo Comin", title = "Iterative Spaced Seed Hashing: Closing the Gap Between Spaced Seed Hashing and $k$-mer Hashing", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "223--233", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0298", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/hash.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0298; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0298", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2019", } @Article{Fiosina:2020:EDL, author = "Jelena Fiosina and Maksims Fiosins and Stefan Bonn", title = "Explainable Deep Learning for Augmentation of Small {RNA} Expression Profiles", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "234--247", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0320", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0320; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0320", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 December 2019", } @Article{Desai:2020:CSU, author = "Heta P. Desai and Anuja P. Parameshwaran and Rajshekhar Sunderraman and Michael Weeks", title = "Comparative Study Using Neural Networks for {16S} Ribosomal Gene Classification", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "248--258", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0436", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0436; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0436", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 February 2020", } @Article{Wimberley:2020:PAC, author = "Charles E. Wimberley and Steffen Heber", title = "{PeakPass}: Automating {ChIP-Seq} Blacklist Creation", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "259--268", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0295", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0295; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0295", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 December 2019", } @Article{Andersen:2020:CGT, author = "Jakob L. Andersen and Daniel Merkle and Peter S. Rasmussen", title = "Combining Graph Transformations and Semigroups for Isotopic Labeling Design", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "269--287", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0291", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0291; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0291", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 November 2019", } @Article{Hernandez-lopez:2020:TDT, author = "Ana A. Hernandez-lopez and Claudio Alberti and Marco Mattavelli", title = "Toward a Dynamic Threshold for Quality Score Distortion in Reference-Based Alignment", journal = j-J-COMPUT-BIOL, volume = "27", number = "2", pages = "288--300", month = feb, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0333", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Feb 11 17:17:47 MST 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0333; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0333", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 December 2019", } @Article{Istrail:2020:PSI, author = "Sorin Istrail", title = "Preface Special Issue: {RECOMB 2018}", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "301", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.29026.si", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.29026.si", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2020", } @Article{Bonnet:2020:DRS, author = "{\'E}douard Bonnet and Pawe{\l} Rz{\k{a}}{\.z}ewski and Florian Sikora", title = "Designing {RNA} Secondary Structures Is Hard", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "302--316", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0420", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0420; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0420", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2020", } @Article{Boroojeny:2020:GTE, author = "Ali Ebrahimpour Boroojeny and Akash Shrestha and Ali Sharifi-Zarchi and Suzanne Renick Gallagher and S. Cenk Sahinalp and Hamidreza Chitsaz", title = "Graph Traversal Edit Distance and Extensions", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "317--329", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0511", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0511; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0511", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2020", } @Article{Chakraborty:2020:CRN, author = "Shounak Chakraborty and Stefan Canzar and Tobias Marschall and Marcel H. Schulz", title = "Chromatyping: Reconstructing Nucleosome Profiles from {NOMe} Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "330--341", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0457", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0457; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0457", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2020", } @Article{Gortler:2020:LFL, author = "Franziska G{\"o}rtler and Marian Sch{\"o}n and Jakob Simeth and Stefan Solbrig and Tilo Wettig and Peter J. Oefner and Rainer Spang and Michael Altenbuchinger", title = "Loss-Function Learning for Digital Tissue Deconvolution", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "342--355", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0462", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0462; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0462", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2020", } @Article{Hoinka:2020:AOW, author = "Jan Hoinka and Yijie Wang and Teresa M. Przytycka", title = "{AptaBlocks} Online: a {Web}-Based Toolkit for the In Silico Design of Oligonucleotide Sticky Bridges", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "356--360", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0470", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0470; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0470", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2020", } @Article{Larson:2020:INN, author = "Gary Larson and Jeffrey L. Thorne and Scott Schmidler", title = "Incorporating Nearest-Neighbor Site Dependence into Protein Evolution Models", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "361--375", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0500", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0500; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0500", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2020", } @Article{Orenstein:2020:RBU, author = "Yaron Orenstein", title = "Reverse {de Bruijn}: Utilizing Reverse Peptide Synthesis to Cover All Amino Acid $k$-mers", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "376--385", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0448", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0448; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0448", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2020", } @Article{Schon:2020:DRP, author = "Marian Sch{\"o}n and Jakob Simeth and Paul Heinrich and Franziska G{\"o}rtler and Stefan Solbrig and Tilo Wettig and Peter J. Oefner and Michael Altenbuchinger and Rainer Spang", title = "{DTD}: an {R} Package for Digital Tissue Deconvolution", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "386--389", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0469", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/s-plus.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0469; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0469", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2020", } @Article{Soule:2020:NLC, author = "Antoine Soul{\'e} and Jean-Marc Steyaert and J{\'e}r{\^o}me Waldisp{\"u}hl", title = "A Nested $2$-Level Cross-Validation Ensemble Learning Pipeline Suggests a Negative Pressure Against Crosstalk {snoRNA-mRNA} Interactions in {{\em Saccharomyces cerevisiae\/}}", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "390--402", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0464", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0464; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0464", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2020", } @Article{Sverchkov:2020:CSN, author = "Yuriy Sverchkov and Yi-hsuan Ho and Audrey Gasch and Mark Craven", title = "Context-Specific Nested Effects Models", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "403--417", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0459", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0459; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0459", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2020", } @Article{Wu:2020:UFI, author = "Yue Wu and Eleazar Eskin and Sriram Sankararaman", title = "A Unifying Framework for Imputing Summary Statistics in Genome-Wide Association Studies", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "418--428", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0449", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0449; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0449", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 February 2020", } @Article{Yamada:2020:CMI, author = "Naomi Yamada and Prashant Kumar Kuntala and B. Franklin Pugh and Shaun Mahony", title = "{ChExMix}: a Method for Identifying and Classifying {Protein--DNA} Interaction Subtypes", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "429--435", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0466", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0466; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0466", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 February 2020", } @Article{Boroojeny:2020:PPA, author = "Ali Ebrahimpour Boroojeny and Akash Shrestha and Ali Sharifi-zarchi and Suzanne Renick Gallagher and S{\"u}leyman Cenk Sahinalp and Hamidreza Chitsaz", title = "{PyGTED}: {Python} Application for Computing Graph Traversal Edit Distance", journal = j-J-COMPUT-BIOL, volume = "27", number = "3", pages = "436--439", month = mar, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0510", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:01 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/python.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0510; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0510", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2020", } @Article{Cowen:2020:PSI, author = "Lenore J. Cowen", title = "Preface Special Issue: {RECOMB 2019}", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "441", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.29027.ljc", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.29027.ljc", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 April 2020", } @Article{Benner:2020:MMS, author = "Philipp Benner and Martin Vingron", title = "{ModHMM}: a Modular Supra-{Bayesian} Genome Segmentation Method", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "442--457", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0280", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0280; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0280", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 December 2019", } @Article{Gong:2020:MDM, author = "Boying Gong and Elizabeth Purdom", title = "{MethCP}: Differentially Methylated Region Detection with Change Point Models", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "458--471", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0326", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0326; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0326", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 March 2020", } @Article{Sahlin:2020:NCL, author = "Kristoffer Sahlin and Paul Medvedev", title = "{De Novo} Clustering of Long-Read Transcriptome Data Using a Greedy, Quality Value-Based Algorithm", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "472--484", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0299", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0299; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0299", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 March 2020", } @Article{Almodaresi:2020:ESE, author = "Fatemeh Almodaresi and Prashant Pandey and Michael Ferdman and Rob Johnson and Rob Patro", title = "An Efficient, Scalable, and Exact Representation of High-Dimensional Color Information Enabled Using {de Bruijn} Graph Search", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "485--499", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0322", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0322; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0322", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 March 2020", } @Article{Kuhnle:2020:ECC, author = "Alan Kuhnle and Taher Mun and Christina Boucher and Travis Gagie and Ben Langmead and Giovanni Manzini", title = "Efficient Construction of a Complete Index for Pan-Genomics Read Alignment", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "500--513", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0309", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0309; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0309", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 March 2020", } @Article{Mun:2020:MRM, author = "Taher Mun and Alan Kuhnle and Christina Boucher and Travis Gagie and Ben Langmead and Giovanni Manzini", title = "Matching Reads to Many Genomes with the $r$-Index", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "514--518", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0316", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0316; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0316", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 March 2020", } @Article{Pan:2020:OOM, author = "Weihua Pan and Tao Jiang and Stefano Lonardi", title = "{OMGS}: Optical Map-Based Genome Scaffolding", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "519--533", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0310", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0310; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0310", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2019", } @Article{Pellegrina:2020:FAF, author = "Leonardo Pellegrina and Cinzia Pizzi and Fabio Vandin", title = "Fast Approximation of Frequent $k$-Mers and Applications to Metagenomics", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "534--549", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0314", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0314; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0314", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2019", } @Article{Jou:2020:MAR, author = "Jonathan D. Jou and Graham T. Holt and Anna U. Lowegard and Bruce R. Donald", title = "Minimization-Aware Recursive {$ K* $}: a Novel, Provable Algorithm that Accelerates Ensemble-Based Protein Design and Provably Approximates the Energy Landscape", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "550--564", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0315", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0315; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0315", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 December 2019", } @Article{Lei:2020:TCN, author = "Haoyun Lei and Bochuan Lyu and E. Michael Gertz and Alejandro A. Sch{\"a}ffer and Xulian Shi and Kui Wu and Guibo Li and Liqin Xu and Yong Hou and Michael Dean and Russell Schwartz", title = "Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "565--598", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0302", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0302; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0302", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 March 2020", } @Article{Mefford:2020:EEA, author = "Joel Mefford and Danny Park and Zhili Zheng and Arthur Ko and Mika Ala-Korpela and Markku Laakso and P{\"a}ivi Pajukanta and Jian Yang and John Witte and Noah Zaitlen", title = "Efficient Estimation and Applications of Cross-Validated Genetic Predictions to Polygenic Risk Scores and Linear Mixed Models", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "599--612", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0325", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0325; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0325", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 February 2020", } @Article{Kim:2020:HMS, author = "Younhun Kim and Frederic Koehler and Ankur Moitra and Elchanan Mossel and Govind Ramnarayan", title = "How Many Subpopulations Is Too Many? {Exponential} Lower Bounds for Inferring Population Histories", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "613--625", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0318", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0318; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0318", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2019", } @Article{Karasikov:2020:SBR, author = "Mikhail Karasikov and Harun Mustafa and Amir Joudaki and Sara Javadzadeh-no and Gunnar R{\"a}tsch and Andr{\'e} Kahles", title = "Sparse Binary Relation Representations for Genome Graph Annotation", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "626--639", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0324", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0324; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0324", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2019", } @Article{Jain:2020:CSG, author = "Chirag Jain and Haowen Zhang and Yu Gao and Srinivas Aluru", title = "On the Complexity of Sequence-to-Graph Alignment", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "640--654", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0066", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0066; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0066", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2020", } @Article{Brand:2020:LRM, author = "Lodewijk Brand and Xue Yang and Kai Liu and Saad Elbeleidy and Hua Wang and Hao Zhang and Feiping Nie", title = "Learning Robust Multilabel Sample Specific Distances for Identifying {HIV-1} Drug Resistance", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "655--672", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0329", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0329; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0329", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 November 2019", } @Article{Anonymous:2020:RIP, author = "Anonymous", title = "{{\em Retraction of\/}}: {Identification of Prognosis Biomarkers of Prostatic Cancer in a Cohort of 498 Patients from TCGA, by Chen Z, Hu H. (J Comput Biol Dec 2019: epub ahead of print; DOI: 10.1089/cmb.2019.0224)}", journal = j-J-COMPUT-BIOL, volume = "27", number = "4", pages = "673", month = apr, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0224.retract", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:02 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0224.retract", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 March 2020", } @Article{Gusev:2020:ASS, author = "Yury Gusev and Svyatoslav Mazilov and Irina Volokhina and Mikhail Chumakov", title = "Agrobacterial, Single-Stranded {DNA-Binding} Protein {VirE2} and Its Complexes", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "675--682", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0243; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0243", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2019", } @Article{Garcia-Maya:2020:IWB, author = "Brenda Ivette Garcia-Maya and Nikolaos Limnios", title = "Identification of Words in Biological Sequences Under the Semi-{Markov} Hypothesis", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "683--697", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0253", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0253; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0253", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 September 2019", } @Article{Zhang:2020:BNB, author = "Lixia Zhang and Leonardo O. Rodrigues and Niven R. Narain and Viatcheslav R. Akmaev", title = "{{\em bAIcis\/}}: a Novel {Bayesian} Network Structural Learning Algorithm and Its Comprehensive Performance Evaluation Against Open-Source Software", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "698--708", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0210", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/gnu.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0210; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0210", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2019", } @Article{Li:2020:RMR, author = "Zhicheng Li and Shijian Li and Xian Wei and Xubiao Peng and Qing Zhao", title = "Recovering the Missing Regions in Crystal Structures from the Nuclear Magnetic Resonance Measurement Data Using Matrix Completion Method", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "709--717", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0107", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0107; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0107", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2019", } @Article{Zhao:2020:CND, author = "Jingwei Zhao and Le Wang and Daliang Kong and Guozhang Hu and Bo Wei", title = "Construction of Novel {DNA} Methylation-Based Prognostic Model to Predict Survival in Glioblastoma", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "718--728", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0125", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0125; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0125", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 August 2019", } @Article{Li:2020:PNA, author = "Lei Li and Linhua Jiang and Sihua Peng", title = "Protein Network Analysis of the Fifth Chromosome of Zebrafish", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "729--737", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0157", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0157; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0157", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 August 2019", } @Article{Jasrotia:2020:GWA, author = "Rahul Singh Jasrotia and Sarika Jaiswal and Pramod Kumar Yadav and Mustafa Raza and Mir Asif Iquebal and Anil Rai and Dinesh Kumar", title = "Genome-Wide Analysis of {HSP70} Family Protein in \bioname{Vigna radiata} and Coexpression Analysis Under Abiotic and Biotic Stress", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "738--754", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0166", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0166; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0166", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 August 2019", } @Article{Dey:2020:GBA, author = "Lopamudra Dey and Anirban Mukhopadhyay", title = "A Graph-Based Approach for Finding the Dengue Infection Pathways in Humans Using Protein--Protein Interactions", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "755--768", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0171", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0171; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0171", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2019", } @Article{Lu:2020:TSE, author = "Ying Lu and Qixiu Lu and Houlin Liu and Jixiang Yu and Chunlei Xin and Yingping Liu and Yanfang Liu and Linlin Fan", title = "Time-Series Expression Analysis of Epidermal Stem Cells from High Fat Diet Mice", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "769--778", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0172", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0172; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0172", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2019", } @Article{Zhang:2020:SBA, author = "Guochang Zhang and Juan Li and Hong Sun and Guanzheng Yang", title = "Screening for the Biomarkers Associated with Myocardial Infarction by Bioinformatics Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "779--785", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0180", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0180; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0180", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2019", } @Article{Baeissa:2020:III, author = "Hanadi M. Baeissa and Frances M. G. Pearl", title = "Identifying the Impact of Inframe Insertions and Deletions on Protein Function in Cancer", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "786--795", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0192", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0192; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0192", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 August 2019", } @Article{Hanson:2020:GKY, author = "Jack Hanson and Kuldip K. Paliwal and Thomas Litfin and Yuedong Yang and Yaoqi Zhou", title = "Getting to Know Your Neighbor: Protein Structure Prediction Comes of Age with Contextual Machine Learning", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "796--814", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0193", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0193; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0193", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 August 2019", } @Article{Xu:2020:NMB, author = "Yangchun Xu and Ling Wang and Lanxiang Jiang and Xuan Zhang", title = "Novel {MicroRNA} Biomarkers, {{\em miR-142-5p}}, {{\em miR-550a}}, {{\em miR-1826}}, and {{\em miR-1201}}, Were Identified for Primary Melanoma", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "815--824", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0198", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0198; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0198", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 September 2019", } @Article{Wang:2020:ISC, author = "Xuedong Wang and Xiaoxi Wang and Xiaoqin Li and Yu Chang", title = "Identification of Specific Candidate Diagnostic Biomarkers for Lung Squamous Cell Carcinoma Based on Methylation", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "825--833", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0213", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0213; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0213", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 September 2019", } @Article{Wu:2020:DMM, author = "Xihai Wu and Yunhui Han and Fangmei Liu and Lihong Ruan", title = "Downregulations of {miR-449a} and {miR-145-5p} Act as Prognostic Biomarkers for Endometrial Cancer", journal = j-J-COMPUT-BIOL, volume = "27", number = "5", pages = "834--844", month = may, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0215", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue Jun 2 19:30:04 MDT 2020", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0215; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0215", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 September 2019", } @Article{Majumdar:2020:IFS, author = "Sayanti Guha Majumdar and Anil Rai and Dwijesh C. Mishra", title = "Integrated Framework for Selection of Additive and Nonadditive Genetic Markers for Genomic Selection", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "845--855", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0223", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0223; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0223", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2019", } @Article{Zhang:2020:AAK, author = "Tongchuan Zhang and Guodong Hu and Yuedong Yang and Jihua Wang and Yaoqi Zhou", title = "All-Atom Knowledge-Based Potential for {RNA} Structure Discrimination Based on the Distance-Scaled Finite Ideal-Gas Reference State", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "856--867", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0251", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0251; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0251", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2019", } @Article{Alyami:2020:NUH, author = "Sultan Alyami and Chun-Hsi Huang", title = "Nongreedy Unbalanced {Huffman} Tree Compressor for Single and Multifasta Files", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "868--876", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0249", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/datacompression.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0249; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0249", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 September 2019", } @Article{Feng:2020:IAD, author = "Ye Feng and Chunyu Shi and Dayu Wang and Xuefeng Wang and Zhi Chen", title = "Integrated Analysis of {DNA} Copy Number Changes and Gene Expression Identifies Key Genes in Gastric Cancer", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "877--887", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0149; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0149", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 September 2019", } @Article{Yu:2020:IBI, author = "Fan Yu and Zhong-Sen Le and Li-Hua Chen and Hong Qian and Bo Yu and Wen-Hua Chen", title = "Identification of Biomolecular Information in Rotenone-Induced Cellular Model of {Parkinson}'s Disease by Public Microarray Data Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "888--903", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 October 2019", } @Article{Ruan:2020:IPG, author = "Sha-Sha Ruan and Yi-Chen Xiao and Pei-Cheng He and Yi Wang and Tao Ma", title = "Identification of Potential Gene Signatures Related to Sleep Deprivation", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "904--913", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0177", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0177; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0177", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 October 2019", } @Article{Mo:2020:KRE, author = "Lujiao Mo and Guanhua Xu and Channi Wu and Kanda Pan and Ping Pan and Lingfeng Yu and Xiaoyuan Shen", title = "Key Regulatory Effect of Activated {{\em HIF-1$ \alpha $ \slash VEGFA\/}} Signaling Pathway in Systemic Capillary Leak Syndrome Confirmed by Bioinformatics Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "914--922", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0222", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0222; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0222", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 September 2019", } @Article{Dong:2020:IMG, author = "Xihua Dong and Xiaoou Yu and Hua Li and Hui Kang", title = "Identification of Marker Genes and Pathways in Patients with Primary Biliary Cholangitis", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "923--933", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0230", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0230; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0230", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2019", } @Article{Chen:2020:LRM, author = "Chian Chen and Hsiuying Wang", title = "Logistic Regression Method for Ligand Discovery", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "934--940", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0232", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0232; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0232", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 September 2019", } @Article{Jukan:2020:VPC, author = "Nermin Jukan and David Zagor{\v{s}}ek and Julija Lazarevi{\v{c}} and Irena Prelo{\v{z}}nik Zupan and Nata{\v{s}}a Debeljak and Miha Mo{\v{s}}kon", title = "{ViDis}: a Platform for Constructing and Sharing of Medical Algorithms", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "941--947", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0238", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0238; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0238", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 October 2019", } @Article{Zhao:2020:HEF, author = "Teng Zhao and Kun Qian and Yi Zhang", title = "High Expression of {{\em FGF5\/}} Is an Independent Prognostic Factor for Poor Overall Survival and Relapse-Free Survival in Lung Adenocarcinoma", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "948--957", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0241", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0241; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0241", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 September 2019", } @Article{Jiang:2020:ITA, author = "Fangping Jiang and Hong Fan and Lian Luo and Yun Li", title = "An Integrative Transcriptome Analysis Reveals Consistently Dysregulated Long Noncoding {RNAs} and Their Transcriptional Regulation Relationships in Heart Failure", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "958--964", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0246", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0246; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0246", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 September 2019", } @Article{Bai:2020:OCK, author = "Lianmei Bai and Yu Ren and Tianqing Cui", title = "Overexpression of {{\em CDCA5}}, {{\em KIF4A}}, {{\em TPX2}}, and {{\em FOXM1\/}} Coregulated Cell Cycle and Promoted Hepatocellular Carcinoma Development", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "965--974", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0254", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0254; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0254", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 October 2019", } @Article{Kanhaiya:2020:IDT, author = "Krishna Kanhaiya and Dwitiya Tyagi-Tiwari", title = "Identification of Drug Targets in Breast Cancer Metabolic Network", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "975--986", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0258", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0258; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0258", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2019", } @Article{Liu:2020:AGE, author = "Ying Liu and Shenghua Xiong and Shiying Liu and Jie Chen and Hao Yang and Gang Liu and Gengmi Li", title = "Analysis of Gene Expression in Bladder Cancer: Possible Involvement of Mitosis and Complement and Coagulation Cascades Signaling Pathway", journal = j-J-COMPUT-BIOL, volume = "27", number = "6", pages = "987--998", month = jun, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0237", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:48 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0237; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0237", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 September 2019", } @Article{AlvesPinto:2020:SIP, author = "Icaro {Alves Pinto} and Nelson Jos{\'e} {Freitas Da Silveira}", title = "In Silico Identification of Potential Inhibitors of the {Wnt} Signaling Pathway in Human Breast Cancer", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "999--1010", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0311", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0311; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0311", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2019", } @Article{Mongia:2020:DDM, author = "Aanchal Mongia and Debarka Sengupta and Angshul Majumdar", title = "{deepMc}: Deep Matrix Completion for Imputation of Single-Cell {RNA-seq} Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1011--1019", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0278", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0278; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0278", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 October 2019", } @Article{Subramanian:2020:RTR, author = "Sai H. Sankara Subramanian and Karpaga Raja Sundari Balachandran and Vijaya Raghavan Rangamaran and Dharani Gopal", title = "{RemeDB}: Tool for Rapid Prediction of Enzymes Involved in Bioremediation from High-Throughput Metagenome Data Sets", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1020--1029", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0345", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0345; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0345", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2019", } @Article{Gu:2020:SPR, author = "Yifan Gu and Guoqing Chen and Yibao Du", title = "Screening of Prognosis-Related Genes in Primary Breast Carcinoma Using Genomic Expression Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1030--1040", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0131", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0131; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0131", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 November 2019", } @Article{Wang:2020:PLS, author = "Weiqing Wang and Shaohua Wang and Xiao Chu and Hui Liu and Ming Xiang", title = "Predicting the Lung Squamous Cell Carcinoma Diagnosis and Prognosis Markers by Unique {DNA} Methylation and Gene Expression Profiles", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1041--1054", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0138", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0138; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0138", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 November 2019", } @Article{Jia:2020:IAM, author = "Xiaochen Jia and Yehui Shi and Yuehong Zhu and Wenjing Meng and Lihong He and Yongsheng Jia and Zhongsheng Tong", title = "Integrated Analysis of {mRNA--miRNA--lncRNA} {ceRNA} Network in Human {HR+\slash Her-2-} Breast Cancer and Triple Negative Breast Cancer", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1055--1066", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0152", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0152; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0152", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2019", } @Article{Tian:2020:DPM, author = "Yingxuan Tian and Min Yu and Li Sun and Linghua Liu and Jun Wang and Ke Hui and Qiaofeng Nan and Xinyu Nie and Yajuan Ren and Xiaoping Ren", title = "Distinct Patterns of {mRNA} and {lncRNA} Expression Differences Between Lung Squamous Cell Carcinoma and Adenocarcinoma", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1067--1078", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0164", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0164; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0164", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 November 2019", } @Article{Zhang:2020:SIK, author = "Meng Zhang and Chen-Yi Di and Peng Guo and Ling-Bing Meng and Meng-Jie Shan and Yong Qiu and Pei-Yuan Guo and Ke-Qin Dong and Qi Xie and Qiang Wang", title = "Screening and Identification of Key Biomarkers in Pancreatic Cancer: Evidence from Bioinformatic Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1079--1091", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0189", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0189; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0189", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2019", } @Article{Zeng:2020:PRR, author = "Tian Zeng and Can Chen and Pan Yang and Wenwei Zuo and Xiaoqing Liu and Yanling Zhang", title = "A Protective Role for {RHOJ} in {NonSmall} Cell Lung Cancer Based on Integrated Bioinformatics Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1092--1103", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0209", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0209; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0209", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2019", } @Article{Wang:2020:SCG, author = "Ruike Wang and Xia Du and Yaqin Zhi", title = "Screening of Critical Genes Involved in Metastasis and Prognosis of High-Grade Serous Ovarian Cancer by Gene Expression Profile Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1104--1114", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0235", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0235; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0235", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 November 2019", } @Article{Niu:2020:WGC, author = "Xiaoguang Niu and Yongtao Xu and Ni Gao and Aiwu Li", title = "Weighted Gene Coexpression Network Analysis Reveals the Critical {lncRNAs} and {mRNAs} in Development of {Hirschsprung}'s Disease", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1115--1129", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0261", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0261; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0261", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 October 2019", } @Article{Deng:2020:PNB, author = "Chao Deng and Timothy Daley and Peter Calabrese and Jie Ren and Andrew D. Smith", title = "Predicting the Number of Bases to Attain Sufficient Coverage in High-Throughput Sequencing Experiments", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1130--1143", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0264", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0264; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0264", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 November 2019", } @Article{Saurabh:2020:SIC, author = "Kumar Saurabh and Maxim Solovchuk and Tony Wen Hann Sheu", title = "Solution of Ion Channel Flow Using Immersed Boundary--Lattice {Boltzmann} Methods", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1144--1156", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0265", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0265; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0265", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 November 2019", } @Article{Asiaee:2020:EGE, author = "Amir Asiaee and Zachary B. Abrams and Samantha Nakayiza and Deepa Sampath and Kevin R. Coombes", title = "Explaining Gene Expression Using Twenty-One {MicroRNAs}", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1157--1170", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0321", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0321; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0321", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 December 2019", } @Article{Pungpapong:2020:IBK, author = "Vitara Pungpapong and Min Zhang and Dabao Zhang", title = "Integrating Biological Knowledge Into Case--Control Analysis Through Iterated Conditional {Modes/Medians} Algorithm", journal = j-J-COMPUT-BIOL, volume = "27", number = "7", pages = "1171--1179", month = jul, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0319", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:50 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0319; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0319", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 November 2019", } @Article{Deblasio:2020:MAT, author = "Dan Deblasio and Kwanho Kim and Carl Kingsford", title = "More Accurate Transcript Assembly via Parameter Advising", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1181--1189", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0286", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0286; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0286", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 April 2020", } @Article{Trong:2020:SGA, author = "Trung Ngo Trong and Juha Mehtonen and Gerardo Gonz{\'a}lez and Roger Kramer and Ville Hautam{\"a}ki and Merja Hein{\"a}niemi", title = "Semisupervised Generative Autoencoder for Single-Cell Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1190--1203", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0337", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0337; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0337", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 December 2019", } @Article{Chen:2020:MMI, author = "Zhenghao Chen and Ilya Soifer and Hugo Hilton and Leeat Keren and Vladimir Jojic", title = "Modeling Multiplexed Images with {{\em Spatial--LDA\/}} Reveals Novel Tissue Microenvironments", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1204--1218", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0340", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0340; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0340", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 April 2020", } @Article{Carter:2020:CPF, author = "Brandon Carter and Maxwell Bileschi and Jamie Smith and Theo Sanderson and Drew Bryant and David Belanger and Lucy J. Colwell", title = "Critiquing Protein Family Classification Models Using Sufficient Input Subsets", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1219--1231", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0339", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0339; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0339", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 December 2019", } @Article{Gorczak:2020:CFA, author = "Katarzyna G{\'o}rczak and J{\"u}rgen Claesen and Tomasz Burzykowski", title = "A Conceptual Framework for Abundance Estimation of Genomic Targets in the Presence of Ambiguous Short Sequencing Reads", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1232--1247", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0272", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0272; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0272", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 December 2019", } @Article{Costa:2020:APA, author = "Evaldo Bezerra Costa and Gabriel Pereira Silva and Marcello Goulart Teixeira", title = "An Approach to Parallel Algorithms for Long {DNA} Sequences Alignment on Manycore Architecture", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1248--1252", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0362", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0362; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0362", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 January 2020", } @Article{Pala:2020:EME, author = "El{\.I}f Pala and Tuba Denk{\c{c}}eken", title = "Evaluation of {miRNA} Expression Profiles in Schizophrenia Using Principal-Component Analysis-Based Unsupervised Feature Extraction Method", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1253--1263", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0412", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0412; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0412", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2019", } @Article{Cui:2020:MIL, author = "Danni Cui and Yingying Liu and Gang Liu and Lei Liu", title = "A Multiple-Instance Learning-Based Convolutional Neural Network Model to Detect the {{\em IDH1\/}} Mutation in the Histopathology Images of Glioma Tissues", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1264--1272", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0410", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0410; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0410", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2020", } @Article{Pepe:2020:AAM, author = "Daniele Pepe and Jin Hwan Do", title = "Analyzing Apomorphine-Mediated Effects in a Cell Model for {Parkinson}'s Disease with Partial Least Squares Structure Equation Modeling", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1273--1282", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0386", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0386; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0386", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2019", } @Article{Pirro:2020:HPT, author = "Stefano Pirr{\`o} and Filomena Spada and Emanuela Gadaleta and Federica Ferrentino and Graeme J. Thorn and Gianni Cesareni and Claude Chelala", title = "{HiPPO} and {PANDA}: Two Bioinformatics Tools to Support Analysis of Mass Cytometry Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1283--1294", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0384", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0384; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0384", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2019", } @Article{Duan:2020:MBC, author = "Xin Duan and Kejun Wang and Jia Ke and Ping Lan and Feng Gao and Xiaojian Wu", title = "Multiomics-Based Colorectal Cancer Molecular Subtyping Using Local Scaling Network Fusion", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1295--1302", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0252", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0252; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0252", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 December 2019", } @Article{Cong:2020:PRP, author = "Ruochen Cong and Jushun Yang and Jie Zhou and Jianhua Shi and Yihua Zhu and Jianfeng Zhu and Jing Xiao and Ping Wang and Ying He and Bosheng He", title = "The Potential Role of Protein Tyrosine Phosphatase, Receptor Type {C} {(CD45)} in the Intestinal Ischemia--Reperfusion Injury", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1303--1312", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0244; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0244", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2019", } @Article{Mahmud:2020:EDT, author = "A. K. M. Firoj Mahmud and Doo Yang and Per Stenberg and Ilya Ioshikhes and Soumyadeep Nandi", title = "Exploring a \bioname{Drosophila} Transcription Factor Interaction Network to Identify Cis-Regulatory Modules", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1313--1328", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0160", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0160; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0160", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2019", } @Article{Xu:2020:PEP, author = "Chunling Xu and Huayi Lu and Fuqiang Li and Guanfang Su", title = "Protein Expression Profile on Differentiation of Bone Marrow {Mesenchymal} Stem Cells into Retinal Ganglion-Like Cells", journal = j-J-COMPUT-BIOL, volume = "27", number = "8", pages = "1329--1336", month = aug, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0024", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:52 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0024; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0024", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 December 2019", } @Article{Ahsen:2020:RPS, author = "Mehmet Eren Ahsen and Robert Vogel and Gustavo A. Stolovitzky", title = "\pkg{R/PY-SUMMA}: an {R/Python} Package for Unsupervised Ensemble Learning for Binary Classification Problems in Bioinformatics", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1337--1340", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0348", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/python.bib; https://www.math.utah.edu/pub/tex/bib/s-plus.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0348; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0348", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2020", } @Article{Fan:2020:IPB, author = "Zongjiang Fan and Wanqiu Zhao and Shengning Fan and Chunxiao Li and Jing Qiao and Yongqing Xu", title = "Identification of Potential Biomarkers for Intervertebral Disc Degeneration Using the Genome-Wide Expression Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1341--1349", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0103", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0103; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0103", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2020", } @Article{Fan:2020:VKE, author = "Jianye Fan and Shoubin Dong and Bo Wang", title = "Variant-Kudu: an Efficient Tool kit Leveraging Distributed Bitmap Index for Analysis of Massive Genetic Variation Datasets", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1350--1360", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0344", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0344; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0344", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2020", } @Article{Karami:2020:NAS, author = "Amirhossein Karami and Afshin Fayyaz Movaghar and Sabine Mercier and Louis Ferre", title = "New Approximate Statistical Significance of Gapped Alignments Based on the Greedy Extension Model", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1361--1372", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0203", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0203; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0203", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 January 2020", } @Article{Wang:2020:MM, author = "Yue Wang and Andrey Minarsky and Robert Penner and Christophe Soul{\'e} and Nadya Morozova", title = "Model of Morphogenesis", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1373--1383", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0414", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0414; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0414", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 February 2020", } @Article{Aouabed:2020:VMB, author = "Haithem Aouabed and Rodrigo Santamar{\'\i}A and Mourad Elloumi", title = "{VisBicluster}: a Matrix-Based Bicluster Visualization of Expression Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1384--1396", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0385", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0385; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0385", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 February 2020", } @Article{Chen:2020:APP, author = "Xiaoxia Chen and Hao Li and Lichao Tian and Qinwei Li and Jinxiang Luo and Yongqiang Zhang", title = "Analysis of the Physicochemical Properties of Acaricides Based on {Lipinski}'s Rule of Five", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1397--1406", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0323", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0323; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0323", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 February 2020", } @Article{Alqahtani:2020:SMA, author = "Fahad Alqahtani and Ion I. M{\u{a}}ndoiu", title = "Statistical Mitogenome Assembly with {RepeaTs}", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1407--1421", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0505", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0505; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0505", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 February 2020", } @Article{Yamada:2020:IPA, author = "Kohei Yamada and Zhi-zhong Chen and Lusheng Wang", title = "Improved Practical Algorithms for Rooted Subtree Prune and Regraft {(rSPR)} Distance and Hybridization Number", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1422--1432", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0432", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0432; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0432", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 February 2020", } @Article{Shi:2020:IPM, author = "Yu Shi and Shan Zhu and Jianxin Yang and Minghai Shao and Wenxiu Ding and Wanrong Jiang and Xinchen Sun and Ninghua Yao", title = "Investigation of Potential Mechanisms Associated with Non-small Cell Lung Cancer", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1433--1442", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0081", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0081; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0081", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 February 2020", } @Article{Wang:2020:CPR, author = "Feiqi Wang and Tatsuya Akutsu and Tomoya Mori", title = "Comparison of Pseudoknotted {RNA} Secondary Structures by Topological Centroid Identification and Tree Edit Distance", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1443--1451", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0512", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0512; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0512", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 February 2020", } @Article{Lo:2020:PMT, author = "Shih-Chiang Lo and Chao-Xuan You and Che-Chi Shu", title = "A Practicable Method of Tuning the Noise Intensity at Protein Level", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1452--1460", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2018.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2018.0151; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2018.0151", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 February 2020", } @Article{Elliott:2020:KSP, author = "Lloyd T. Elliott", title = "Kinship Solutions for Partially Observed Multiphenotype Data", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1461--1470", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0440", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0440; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0440", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2020", } @Article{Urban:2020:MAH, author = "Paulina Urban and Vahid Rezaei Tabar and Micha{\l} Denkiewicz and Grzegorz Bokota and Nirmal Das and Subhadip Basu and Dariusz Plewczynski", title = "The Mixture of Autoregressive Hidden {Markov} Models of Morphology for Dentritic Spines During Activation Process", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1471--1485", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0383", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0383; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0383", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 March 2020", } @Article{Zhang:2020:ISA, author = "Weina Zhang and Yilun Zhang", title = "Integrated Survival Analysis of {mRNA} and {microRNA} Signature of Patients with Breast Cancer Based on {Cox} Model", journal = j-J-COMPUT-BIOL, volume = "27", number = "9", pages = "1486--1494", month = sep, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0495", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:54 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0495; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0495", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 March 2020", } @Article{Penner:2020:BFE, author = "Robert C. Penner", title = "Backbone Free Energy Estimator Applied to Viral Glycoproteins", journal = j-J-COMPUT-BIOL, volume = "27", number = "10", pages = "1495--1508", month = oct, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0120", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:56 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0120; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0120", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 April 2020", } @Article{Qiu:2020:CPE, author = "Yier Qiu and Guowen Lu and Yingjie Wu", title = "Coexpression of {PBX1} and {EMP2} as Prognostic Biomarkers in Estrogen Receptor-Negative Breast Cancer via Data Mining", journal = j-J-COMPUT-BIOL, volume = "27", number = "10", pages = "1509--1518", month = oct, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0491", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:56 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0491; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0491", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 March 2020", } @Article{Tang:2020:IBR, author = "Yiyang Tang and Lihuang Zha and Xiaofang Zeng and Zaixin Yu", title = "Identification of Biomarkers Related to Systemic Sclerosis With or Without Pulmonary Hypertension Using Co-expression Analysis", journal = j-J-COMPUT-BIOL, volume = "27", number = "10", pages = "1519--1531", month = oct, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0492", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:56 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0492; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0492", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2020", } @Article{Zhang:2020:ISM, author = "Shusen Zhang and Yuanyuan Lu and Zhongxin Liu and Xiaopeng Li and Zhihua Wang and Zhigang Cai", title = "Identification Six Metabolic Genes as Potential Biomarkers for Lung Adenocarcinoma", journal = j-J-COMPUT-BIOL, volume = "27", number = "10", pages = "1532--1543", month = oct, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0454", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:56 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0454; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0454", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2020", } @Article{Zou:2020:TSC, author = "Pan Zou and Lijin Duan and Shasha Zhang and Xue Bai and Zhenghui Liu and Fengmei Jin and Haibo Sun and Wentao Xu and Rui Chen", title = "Target Specificity of the {CRISPR-Cas9} System in \bioname{Arabidopsis thaliana}, \bioname{Oryza sativa}, and \bioname{Glycine max} Genomes", journal = j-J-COMPUT-BIOL, volume = "27", number = "10", pages = "1544--1552", month = oct, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0453", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:56 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0453; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0453", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2020", } @Article{Shu:2020:TMB, author = "Yongqian Shu and Xiaohong Wu and Jia Shen and Dongdong Luo and Xiang Li and Hailong Wang and Yuanhua Tom Tang", title = "Tumor Mutation Burden Computation in Two Pan-Cancer Precision Medicine Next-Generation Sequencing Panels", journal = j-J-COMPUT-BIOL, volume = "27", number = "10", pages = "1553--1560", month = oct, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0055", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:56 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0055; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0055", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 April 2020", } @Article{Zoller:2020:NPI, author = "Roni Zoller and Meirav Zehavi and Michal Ziv-Ukelson", title = "A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation", journal = j-J-COMPUT-BIOL, volume = "27", number = "11", pages = "1561--1580", month = nov, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0472", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:57 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0472; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0472", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 April 2020", } @Article{Liu:2020:CRF, author = "Xiyuan Liu and Di Gao and Gang Shen", title = "Conditional Random Fields with Least Absolute Shrinkage and Selection Operator to Classifying the Barley Genes Based on Expression Level Affected by the Fungal Infection", journal = j-J-COMPUT-BIOL, volume = "27", number = "11", pages = "1581--1594", month = nov, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0428", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:57 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0428; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0428", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 March 2020", } @Article{Chang:2020:BAS, author = "Xin Chang and Mei-Feng Yang and Wei Fan and Li-Sheng Wang and Jun Yao and Zhao-Shen Li and De-Feng Li", title = "Bioinformatic Analysis Suggests That Three Hub Genes May Be a Vital Prognostic Biomarker in Pancreatic Ductal Adenocarcinoma", journal = j-J-COMPUT-BIOL, volume = "27", number = "11", pages = "1595--1609", month = nov, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0367", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:57 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0367; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0367", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 March 2020", } @Article{Prajapati:2020:GPP, author = "Rutvi Prajapati and Isaac Arnold Emerson", title = "Gene Prioritization in {Parkinson}'s Disease Using Human Protein--Protein Interaction Network", journal = j-J-COMPUT-BIOL, volume = "27", number = "11", pages = "1610--1621", month = nov, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0281", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:57 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0281; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0281", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 April 2020", } @Article{Penner:2020:CHF, author = "Robert C. Penner", title = "Conserved High Free Energy Sites in Human Coronavirus Spike Glycoprotein Backbones", journal = j-J-COMPUT-BIOL, volume = "27", number = "11", pages = "1622--1630", month = nov, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0193", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:57 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0193; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0193", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 May 2020", } @Article{Wang:2020:MAD, author = "Rong Wang and Lei Fu and Jinbin Li and Di Zhao and Yulan Zhao and Ling Yin", title = "Microarray Analysis for Differentially Expressed Genes Between Stromal and Epithelial Cells in Development and Metastasis of Invasive Breast Cancer", journal = j-J-COMPUT-BIOL, volume = "27", number = "12", pages = "1631--1643", month = dec, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0154", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:58 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0154; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0154", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 May 2020", } @Article{Wang:2020:CRT, author = "Xiaojie Wang and Yiyi Zhang and Waleed M. Ghareeb and Shuangming Lin and Xingrong Lu and Ying Huang and Shenghui Huang and Zongbin Xu and Pan Chi", title = "A Comprehensive Repertoire of Transfer {RNA}-Derived Fragments and Their Regulatory Networks in Colorectal Cancer", journal = j-J-COMPUT-BIOL, volume = "27", number = "12", pages = "1644--1655", month = dec, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0305", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:58 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0305; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0305", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2020", } @Article{Hu:2020:CAI, author = "Maolin Hu and Jiangling Xie and Zhifeng Liu and Xuan Wang and Ming Liu and Jianye Wang", title = "Comprehensive Analysis Identifying {Wnt} Ligands Gene Family for Biochemical Recurrence in Prostate Adenocarcinoma and Construction of a Nomogram", journal = j-J-COMPUT-BIOL, volume = "27", number = "12", pages = "1656--1667", month = dec, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0397", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:58 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0397; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0397", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2020", } @Article{Ye:2020:DMH, author = "Yusong Ye and Zhuoqin Yang and Jinzhi Lei", title = "{DNA} Methylation Heterogeneity Induced by Collaborations Between Enhancers", journal = j-J-COMPUT-BIOL, volume = "27", number = "12", pages = "1668--1677", month = dec, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0413", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:58 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0413; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0413", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 April 2020", } @Article{Li:2020:DTI, author = "Baoshan Li and Yi Jiang and Jingxin Chu and Qian Zhou", title = "Drug-Target Interaction Network Analysis of Gene-Phenotype Connectivity Maintained by Genistein", journal = j-J-COMPUT-BIOL, volume = "27", number = "12", pages = "1678--1687", month = dec, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0443", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:58 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0443; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0443", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2020", } @Article{Sun:2020:NMB, author = "Nan Sun and Rui Dong and Shaojun Pei and Changchuan Yin and Stephen S.-T. Yau", title = "A New Method Based on Coding Sequence Density to Cluster Bacteria", journal = j-J-COMPUT-BIOL, volume = "27", number = "12", pages = "1688--1698", month = dec, year = "2020", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0509", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:23:58 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0509; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0509", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2020", } @Article{Wekesa:2021:PPF, author = "Jael Sanyanda Wekesa and Yushi Luan and Jun Meng", title = "Predicting Protein Functions Based on Differential Co-expression and Neighborhood Analysis", journal = j-J-COMPUT-BIOL, volume = "28", number = "1", pages = "1--18", month = jan, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0120", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:00 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0120; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0120", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2020", } @Article{Collins:2021:MAE, author = "Obiora Cornelius Collins and Kevin Jan Duffy", title = "Mathematical Analyses on the Effects of Control Measures for a Waterborne Disease Model with Socioeconomic Conditions", journal = j-J-COMPUT-BIOL, volume = "28", number = "1", pages = "19--32", month = jan, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0352", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:00 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0352; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0352", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2020", } @Article{Cao:2021:IMD, author = "Buwen Cao and Shuguang Deng and Hua Qin and Jiawei Luo and Guanghui Li and Cheng Liang", title = "Inferring {MicroRNA}-Disease Associations Based on the Identification of a Functional Module", journal = j-J-COMPUT-BIOL, volume = "28", number = "1", pages = "33--42", month = jan, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0106", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:00 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0106; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0106", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 June 2020", } @Article{Sharma:2021:ISI, author = "Vishnu Kumar Sharma and Prasad V. Bharatam", title = "Identification of Selective Inhibitors of {{\em Ld\/}} {DHFR} Enzyme Using Pharmacoinformatic Methods", journal = j-J-COMPUT-BIOL, volume = "28", number = "1", pages = "43--59", month = jan, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0332", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:00 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0332; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0332", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 March 2020", } @Article{Yin:2021:IPH, author = "Yang Yin and Yang-fan Zou and Yu Xiao and Tian-xi Wang and Ya-ni Wang and Zhi-cheng Dong and Yu-hu Huo and Bo-chen Yao and Ling-bing Meng and Shuang-xia Du", title = "Identification of Potential Hub Genes of Atherosclerosis Through Bioinformatic Analysis", journal = j-J-COMPUT-BIOL, volume = "28", number = "1", pages = "60--78", month = jan, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0334", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:00 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0334; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0334", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 April 2020", } @Article{Zhao:2021:IDE, author = "Enfa Zhao and Hang Xie and Yushun Zhang", title = "Identification of Differentially Expressed Genes Associated with Idiopathic Pulmonary Arterial Hypertension by Integrated Bioinformatics Approaches", journal = j-J-COMPUT-BIOL, volume = "28", number = "1", pages = "79--88", month = jan, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0433", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:00 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0433; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0433", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 June 2020", } @Article{Tang:2021:SCF, author = "Wan Tang and Degong Mu and Ling Han and Xianmin Guo and Bing Han and Dong Song", title = "Screening of Clinical Factors Related to Prognosis of Breast Cancer Based on the {Cox} Proportional Risk Model", journal = j-J-COMPUT-BIOL, volume = "28", number = "1", pages = "89--98", month = jan, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0110", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:00 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", note = "See retraction notice \cite{Anonymous:2022:RSC}.", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0110; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0110", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 August 2020", } @Article{Chen:2021:EDM, author = "Yanwei Chen and Keke Wang and Mengyuan Shang and Shuangshuang Zhao and Zheng Zhang and Haizhen Yang and Zheming Chen and Rui Du and Qilong Wang and Baoding Chen", title = "Exploration of {DNA} Methylation-Driven Genes in Papillary Thyroid Carcinoma Based on the Cancer Genome Atlas", journal = j-J-COMPUT-BIOL, volume = "28", number = "1", pages = "99--114", month = jan, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0471", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:00 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0471; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0471", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 August 2020", } @Article{Mandoiu:2021:SII, author = "Ion Mandoiu and T. M. Murali and Giri Narasimhan and Sanguthevar Rajasekaran and Pavel Skums and Alexander Zelikovsky", title = "Special Issue: {9th International Computational Advances in Bio and Medical Sciences (ICCABS 2019)}", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "115--116", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29034.im", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/pdf/10.1089/cmb.2021.29034.im", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 February 2021", } @Article{Mohebbi:2021:HMT, author = "Mohammad Mohebbi and Liang Ding and Russell L. Malmberg and Liming Cai", title = "Human {MicroRNA} Target Prediction via Multi-Hypotheses Learning", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "117--132", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0227", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0227; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0227", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 November 2020", } @Article{Kuang:2021:DLS, author = "Shuzhen Kuang and Liangjiang Wang", title = "Deep Learning of Sequence Patterns for {CCCTC}-Binding Factor-Mediated Chromatin Loop Formation", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "133--145", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0225", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0225; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0225", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 November 2020", } @Article{Yin:2021:DAS, author = "Wutao Yin and Sakib Mostafa and Fang-xiang Wu", title = "Diagnosis of Autism Spectrum Disorder Based on Functional Brain Networks with Deep Learning", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "146--165", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0252", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0252; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0252", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 October 2020", } @Article{Syed:2021:MLM, author = "Khajamoinuddin Syed and William Sleeman and Payal Soni and Michael Hagan and Jatinder Palta and Rishabh Kapoor and Preetam Ghosh", title = "Machine-Learning Models for Multicenter Prostate Cancer Treatment Plans", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "166--184", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0188", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0188; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0188", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 September 2020", } @Article{Hayes:2021:CVD, author = "Matthew Hayes and Derrick Mullins and Angela Nguyen", title = "Complex Variant Discovery Using Discordant Cluster Normalization", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "185--194", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0249", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0249; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0249", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2020", } @Article{Chen:2021:OFB, author = "Hsin-Hao Chen and Chung-Chin Lu", title = "Optimized Fluorescence-Based Detection in Single Molecule Synthesis Process", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "195--208", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0226", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0226; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0226", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 November 2020", } @Article{Thapa:2021:MGD, author = "Ishwor Thapa and Hesham Ali", title = "A Multiomics Graph Database System for Biological Data Integration and Cancer Informatics", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "209--219", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0231", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0231; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0231", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2020", } @Article{Cheng:2021:ANP, author = "Chu-Yu Cheng and Chung-Chin Lu", title = "The Agility of a Neuron: Phase Shift Between Sinusoidal Current Input and Firing Rate Curve", journal = j-J-COMPUT-BIOL, volume = "28", number = "2", pages = "220--234", month = feb, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0224", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:01 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0224; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0224", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 November 2020", } @Article{Alexandrino:2021:GRD, author = "Alexsandro Oliveira Alexandrino and Andre Rodrigues Oliveira and Ulisses Dias and Zanoni Dias", title = "Genome Rearrangement Distance with Reversals, Transpositions, and Indels", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "235--247", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0121", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0121; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0121", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 October 2020", } @Article{Barrett:2021:MFL, author = "Christopher Barrett and Andrei C. Bura and Qijun He and Fenix W. Huang and Thomas J. X. Li and Michael S. Waterman and Christian M. Reidys", title = "Multiscale Feedback Loops in {SARS-CoV-2} Viral Evolution", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "248--256", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0343", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0343; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0343", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 December 2020", } @Article{Castellani:2021:ECE, author = "Gastone Castellani and Leon N. Cooper and Luciana Renata {De Oliveira} and Brian S. Blais", title = "Energy Consumption and Entropy Production in a Stochastic Formulation of {BCM} Learning", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "257--268", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0118", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0118; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0118", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 December 2020", } @Article{Wang:2021:FAC, author = "Jiasong Wang and Changchuan Yin", title = "A Fast Algorithm for Computing the {Fourier} Spectrum of a Fractional Period", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "269--282", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0269", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0269; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0269", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 December 2020", } @Article{Guerra:2021:RSM, author = "Concettina Guerra and Sarang Joshi and Yinquan Lu and Francesco Palini and Umberto Ferraro Petrillo and Jarek Rossignac", title = "Rank-Similarity Measures for Comparing Gene Prioritizations: a Case Study in Autism", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "283--295", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0244; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0244", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 October 2020", } @Article{Oill:2021:PAR, author = "Angela M. Taravella Oill and Anagha J. Deshpande and Heini M. Natri and Melissa A. Wilson", title = "{PopInf}: an Approach for Reproducibly Visualizing and Assigning Population Affiliation in Genomic Samples of Uncertain Origin", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "296--303", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0434", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0434; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0434", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 October 2020", } @Article{Wang:2021:GRP, author = "Xiao Wang and Dan Hao and Haja N. Kadarmideen", title = "\pkg{GeneDMRs}: an {R} Package for Gene-Based Differentially Methylated Regions Analysis", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "304--316", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0081", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/s-plus.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0081; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2020.0081", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 November 2020", } @Article{Xia:2021:SIK, author = "Yijun Xia and Juan Xie and Jun Zhao and Yin Lou and Dongsheng Cao", title = "Screening and Identification of Key Biomarkers in Melanoma: Evidence from Bioinformatic Analyses", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "317--329", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0400", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0400; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0400", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 September 2020", } @Article{Yang:2021:IAL, author = "Jie Yang and Qing-chun Xu and Zhen-yu Wang and Xun Lu and Liu-kui Pan and Jun Wu and Chen Wang", title = "Integrated Analysis of an {lncRNA}-Associated {ceRNA} Network Reveals Potential Biomarkers for Hepatocellular Carcinoma", journal = j-J-COMPUT-BIOL, volume = "28", number = "3", pages = "330--344", month = mar, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0250", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Mar 31 17:24:03 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0250; https://www.liebertpub.com/doi/pdf/10.1089/cmb.2019.0250", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 November 2020", } @Article{Schwartz:2021:RSIa, author = "Russell Schwartz", title = "{RECOMB 2020} Special Issue", journal = j-J-COMPUT-BIOL, volume = "28", number = "4", pages = "345", month = apr, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29028.rs", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:33 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 April 2021", } @Article{Guo:2021:CSE, author = "Yuzhi Guo and Jiaxiang Wu and Hehuan Ma and Sheng Wang and Junzhou Huang", title = "Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning", journal = j-J-COMPUT-BIOL, volume = "28", number = "4", pages = "346--361", month = apr, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0416", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:33 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2021", } @Article{Guo:2021:ENE, author = "Yuzhi Guo and Jiaxiang Wu and Hehuan Ma and Sheng Wang and Junzhou Huang", title = "{EPTool}: a New Enhancing {PSSM} Tool for Protein Secondary Structure Prediction", journal = j-J-COMPUT-BIOL, volume = "28", number = "4", pages = "362--364", month = apr, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0417", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:33 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 December 2020", } @Article{Caylak:2021:PET, author = "Gizem Caylak and Oznur Tastan and A. Ercument Cicek", title = "{Potpourri}: an Epistasis Test Prioritization Algorithm via Diverse {SNP} Selection", journal = j-J-COMPUT-BIOL, volume = "28", number = "4", pages = "365--377", month = apr, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0429", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:33 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 December 2020", } @Article{Caylak:2021:TDC, author = "Gizem Caylak and Oznur Tastan and A. Ercument Cicek", title = "A Tool for Detecting Complementary Single Nucleotide Polymorphism Pairs in Genome-Wide Association Studies for Epistasis Testing", journal = j-J-COMPUT-BIOL, volume = "28", number = "4", pages = "378--380", month = apr, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0430", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:33 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 December 2020", } @Article{Rahman:2021:RMS, author = "Amatur Rahman and Paul Medevedev", title = "Representation of $k$-Mer Sets Using Spectrum-Preserving String Sets", journal = j-J-COMPUT-BIOL, volume = "28", number = "4", pages = "381--394", month = apr, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0431", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:33 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 December 2020", } @Article{Zheng:2021:LDS, author = "Hongyu Zheng and Carl Kingsford and Guillaume Mar{\c{c}}ais", title = "Lower Density Selection Schemes via Small Universal Hitting Sets with Short Remaining Path Length", journal = j-J-COMPUT-BIOL, volume = "28", number = "4", pages = "395--409", month = apr, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0432", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:33 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 December 2020", } @Article{Bohnenkamper:2021:CRD, author = "Leonard Bohnenk{\"a}mper and Mar{\'\i}lia D. V. Braga and Daniel Doerr and Jens Stoye", title = "Computing the Rearrangement Distance of Natural Genomes", journal = j-J-COMPUT-BIOL, volume = "28", number = "4", pages = "410--431", month = apr, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0434", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:33 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 December 2020", } @Article{Schwartz:2021:RSIb, author = "Russell Schwartz", title = "{RECOMB 2020} Special Issue", journal = j-J-COMPUT-BIOL, volume = "28", number = "5", pages = "433--434", month = may, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29035.Sch", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:35 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2021", } @Article{Paige:2021:RGP, author = "Brooks Paige and James Bell and Aur{\'e}lien Bellet and Adri{\`a} Gasc{\'o}n and Daphne Ezer", title = "Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores", journal = j-J-COMPUT-BIOL, volume = "28", number = "5", pages = "435--451", month = may, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0445", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:35 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 January 2021", } @Article{Legried:2021:PTS, author = "Brandon Legried and Erin K. Molloy and Tandy Warnow and S{\'e}bastien Roch", title = "Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss", journal = j-J-COMPUT-BIOL, volume = "28", number = "5", pages = "452--468", month = may, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0424", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:35 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 December 2020", } @Article{Reyna:2021:NNS, author = "Matthew A. Reyna and Uthsav Chitra and Rebecca Elyanow and Benjamin J. Raphael", title = "{NetMix}: a Network-Structured Mixture Model for Reduced-Bias Estimation of Altered Subnetworks", journal = j-J-COMPUT-BIOL, volume = "28", number = "5", pages = "469--484", month = may, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0435", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:35 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 January 2021", } @Article{Dizaji:2021:DLS, author = "Kamran Ghasedi Dizaji and Wei Chen and Heng Huang", title = "Deep Large-Scale Multitask Learning Network for Gene Expression Inference", journal = j-J-COMPUT-BIOL, volume = "28", number = "5", pages = "485--500", month = may, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0438", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:35 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 May 2021", } @Article{Ge:2021:SAA, author = "Songwei Ge and Haohan Wang and Amir Alavi and Eric Xing and Ziv Bar-joseph", title = "Supervised Adversarial Alignment of Single-Cell {RNA-seq} Data", journal = j-J-COMPUT-BIOL, volume = "28", number = "5", pages = "501--513", month = may, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0439", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:35 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 January 2021", } @Article{Sefer:2021:MLS, author = "Emre Sefer and Carl Kingsford", title = "Metric Labeling and Semimetric Embedding for Protein Annotation Prediction", journal = j-J-COMPUT-BIOL, volume = "28", number = "5", pages = "514--525", month = may, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0425", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Wed Jun 9 08:40:35 MDT 2021", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 December 2020", } @Article{Galas:2021:TIT, author = "David J. Galas and James Kunert-graf and Lisa Uechi and Nikita A. Sakhanenko", title = "Toward an Information Theory of Quantitative Genetics", journal = j-J-COMPUT-BIOL, volume = "28", number = "6", pages = "527--559", month = jun, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0032", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:38 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0032; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0032", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 December 2020", } @Article{Benner:2021:CLR, author = "Philipp Benner", title = "Computing Leapfrog Regularization Paths with Applications to Large-Scale {$K$}-mer Logistic Regression", journal = j-J-COMPUT-BIOL, volume = "28", number = "6", pages = "560--569", month = jun, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0284", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:38 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0284; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0284", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 March 2021", } @Article{Yourdkhani:2021:PIP, author = "Samaneh Yourdkhani and Elizabeth S. Allman and John A. Rhodes", title = "Parameter Identifiability for a Profile Mixture Model of Protein Evolution", journal = j-J-COMPUT-BIOL, volume = "28", number = "6", pages = "570--586", month = jun, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0315", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:38 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0315; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0315", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2021", } @Article{Wang:2021:EGS, author = "Shijia Wang and Shufei Ge and Caroline Colijn and Priscila Biller and Liangliang Wang and Lloyd T. Elliott", title = "Estimating Genetic Similarity Matrices Using Phylogenies", journal = j-J-COMPUT-BIOL, volume = "28", number = "6", pages = "587--600", month = jun, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0375", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:38 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0375; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0375", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 April 2021", } @Article{Soto:2021:TTD, author = "Carlos Soto and Darshan Bryner and Nicola Neretti and Anuj Srivastava", title = "Toward a Three-Dimensional Chromosome Shape Alphabet", journal = j-J-COMPUT-BIOL, volume = "28", number = "6", pages = "601--618", month = jun, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0383", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:38 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0383; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0383", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 March 2021", } @Article{Jung:2021:BEE, author = "Jinuk Jung and Hyunwhan Joe and Kyungsik Ha and Jin-muk Lim and Hong-gee Kim", title = "Biomedical Entity Explorer: a {Web} Server for Biomedical Entity Exploration", journal = j-J-COMPUT-BIOL, volume = "28", number = "6", pages = "619--628", month = jun, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0364", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:38 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0364; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0364", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 June 2021", } @Article{Innis:2021:GPC, author = "Sarah E. Innis and Kelsie Reinaltt and Mete Civelek and Warren D. Anderson", title = "{GSEAplot}: a Package for Customizing Gene Set Enrichment Analysis in {R}", journal = j-J-COMPUT-BIOL, volume = "28", number = "6", pages = "629--631", month = jun, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0426", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:38 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/s-plus.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0426; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0426", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2021", } @Article{Anonymous:2021:JCP, author = "Anonymous", title = "{{\em JCB\/}} Call for Papers for the Special Issue on {``40 Years of Computational Biology: In Honor of Professor Michael Waterman's 80th Birthday''}", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "633--635", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29043.cfp", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/fpi/10.1089/cmb.2021.29043.cfp; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.29043.cfp", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 June 2021", } @Article{Cai:2021:SIIa, author = "Zhipeng Cai and Pavel Skums and Yuri Porozov and Alexander Zelikovsky", title = "Special Issue: {16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020)}", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "636", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29038.zc", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.29038.zc", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 May 2021", } @Article{Dai:2021:NME, author = "Wei Dai and Bingxi Chen and Wei Peng and Xia Li and Jiancheng Zhong and Jianxin Wang", title = "A Novel Multi-Ensemble Method for Identifying Essential Proteins", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "637--649", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0527", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0527; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0527", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 January 2021", } @Article{Zhu:2021:PVR, author = "Lingzhi Zhu and Cheng Yan and Guihua Duan", title = "Prediction of Virus--Receptor Interactions Based on Improving Similarities", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "650--659", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0544", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0544; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0544", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 January 2021", } @Article{Wu:2021:NPD, author = "Gaoyan Wu and Mengyun Yang and Yaohang Li and Jianxin Wang", title = "{De Novo} Prediction of Drug--Target Interactions Using {Laplacian} Regularized {Schatten} $p$-Norm Minimization", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "660--673", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0538", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0538; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0538", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 January 2021", } @Article{Liu:2021:ERA, author = "Chun-cheng Liu and Tao-chuan Shih and Tun-wen Pai and Chin-hwa Hu and Wen-shyong Tzou", title = "Enhanced Over-Representation Analysis for the Differential Regulation of {\em {Birc5a\/}} and {\em {HIF2\/}} $ \alpha $-Knockdown Approaches", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "674--686", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0556", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0556; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0556", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 January 2021", } @Article{Wang:2021:EPP, author = "Nian Wang and Min Zeng and Yiming Li and Fang-xiang Wu and Min Li", title = "Essential Protein Prediction Based on {node2vec} and {XGBoost}", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "687--700", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0543", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0543; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0543", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2021", } @Article{Nojgaard:2021:CGS, author = "Nikolai N{\o}jgaard and Walter Fontana and Marc Hellmuth and Daniel Merkle", title = "{Cayley} Graphs of Semigroups Applied to Atom Tracking in Chemistry", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "701--715", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0548", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0548; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0548", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2021", } @Article{Cheloshkina:2021:RCB, author = "Kseniia Cheloshkina and Islam Bzhikhatlov and Maria Poptsova", title = "Randomness in Cancer Breakpoint Prediction", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "716--731", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0551", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0551; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0551", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2021", } @Article{Chen:2021:CIS, author = "Zhineng Chen and Sai Wang and Caiyan Jia and Kai Hu and Xiongjun Ye and Xuanya Li and Xieping Gao", title = "{CRDet}: Improving Signet Ring Cell Detection by Reinforcing the Classification Branch", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "732--743", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0555", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0555; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0555", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 June 2021", } @Article{Anonymous:2021:RSP, author = "Anonymous", title = "{{\em Retraction of:\/}} {A Study of Potential SARS-CoV-2 Antiviral Drugs and Preliminary Research of Their Molecular Mechanism, Based on Anti-SARS-CoV Drug Screening and Molecular Dynamics Simulation (doi: 10.1089/cmb.2020.0112)}", journal = j-J-COMPUT-BIOL, volume = "28", number = "7", pages = "744", month = jul, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0112.retract", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:39 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0112.retract", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 June 2021", } @Article{Cai:2021:SIIb, author = "Zhipeng Cai and Pavel Skums and Yuri Porozov and Alexander Zelikovsky", title = "Special Issue: {16th International Symposium on Bioinformatics Research and Applications (ISBRA 2020)}", journal = j-J-COMPUT-BIOL, volume = "28", number = "8", pages = "745--746", month = aug, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29041.zc", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:41 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.29041.zc", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2021", } @Article{Myasnikova:2021:QAD, author = "Ekaterina M. Myasnikova and Marat A. Sabirov and Alexander V. Spirov", title = "Quantitative Analysis of the Dynamics of Maternal Gradients in the Early \bioname{Drosophila} Embryo", journal = j-J-COMPUT-BIOL, volume = "28", number = "8", pages = "747--757", month = aug, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0571", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:41 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0571; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0571", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2021", } @Article{Paszek:2021:TDL, author = "Jaros{\l}aw Paszek and Alexey Markin and Pawe{\l} G{\'o}recki and Oliver Eulenstein", title = "Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming", journal = j-J-COMPUT-BIOL, volume = "28", number = "8", pages = "758--773", month = aug, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0011", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:41 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0011; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0011", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2021", } @Article{Gu:2021:SGS, author = "Wenyan Gu and Aizhong Zhou and Lusheng Wang and Shiwei Sun and Xuefeng Cui and Daming Zhu", title = "{SVLR}: Genome Structural Variant Detection Using Long-Read Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "28", number = "8", pages = "774--788", month = aug, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0048", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:41 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0048; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0048", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 May 2021", } @Article{Yang:2021:FAA, author = "Wen Yang and Lusheng Wang", title = "Fast and Accurate Algorithms for Mapping and Aligning Long Reads", journal = j-J-COMPUT-BIOL, volume = "28", number = "8", pages = "789--803", month = aug, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0603", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:41 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0603; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0603", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 June 2021", } @Article{Huang:2021:IID, author = "Qiuyue Huang and Jun Wang and Xiangliang Zhang and Maozu Guo and Guoxian Yu", title = "{IsoDA}: Isoform--Disease Association Prediction by Multiomics Data Fusion", journal = j-J-COMPUT-BIOL, volume = "28", number = "8", pages = "804--819", month = aug, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0626", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:41 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0626; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0626", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 April 2021", } @Article{Moussa:2021:STI, author = "Marmar Moussa and Ion I. M{\u{a}}ndoiu", title = "{SC1}: a Tool for Interactive {Web}-Based Single-Cell {RNA-Seq} Data Analysis", journal = j-J-COMPUT-BIOL, volume = "28", number = "8", pages = "820--841", month = aug, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0051", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:41 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0051; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0051", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2021", } @Article{Rondel:2021:PAA, author = "Filipp Martin Rondel and Roya Hosseini and Bikram Sahoo and Sergey Knyazev and Igor Mandric and Frank Stewart and Ion I. M{\u{a}}ndoiu and Bogdan Pasaniuc and Yuri Porozov and Alexander Zelikovsky", title = "Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data", journal = j-J-COMPUT-BIOL, volume = "28", number = "8", pages = "842--855", month = aug, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0053", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:41 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0053; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0053", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 July 2021", } @Article{Malikic:2021:SHT, author = "Salem Maliki{\'c} and Farid Rashidi Mehrabadi and Erfan Sadeqi Azer and Mohammad Haghir Ebrahimabadi and Suleyman Cenk Sahinalp", title = "Studying the History of Tumor Evolution from Single-Cell Sequencing Data by Exploring the Space of Binary Matrices", journal = j-J-COMPUT-BIOL, volume = "28", number = "9", pages = "857--879", month = sep, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0595", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:42 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0595; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0595", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 July 2021", } @Article{Li:2021:NRL, author = "Caesar Z. Li and Eric S. Kawaguchi and Gang Li", title = "A New $ \ell_0$-Regularized Log-Linear {Poisson} Graphical Model with Applications to {RNA} Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "28", number = "9", pages = "880--891", month = sep, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0558", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:42 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0558; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0558", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2021", } @Article{Thanh:2021:CKF, author = "Vo Hong Thanh and Dani Korpela and Pekka Orponen", title = "Cotranscriptional Kinetic Folding of {RNA} Secondary Structures Including Pseudoknots", journal = j-J-COMPUT-BIOL, volume = "28", number = "9", pages = "892--908", month = sep, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0606", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:42 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0606; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0606", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 April 2021", } @Article{Thomas:2021:MNT, author = "Sunil Thomas", title = "Mapping the Nonstructural Transmembrane Proteins of Severe Acute Respiratory Syndrome Coronavirus 2", journal = j-J-COMPUT-BIOL, volume = "28", number = "9", pages = "909--921", month = sep, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0627", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:42 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0627; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0627", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 June 2021", } @Article{Wang:2021:EVP, author = "Shisheng Wang and Yi Zhong and Jingqiu Cheng and Hao Yang", title = "{EnrichVisBox}: a Versatile and Powerful {Web} Toolbox for Visualizing Complex Functional Enrichment Results of Omics Data", journal = j-J-COMPUT-BIOL, volume = "28", number = "9", pages = "922--930", month = sep, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0564", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:42 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0564; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0564", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 July 2021", } @Article{Feltes:2021:BTM, author = "Bruno C{\'e}sar Feltes and Joice {De Faria Poloni} and M{\'a}rcio Dorn", title = "Benchmarking and Testing Machine Learning Approaches with {BARRA:CuRDa}, a {{\em Curated RNA-Seq Database\/}} for Cancer Research", journal = j-J-COMPUT-BIOL, volume = "28", number = "9", pages = "931--944", month = sep, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0463", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:42 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0463; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0463", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 July 2021", } @Article{Orlovich:2021:SFS, author = "Yury Orlovich and Kirill Kukharenko and Volker Kaibel and Pavel Skums", title = "Scale-Free Spanning Trees and Their Application in Genomic Epidemiology", journal = j-J-COMPUT-BIOL, volume = "28", number = "10", pages = "945--960", month = oct, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0500", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:44 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0500; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0500", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 September 2021", } @Article{Liu:2021:COP, author = "Junfeng Liu and Yi Wang and Hongyu Zhao", title = "Calculating Orthologous Protein-Coding Sequence Set Probability Using the {Poisson} Process", journal = j-J-COMPUT-BIOL, volume = "28", number = "10", pages = "961--974", month = oct, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0507", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:44 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0507; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0507", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 September 2021", } @Article{Gopal:2021:IRD, author = "Jeyakodi Gopal and Vigneshwar Suriya Prakash Sinnarasan and Amouda Venkatesan", title = "Identification of Repurpose Drugs by Computational Analysis of Disease--Gene--Drug Associations", journal = j-J-COMPUT-BIOL, volume = "28", number = "10", pages = "975--984", month = oct, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0356", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:44 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0356; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0356", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 July 2021", } @Article{Nation:2021:CAF, author = "J. B. Nation and Justin Cabot-Miller and Oren Segal and Robert Lucito and Kira Adaricheva", title = "Combining Algorithms to Find Signatures That Predict Risk in Early-Stage Stomach Cancer", journal = j-J-COMPUT-BIOL, volume = "28", number = "10", pages = "985--1006", month = oct, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0568", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:44 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0568; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0568", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 September 2021", } @Article{Zhang:2021:ICD, author = "Wei Zhang and Shu-lin Wang and Yue Liu", title = "Identification of Cancer Driver Modules Based on Graph Clustering from Multiomics Data", journal = j-J-COMPUT-BIOL, volume = "28", number = "10", pages = "1007--1020", month = oct, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0052", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:44 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0052; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0052", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 September 2021", } @Article{Petrovs:2021:IWA, author = "Rudolfs Petrovs and Egils Stalidzans and Agris Pentjuss", title = "{IMFLer}: a {Web} Application for Interactive Metabolic Flux Analysis and Visualization", journal = j-J-COMPUT-BIOL, volume = "28", number = "10", pages = "1021--1032", month = oct, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0056", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:44 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0056; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0056", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 August 2021", } @Article{Jha:2021:SII, author = "Sumit Kumar Jha and Ion M{\u{a}}ndoiu and Sanguthevar Rajasekaran and Pavel Skums and Alexander Zelikovsky", title = "Special Issue: {10th International Computational Advances in Bio and Medical Sciences (ICCABS 2020)}", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1033--1034", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29048.skj", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.29048.skj", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 November 2021", } @Article{Fu:2021:JCS, author = "Xuecong Fu and Haoyun Lei and Yifeng Tao and Kerstin Heselmeyer-haddad and Irianna Torres and Michael Dean and Thomas Ried and Russell Schwartz", title = "Joint Clustering of Single-Cell Sequencing and Fluorescence In Situ Hybridization Data for Reconstructing Clonal Heterogeneity in Cancers", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1035--1051", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0255", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0255; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0255", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 October 2021", } @Article{Andreace:2021:MMR, author = "Francesco Andreace and Cinzia Pizzi and Matteo Comin", title = "{MetaProb 2}: Metagenomic Reads Binning Based on Assembly Using Minimizers and {$K$}-Mers Statistics", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1052--1062", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0270", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0270; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0270", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 August 2021", } @Article{Arango-argoty:2021:MFW, author = "Gustavo A. Arango-argoty and Lenwood S. Heath and Amy Pruden and Peter J. Vikesland and Liqing Zhang", title = "{MetaMLP}: a Fast Word Embedding Based Classifier to Profile Target Gene Databases in Metagenomic Samples", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1063--1074", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0273", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0273; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0273", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 October 2021", } @Article{Basher:2021:MPP, author = "Abdur Rahman M. A. Basher and Ryan J. Mclaughlin and Steven J. Hallam", title = "Metabolic Pathway Prediction Using Non-Negative Matrix Factorization with Improved Precision", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1075--1103", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0258", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0258; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0258", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 September 2021", } @Article{Saha:2021:NPN, author = "Subrata Saha and Ahmed Soliman and Sanguthevar Rajasekaran", title = "A Novel Pathway Network Analytics Method Based on Graph Theory", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1104--1112", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0257", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0257; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0257", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 August 2021", } @Article{Melnyk:2021:AZI, author = "Andrew Melnyk and Fatemeh Mohebbi and Sergey Knyazev and Bikram Sahoo and Roya Hosseini and Pavel Skums and Alex Zelikovsky and Murray Patterson", title = "From Alpha to Zeta: Identifying Variants and Subtypes of {SARS-CoV-2} Via Clustering", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1113--1129", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0302", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0302; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0302", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2021", } @Article{Novikov:2021:SRS, author = "Daniel Novikov and Sergey Knyazev and Mark Grinshpon and Pelin Icer and Pavel Skums and Alex Zelikovsky", title = "Scalable Reconstruction of {SARS-CoV-2} Phylogeny with Recurrent Mutations", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1130--1141", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0306", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0306; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0306", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2021", } @Article{Ali:2021:SFD, author = "Sarwan Ali and Simone Ciccolella and Lorenzo Lucarella and Gianluca {Della Vedova} and Murray Patterson", title = "Simpler and Faster Development of Tumor Phylogeny Pipelines", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1142--1155", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0271", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0271; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0271", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2021", } @Article{Xu:2021:AFP, author = "Qiaoji Xu and Lingling Jin and Yue Zhang and Xiaomeng Zhang and Chunfang Zheng and James H. Leebens-mack and David Sankoff", title = "Ancestral Flowering Plant Chromosomes and Gene Orders Based on Generalized Adjacencies and Chromosomal Gene Co-Occurrences", journal = j-J-COMPUT-BIOL, volume = "28", number = "11", pages = "1156--1179", month = nov, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0340", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:45 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0340; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0340", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 November 2021", } @Article{Llabres:2021:GRF, author = "Merc{\`e} Llabr{\'e}s and Francesc Rossell{\'o} and Gabriel Valiente", title = "The Generalized {Robinson--Foulds} Distance for Phylogenetic Trees", journal = j-J-COMPUT-BIOL, volume = "28", number = "12", pages = "1181--1195", month = dec, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0342", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:47 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0342; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0342", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 October 2021", } @Article{Nourani:2021:GGO, author = "Esmaeil Nourani", title = "{GoVec}: Gene Ontology Representation Learning Using Weighted Heterogeneous Graph and Meta-Path", journal = j-J-COMPUT-BIOL, volume = "28", number = "12", pages = "1196--1207", month = dec, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0069", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:47 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0069; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0069", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2021", } @Article{Liu:2021:NFS, author = "Shaoxun Liu and Yi Kou and Lin Chen", title = "Novel Few-Shot Learning Neural Network for Predicting Carbohydrate-Active Enzyme Affinity Toward Fructo-Oligosaccharides", journal = j-J-COMPUT-BIOL, volume = "28", number = "12", pages = "1208--1218", month = dec, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0091", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:47 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0091; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0091", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 December 2021", } @Article{Chen:2021:ILI, author = "Xuejun Chen and Zhenran Jiang", title = "{ISFMDA}: Learning Interactions of Selected Features-Based Method for Predicting Potential {MicroRNA-Disease} Associations", journal = j-J-COMPUT-BIOL, volume = "28", number = "12", pages = "1219--1227", month = dec, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:47 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0149; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0149", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2021", } @Article{Dhankhar:2021:SSA, author = "Poonam Dhankhar and Vikram Dalal and Viney Kumar", title = "Screening of Severe Acute Respiratory Syndrome Coronavirus 2 {RNA-Dependent} {RNA} Polymerase Inhibitors Using Computational Approach", journal = j-J-COMPUT-BIOL, volume = "28", number = "12", pages = "1228--1247", month = dec, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2020.0639", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:47 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2020.0639; https://www.liebertpub.com/doi/reader/10.1089/cmb.2020.0639", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 November 2021", } @Article{Sapra:2021:PDM, author = "Dikscha Sapra and Harpreet Kaur and Anjali Dhall and Gajendra P. S. Raghava", title = "{ProCanBio}: a Database of Manually Curated Biomarkers for Prostate Cancer", journal = j-J-COMPUT-BIOL, volume = "28", number = "12", pages = "1248--1257", month = dec, year = "2021", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0348", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:47 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0348; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0348", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 December 2021", } @Article{Anonymous:2022:AR, author = "Anonymous", title = "Acknowledgment of Reviewers 2021", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "1", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.29053.ack", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.29053.ack", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2022", } @Article{Peng:2022:RSIa, author = "Jian Peng", title = "{RECOMB} 2021 Special Issue", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "2", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29050.jp", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.29050.jp", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2022", } @Article{Demetci:2022:SSCa, author = "Pinar Demetci and Rebecca Santorella and Bj{\"o}rn Sandstede and William Stafford Noble and Ritambhara Singh", title = "{SCOT}: Single-Cell Multi-Omics Alignment with Optimal Transport", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "3--18", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0446", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0446; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0446", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2022", } @Article{Demetci:2022:SCM, author = "Pinar Demetci and Rebecca Santorella and Bj{\"o}rn Sandstede and William Stafford Noble and Ritambhara Singh", title = "Single-Cell Multiomics Integration by {SCOT}", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "19--22", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0477", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0477; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0477", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 January 2022", } @Article{Sun:2022:SSC, author = "Tianyi Sun and Dongyuan Song and Wei Vivian Li and Jingyi Jessica Li", title = "Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by {scDesign2}", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "23--26", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0440", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0440; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0440", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 January 2022", } @Article{Shrivastava:2022:GDL, author = "Harsh Shrivastava and Xiuwei Zhang and Le Song and Srinivas Aluru", title = "{GRNUlar}: a Deep Learning Framework for Recovering Single-Cell Gene Regulatory Networks", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "27--44", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0437", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0437; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0437", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2022", } @Article{Nasser:2022:DUN, author = "Rami Nasser and Yonina C. Eldar and Roded Sharan", title = "Deep Unfolding for Non-Negative Matrix Factorization with Application to Mutational Signature Analysis", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "45--55", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0438", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0438; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0438", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 January 2022", } @Article{Franzese:2022:SDT, author = "Nicholas Franzese and Jason Fan and Roded Sharan and Mark D. M. Leiserson", title = "{ScalpelSig} Designs Targeted Genomic Panels from Data to Detect Activity of Mutational Signatures", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "56--73", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0453", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0453; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0453", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 January 2022", } @Article{Zaharias:2022:RED, author = "Paul Zaharias and Martin Grosshauser and Tandy Warnow", title = "Re-evaluating Deep Neural Networks for Phylogeny Estimation: The Issue of Taxon Sampling", journal = j-J-COMPUT-BIOL, volume = "29", number = "1", pages = "74--89", month = jan, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0383", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:48 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0383; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0383", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 January 2022", } @Article{Peng:2022:RSIb, author = "Jian Peng", title = "{RECOMB 2021} Special Issue", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "91", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.29051.jp", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.29051.jp", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 February 2022", } @Article{Kong:2022:PDL, author = "Lupeng Kong and Fusong Ju and Wei-mou Zheng and Jianwei Zhu and Shiwei Sun and Jinbo Xu and Dongbo Bu", title = "{ProALIGN}: Directly Learning Alignments for Protein Structure Prediction via Exploiting Context-Specific Alignment Motifs", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "92--105", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0430", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0430; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0430", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 January 2022", } @Article{Du:2022:NMH, author = "Yuxuan Du and Sarah M. Laperriere and Jed Fuhrman and Fengzhu Sun", title = "Normalizing Metagenomic {Hi-C} Data and Detecting Spurious Contacts Using Zero-Inflated Negative Binomial Regression", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "106--120", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0439", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0439; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0439", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 January 2022", } @Article{Zheng:2022:DRO, author = "Hongyu Zheng and Cong Ma and Carl Kingsford", title = "Deriving Ranges of Optimal Estimated Transcript Expression due to Nonidentifiability", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "121--139", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0444", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0444; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0444", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 January 2022", } @Article{Shibuya:2022:SMS, author = "Yoshihiro Shibuya and Djamal Belazzougui and Gregory Kucherov", title = "Set-Min Sketch: a Probabilistic Map for Power-Law Distributions with Application to $k$-Mer Annotation", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "140--154", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0429", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0429; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0429", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2022", } @Article{Blanca:2022:SMS, author = "Antonio Blanca and Robert S. Harris and David Koslicki and Paul Medvedev", title = "The Statistics of $k$-mers from a Sequence Undergoing a Simple Mutation Process Without Spurious Matches", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "155--168", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0431", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0431; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0431", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 February 2022", } @Article{Rossi:2022:MPI, author = "Massimiliano Rossi and Marco Oliva and Ben Langmead and Travis Gagie and Christina Boucher", title = "{MONI}: a Pangenomic Index for Finding Maximal Exact Matches", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "169--187", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0290", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0290; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0290", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 January 2022", } @Article{Rossi:2022:FME, author = "Massimiliano Rossi and Marco Oliva and Paola Bonizzoni and Ben Langmead and Travis Gagie and Christina Boucher", title = "Finding Maximal Exact Matches Using the $r$-Index", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "188--194", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0445", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0445; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0445", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 January 2022", } @Article{Shaw:2022:FEF, author = "Jim Shaw and Yun William Yu", title = "\pkg{flopp}: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning", journal = j-J-COMPUT-BIOL, volume = "29", number = "2", pages = "195--211", month = feb, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0436", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:50 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0436; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0436", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 January 2022", } @Article{Tozzo:2022:WDW, author = "Veronica Tozzo and Chlo{\'e}-agathe Azencott and Samuele Fiorini and Emanuele Fava and Andrea Trucco and Annalisa Barla", title = "Where Do We Stand in Regularization for Life Science Studies?", journal = j-J-COMPUT-BIOL, volume = "29", number = "3", pages = "213--232", month = mar, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0371", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:52 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2019.0371; https://www.liebertpub.com/doi/reader/10.1089/cmb.2019.0371", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 April 2021", } @Article{Wang:2022:TOL, author = "Haohan Wang and Bryon Aragam and Eric P. Xing", title = "Trade-offs of Linear Mixed Models in Genome-Wide Association Studies", journal = j-J-COMPUT-BIOL, volume = "29", number = "3", pages = "233--242", month = mar, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0157", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:52 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0157; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0157", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 February 2022", } @Article{Alexandrino:2022:LCG, author = "Alexsandro Oliveira Alexandrino and Andre Rodrigues Oliveira and Ulisses Dias and Zanoni Dias", title = "Labeled Cycle Graph for Transposition and Indel Distance", journal = j-J-COMPUT-BIOL, volume = "29", number = "3", pages = "243--256", month = mar, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0279", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:52 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0279; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0279", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 November 2021", } @Article{Park:2022:UMM, author = "Heewon Park and Rui Yamaguchi and Seiya Imoto and Satoru Miyano", title = "Uncovering Molecular Mechanisms of Drug Resistance via Network-Constrained Common Structure Identification", journal = j-J-COMPUT-BIOL, volume = "29", number = "3", pages = "257--275", month = mar, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0314", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:52 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0314; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0314", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 January 2022", } @Article{Hassani:2022:OSF, author = "Hossein Hassani and Zakieh Avazzadeh and J. A. Tenreiro Machado and Praveen Agarwal and Maryam Bakhtiar", title = "Optimal Solution of a Fractional {HIV\slash AIDS} Epidemic Mathematical Model", journal = j-J-COMPUT-BIOL, volume = "29", number = "3", pages = "276--291", month = mar, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0253", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:52 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0253; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0253", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 February 2022", } @Article{Hammoud:2022:CPT, author = "Muhsen Hammoud and Charles Morphy D. Santos and Jo{\~a}o Paulo Gois", title = "Comparing Phylogenetic Trees Side by Side Through {iPhyloC}, a New Interactive {Web}-Based Framework", journal = j-J-COMPUT-BIOL, volume = "29", number = "3", pages = "292--303", month = mar, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0351", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:52 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0351; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0351", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 February 2022", } @Article{Emek:2022:SIB, author = "Yuval Emek and Saket Navlakha", title = "Special Issue: {Biological Distributed Algorithms 2021}", journal = j-J-COMPUT-BIOL, volume = "29", number = "4", pages = "305", month = apr, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.29060.ye", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:53 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.29060.ye", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 April 2022", } @Article{Chandrasekhar:2022:MFA, author = "Arjun Chandrasekhar and Magdalena M. Julkowska", title = "A Mathematical Framework for Analyzing Wild Tomato Root Architecture", journal = j-J-COMPUT-BIOL, volume = "29", number = "4", pages = "306--316", month = apr, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0361", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:53 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0361; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0361", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 March 2022", } @Article{Feldmann:2022:CAR, author = "Michael Feldmann and Andreas Padalkin and Christian Scheideler and Shlomi Dolev", title = "Coordinating Amoebots via Reconfigurable Circuits", journal = j-J-COMPUT-BIOL, volume = "29", number = "4", pages = "317--343", month = apr, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0363", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:53 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0363; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0363", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 March 2022", } @Article{Zhang:2022:ULB, author = "Emily Zhang and Jiajia Zhao and Nancy Lynch", title = "An Upper and Lower Bound for the Convergence Time of House-Hunting in \bioname{Temnothorax} Ant Colonies", journal = j-J-COMPUT-BIOL, volume = "29", number = "4", pages = "344--357", month = apr, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0364", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:53 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0364; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0364", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 February 2022", } @Article{Kunev:2022:ASN, author = "Martin Kunev and Petr Kuznetsov and Denis Sheynikhovich", title = "Agreement in Spiking Neural Networks", journal = j-J-COMPUT-BIOL, volume = "29", number = "4", pages = "358--369", month = apr, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0365", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:53 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0365; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0365", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 March 2022", } @Article{Murray:2022:EDS, author = "Keith T. Murray and Mien Brabeeba Wang and Nancy Lynch", title = "Emergence of Direction-Selective Retinal Cell Types in Task-Optimized Deep Learning Models", journal = j-J-COMPUT-BIOL, volume = "29", number = "4", pages = "370--381", month = apr, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0368", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:53 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0368; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0368", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 March 2022", } @Article{Zhao:2022:PPE, author = "Jiajia Zhao and Nancy Lynch and Stephen C. Pratt", title = "The Power of Population Effect in \bioname{Temnothorax} Ant House-Hunting: a Computational Modeling Approach", journal = j-J-COMPUT-BIOL, volume = "29", number = "4", pages = "382--408", month = apr, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0369", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Apr 8 09:59:53 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0369; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0369", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 January 2022", } @Article{Bigness:2022:ILR, author = "Jeremy Bigness and Xavier Loinaz and Shalin Patel and Erica Larschan and Ritambhara Singh", title = "Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks", journal = j-J-COMPUT-BIOL, volume = "29", number = "5", pages = "409--424", month = may, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0316", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Jun 3 08:22:54 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0316; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0316", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 March 2022", } @Article{Guo:2022:NSO, author = "Qianghui Guo and Yinglie Jin and Mengqin Li and Lisa Hui Sun and Yanyan Xu", title = "On the Number of Saturated and Optimal Extended 2-Regular Simple Stacks in the {Nussinov--Jacobson} Energy Model", journal = j-J-COMPUT-BIOL, volume = "29", number = "5", pages = "425--440", month = may, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0421", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Jun 3 08:22:54 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0421; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0421", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 March 2022", } @Article{Mongia:2022:DGD, author = "Aanchal Mongia and Stuti Jain and Emilie Chouzenoux and Angshul Majumdar", title = "{DeepVir}: Graphical Deep Matrix Factorization for In Silico Antiviral Repositioning --- Application to {COVID-19}", journal = j-J-COMPUT-BIOL, volume = "29", number = "5", pages = "441--452", month = may, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Jun 3 08:22:54 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0108; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0108", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 April 2022", } @Article{Thornton:2022:UDD, author = "Micah Thornton and Monnie Mcgee", title = "Use of {DFT} Distance Metrics for Classification of {SARS-CoV-2} Genomes", journal = j-J-COMPUT-BIOL, volume = "29", number = "5", pages = "453--464", month = may, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0229", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Jun 3 08:22:54 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0229; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0229", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 March 2022", } @Article{Gan:2022:CIS, author = "Luqin Gan and Giuseppe Vinci and Genevera I. Allen", title = "Correlation Imputation for Single-Cell {RNA-seq}", journal = j-J-COMPUT-BIOL, volume = "29", number = "5", pages = "465--482", month = may, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0403", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Jun 3 08:22:54 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0403; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0403", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 March 2022", } @Article{Espitia:2022:MMH, author = "Cristian C. Espitia and Miguel A. Botina and Marco A. Solarte and Ivan Hernandez and Ricardo A. Riascos and Jo{\~a}o F. Meyer", title = "Mathematical Model of {HIV\slash AIDS} Considering Sexual Preferences Under Antiretroviral Therapy, a Case Study in {San Juan de Pasto, Colombia}", journal = j-J-COMPUT-BIOL, volume = "29", number = "5", pages = "483--493", month = may, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0323", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Fri Jun 3 08:22:54 MDT 2022", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0323; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0323", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 May 2022", } @Article{Kumar:2022:SIC, author = "Sandeep Kumar", title = "Special Issue: Computational Intelligence", journal = j-J-COMPUT-BIOL, volume = "29", number = "6", pages = "495--496", month = jun, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.29063.sk", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:20 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.29063.sk", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 May 2022", } @Article{Alkhathlan:2022:PCB, author = "Lina Alkhathlan and Abdul Khader Jilani Saudagar", title = "Predicting and Classifying Breast Cancer Using Machine Learning", journal = j-J-COMPUT-BIOL, volume = "29", number = "6", pages = "497--514", month = jun, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0236", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:20 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0236; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0236", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 December 2021", } @Article{Bezdan:2022:FSH, author = "Timea Bezdan and Miodrag Zivkovic and Nebojsa Bacanin and Amit Chhabra and Muthusamy Suresh", title = "Feature Selection by Hybrid Brain Storm Optimization Algorithm for {COVID-19} Classification", journal = j-J-COMPUT-BIOL, volume = "29", number = "6", pages = "515--529", month = jun, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0256", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:20 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0256; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0256", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 April 2022", } @Article{Altameem:2022:IAG, author = "Ayman Altameem and Basetty Mallikarjuna and Abdul Khader Jilani Saudagar and Meenakshi Sharma and Ramesh Chandra Poonia", title = "Improvement of Automatic Glioma Brain Tumor Detection Using Deep Convolutional Neural Networks", journal = j-J-COMPUT-BIOL, volume = "29", number = "6", pages = "530--544", month = jun, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0280", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:20 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0280; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0280", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 March 2022", } @Article{Harjule:2022:TEM, author = "Priyanka Harjule and Manva Mohd. Tokir and Tanuj Mehta and Shivam Gurjar and Anupam Kumar and Basant Agarwal", title = "Texture Enhancement of Medical Images for Efficient Disease Diagnosis with Optimized Fractional Derivative Masks", journal = j-J-COMPUT-BIOL, volume = "29", number = "6", pages = "545--564", month = jun, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0267", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:20 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0267; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0267", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 March 2022", } @Article{Aziz:2022:CSB, author = "Rabia Musheer Aziz", title = "Cuckoo Search-Based Optimization for Cancer Classification: a New Hybrid Approach", journal = j-J-COMPUT-BIOL, volume = "29", number = "6", pages = "565--584", month = jun, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0410", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:20 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0410; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0410", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2022", } @Article{Kim:2022:INC, author = "Yujung Kim and Jaejik Kim", title = "Identification of New Clusters from Labeled Data Using Mixture Models", journal = j-J-COMPUT-BIOL, volume = "29", number = "6", pages = "585--596", month = jun, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0443", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:20 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0443; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0443", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 April 2022", } @Article{Anonymous:2022:RSC, author = "Anonymous", title = "{{\em Retraction of:\/}} {Screening} of Clinical Factors Related to Prognosis of Breast Cancer Based on the {Cox} Proportional Risk Model (doi: {\tt 10.1089/cmb.2019.0110})", journal = j-J-COMPUT-BIOL, volume = "29", number = "6", pages = "597", month = jun, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2019.0110.retract", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:20 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", note = "See \cite{Tang:2021:SCF}.", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2019.0110.retract", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 June 2022", } @Article{Istrail:2022:SIP, author = "Sorin Istrail and Pavel Pevzner and Fengzhu Sun and Martin Vingron", title = "Special Issue: {Professor Michael Waterman}'s 80th Birthday, Part 1", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "599--600", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.29065.si", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.29065.si", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2022", } @Article{Pevzner:2022:MWC, author = "Pavel Pevzner and Martin Vingron and Christian Reidys and Fengzhu Sun and Sorin Istrail", title = "{Michael Waterman}'s Contributions to Computational Biology and Bioinformatics", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "601--615", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.29066.pp", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.29066.pp; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.29066.pp", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2022", } @Article{Calabrese:2022:QBU, author = "Peter Calabrese", title = "Quantitative Biology Undergraduate Major at the {University of Southern California}", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "616--618", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0605", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0605; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0605", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2022", } @Article{Xu:2022:TTF, author = "Siwei Xu and Mario Skarica and Ahyeon Hwang and Yi Dai and Cheyu Lee and Matthew J. Girgenti and Jing Zhang", title = "Translator: a {{\em Trans\/}}fer {{\em L\/}}earning Approach to Facilitate Single-Cell {{\em AT\/}AC-Seq} Data Analysis fr{\em o\/}m {{\em R\/}}eference Dataset", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "619--633", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0596", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0596; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0596", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2022", } @Article{Zhu:2022:IAM, author = "Mengqiu Zhu and Yinglei Lai", title = "Improvements Achieved by Multiple Imputation for Single-Cell {RNA-Seq} Data in Clustering Analysis and Differential Expression Analysis", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "634--649", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0597", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0597; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0597", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 May 2022", } @Article{Shan:2022:DSM, author = "Xu Shan and Jinyu Chen and Kangning Dong and Wei Zhou and Shihua Zhang", title = "Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "650--663", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0617", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0617; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0617", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2022", } @Article{Liu:2022:SST, author = "Baqiao Liu and Tandy Warnow", title = "Scalable Species Tree Inference with External Constraints", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "664--678", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0543", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0543; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0543", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 February 2022", } @Article{Mehta:2022:PJM, author = "Rohan S. Mehta and Mike Steel and Noah A. Rosenberg", title = "The Probability of Joint Monophyly of Samples of Gene Lineages for All Species in an Arbitrary Species Tree", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "679--703", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0647", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0647; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0647", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 May 2022", } @Article{Chen:2022:SMM, author = "Liang Chen and Hui Wan and Qiuyan He and Shun He and Minghua Deng", title = "Statistical Methods for Microbiome Compositional Data Network Inference: a Survey", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "704--723", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0406", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0406; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0406", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2022", } @Article{Yooseph:2022:VAB, author = "Shibu Yooseph and Sahar Tavakoli", title = "Variational Approximation-Based Model Selection for Microbial Network Inference", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "724--737", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0595", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0595; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0595", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 May 2022", } @Article{Han:2022:LSH, author = "Wontack Han and Haixu Tang and Yuzhen Ye", title = "Locality-Sensitive Hashing-Based $k$-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "738--751", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0640", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0640; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0640", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2022", } @Article{Pardo-diaz:2022:EIG, author = "Javier Pardo-diaz and Mariano Beguerisse-d{\'\i}az and Philip S. Poole and Charlotte M. Deane and Gesine Reinert", title = "Extracting Information from Gene Coexpression Networks of \bioname{Rhizobium leguminosarum}", journal = j-J-COMPUT-BIOL, volume = "29", number = "7", pages = "752--768", month = jul, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0600", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:22 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0600; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0600", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 May 2022", } @Article{Hu:2022:CAH, author = "Ran Hu and Xianghong Jasmine Zhou and Wenyuan Li", title = "Computational Analysis of High-Dimensional {DNA} Methylation Data for Cancer Prognosis", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "769--781", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0002; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0002", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 June 2022", } @Article{Shen:2022:WIM, author = "Chengze Shen and Minhyuk Park and Tandy Warnow", title = "{WITCH}: Improved Multiple Sequence Alignment Through Weighted Consensus Hidden {Markov} Model Alignment", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "782--801", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0585", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0585; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0585", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2022", } @Article{Iv:2022:EIC, author = "Frederick A. Matsen Iv and Peter L. Ralph", title = "Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "802--824", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0644", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0644; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0644", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2022", xxnote = "Check downcased author string??", } @Article{Flomin:2022:DSA, author = "Dan Flomin and David Pellow and Ron Shamir", title = "Data Set-Adaptive Minimizer Order Reduces Memory Usage in $k$-Mer Counting", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "825--838", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0599", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0599; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0599", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 May 2022", } @Article{An:2022:NCT, author = "Shaokun An and Jie Ren and Fengzhu Sun and Lin Wan", title = "A New Context Tree Inference Algorithm for Variable Length {Markov} Chain Model with Applications to Biological Sequence Analyses", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "839--856", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0604", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0604; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0604", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2022", } @Article{Lehmann:2022:RIQ, author = "Kjong-van Lehmann and Andre Kahles and Magdalena Murr and Gunnar R{\"a}tsch", title = "{RNA} Instant Quality Check: Alignment-Free {RNA}-Degradation Detection", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "857--866", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0603", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0603; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0603", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2022", } @Article{Mcloughlin:2022:SDE, author = "Aidan Mcloughlin and Haiyan Huang", title = "Shared Differential Expression-Based Distance Reflects Global Cell Type Relationships in Single-Cell {RNA} Sequencing Data", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "867--879", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0652", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0652; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0652", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 July 2022", } @Article{Jiang:2022:TSG, author = "Wei Jiang and Liang Chen", title = "Tissue Specificity of Gene Expression Evolves Across Mammal Species", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "880--891", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0592", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0592; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0592", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 July 2022", } @Article{Moon:2022:SSD, author = "Sehwan Moon and Jeongyoung Hwang and Hyunju Lee", title = "{SDGCCA}: Supervised Deep Generalized Canonical Correlation Analysis for Multi-Omics Integration", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "892--907", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0598", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0598; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0598", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2022", } @Article{Jiao:2022:GWC, author = "Rong Jiao and Xiangning Chen and Eric Boerwinkle and Momiao Xiong", title = "Genome-Wide Causation Studies of Complex Diseases", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "908--931", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0676", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0676; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0676", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2022", } @Article{Zeng:2022:SDT, author = "Xiangrui Zeng and Ziqian Lin and Mostofa Rafid Uddin and Bo Zhou and Chao Cheng and Jing Zhang and Zachary Freyberg and Min Xu", title = "Structure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series", journal = j-J-COMPUT-BIOL, volume = "29", number = "8", pages = "932--941", month = aug, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0606", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:25 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0606; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0606", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 July 2022", } @Article{Kumar:2022:MLP, author = "Harshit Kumar and Manjit Panigrahi and Anuradha Panwar and Divya Rajawat and Sonali Sonejita Nayak and K. A. Saravanan and Kaiho Kaisa and Subhashree Parida and Bharat Bhushan and Triveni Dutt", title = "Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data", journal = j-J-COMPUT-BIOL, volume = "29", number = "9", pages = "943--960", month = sep, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0447", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:27 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0447; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0447", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 May 2022", } @Article{Shieh:2022:ILP, author = "Yi-kung Shieh and Dao-yuan Peng and Yu-han Chen and Tsung-wei Wu and Chin Lung Lu", title = "An Integer Linear Programming Approach for Scaffolding Based on Exemplar Breakpoint Distance", journal = j-J-COMPUT-BIOL, volume = "29", number = "9", pages = "961--973", month = sep, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0399", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:27 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0399; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0399", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 May 2022", } @Article{Leibovich:2022:ODS, author = "Zehavit Leibovich and Ilan Gronau", title = "Optimal Design of Synthetic {DNA} Sequences Without Unwanted Binding Sites", journal = j-J-COMPUT-BIOL, volume = "29", number = "9", pages = "974--986", month = sep, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0417", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:27 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0417; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0417", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 May 2022", } @Article{Lee:2022:RNM, author = "Sunho Lee and Seokchol Hong and Jonathan Woo and Jae-hak Lee and Kyunghee Kim and Lucia Kim and Kunsoo Park and Jongsun Jung", title = "{RDscan}: a New Method for Improving Germline and Somatic Variant Calling Based on Read Depth Distribution", journal = j-J-COMPUT-BIOL, volume = "29", number = "9", pages = "987--1000", month = sep, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0269", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:27 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0269; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0269", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2022", } @Article{Ren:2022:KNM, author = "Ruohan Ren and Changchuan Yin and Stephen S.-T. Yau", title = "\pkg{kmer2vec}: a Novel Method for Comparing {DNA} Sequences by \pkg{word2vec} Embedding", journal = j-J-COMPUT-BIOL, volume = "29", number = "9", pages = "1001--1021", month = sep, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0536", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:27 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0536; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0536", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 May 2022", } @Article{Zhao:2022:SRU, author = "Minglu Zhao and Ning Tang and Annya L. Dahmani and Yixin Zhu and Federico Rossano and Tao Gao", title = "Sharing Rewards Undermines Coordinated Hunting", journal = j-J-COMPUT-BIOL, volume = "29", number = "9", pages = "1022--1030", month = sep, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0549", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:27 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0549; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0549", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 June 2022", } @Article{Kambhampati:2022:COT, author = "Sandeep Kambhampati and Sean Murphy and Hideki Uosaki and Chulan Kwon", title = "Cross-Organ Transcriptomic Comparison Reveals Universal Factors During Maturation", journal = j-J-COMPUT-BIOL, volume = "29", number = "9", pages = "1031--1044", month = sep, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0349", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:27 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0349; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0349", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 July 2022", } @Article{Vijayakumar:2022:HFR, author = "Saravanan Vijayakumar", title = "Harnessing Fuzzy Rule Based System for Screening Major Histocompatibility Complex Class {I} Peptide Epitopes from the Whole Proteome: an Implementation on the Proteome of \bioname{Leishmania donovani}", journal = j-J-COMPUT-BIOL, volume = "29", number = "9", pages = "1045--1058", month = sep, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0464", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:27 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0464; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0464", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 April 2022", } @Article{Cai:2022:ISB, author = "Zhipeng Cai and Pavel Skums and Alexander Zelikovsky", title = "17th International Symposium on Bioinformatics Research and Applications ({ISBRA 2021})", journal = j-J-COMPUT-BIOL, volume = "29", number = "10", pages = "1059--1060", month = oct, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.29070.zc", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:29 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.29070.zc", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 October 2022", } @Article{Bai:2022:SSC, author = "Tian Bai and Zhenting Zhang and Shuyu Guo and Chen Zhao and Xiao Luo", title = "Semi-Supervised Cell Detection with Reliable Pseudo-Labels", journal = j-J-COMPUT-BIOL, volume = "29", number = "10", pages = "1061--1073", month = oct, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:29 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0108; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0108", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 June 2022", } @Article{Zhu:2022:DRS, author = "Xiaoshu Zhu and Jian Li and Yongchang Lin and Liquan Zhao and Jianxin Wang and Xiaoqing Peng", title = "Dimensionality Reduction of Single-Cell {RNA} Sequencing Data by Combining Entropy and Denoising {AutoEncoder}", journal = j-J-COMPUT-BIOL, volume = "29", number = "10", pages = "1074--1084", month = oct, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0118", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:29 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0118; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0118", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 July 2022", } @Article{Xia:2022:STS, author = "Yixiao Xia and Minchao Jiang and Yizhang Luo and Guanwen Feng and Gangyong Jia and Hua Zhang and Pu Wang and Ruiquan Ge", title = "{SuccSPred2.0}: a Two-Step Model to Predict Succinylation Sites Based on Multifeature Fusion and Selection Algorithm", journal = j-J-COMPUT-BIOL, volume = "29", number = "10", pages = "1085--1094", month = oct, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0109", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:29 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0109; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0109", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 June 2022", } @Article{Xin:2022:DCN, author = "Bin Xin and Yaning Yang and Xiaolan Xie and Jiandong Shang and Zhengyu Liu and Shaoliang Peng", title = "Detecting and Classifying Nuclei Using Multi-Scale Fully Convolutional Network", journal = j-J-COMPUT-BIOL, volume = "29", number = "10", pages = "1095--1103", month = oct, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0111", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:29 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0111; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0111", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2022", } @Article{Chen:2022:SSG, author = "Ming Chen and Wei Jiang and Yi Pan and Jianhua Dai and Yunwen Lei and Chunyan Ji", title = "{SGFNNs}: Signed Graph Filtering-based Neural Networks for Predicting Drug--Drug Interactions", journal = j-J-COMPUT-BIOL, volume = "29", number = "10", pages = "1104--1116", month = oct, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0113", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:29 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0113; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0113", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2022", } @Article{Li:2022:TLB, author = "Hongjia Li and Ge Chen and Shan Gao and Jintao Li and Xiaohua Wan and Fa Zhang", title = "A Transfer Learning-Based Classification Model for Particle Pruning in Cryo-Electron Microscopy", journal = j-J-COMPUT-BIOL, volume = "29", number = "10", pages = "1117--1131", month = oct, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0101", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:29 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0101; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0101", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2022", } @Article{Khandai:2022:DSC, author = "Kaustubh Khandai and Cristian Navarro-martinez and Brendan Smith and Rebecca Buonopane and Soyong Ashley Byun and Murray Patterson", title = "Determining Significant Correlation Between Pairs of Extant Characters in a Small Parsimony Framework", journal = j-J-COMPUT-BIOL, volume = "29", number = "10", pages = "1132--1154", month = oct, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0141", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:29 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0141; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0141", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 June 2022", } @Article{Peer:2022:SIRa, author = "Itsik Pe'er", title = "Special Issue: {RECOMB 2022}, Part 1", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1155", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.29075.ip", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.29075.ip", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2022", } @Article{Mahbub:2022:QBG, author = "Sazan Mahbub and Shashata Sawmya and Arpita Saha and Rezwana Reaz and M. Sohel Rahman and Md. Shamsuzzoha Bayzid", title = "Quartet Based Gene Tree Imputation Using Deep Learning Improves Phylogenomic Analyses Despite Missing Data", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1156--1172", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0212", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0212; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0212", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 September 2022", } @Article{Hill:2022:ITB, author = "Max Hill and Sebastien Roch", title = "Inconsistency of Triplet-Based and Quartet-Based Species Tree Estimation under Intralocus Recombination", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1173--1197", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0265", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0265; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0265", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 September 2022", } @Article{Zhang:2022:MSC, author = "Ran Zhang and Laetitia Meng-papaxanthos and Jean-philippe Vert and William Stafford Noble", title = "Multimodal Single-Cell Translation and Alignment with Semi-Supervised Learning", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1198--1212", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0264", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0264; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0264", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 October 2022", } @Article{Demetci:2022:SSCb, author = "Pinar Demetci and Rebecca Santorella and Manav Chakravarthy and Bjorn Sandstede and Ritambhara Singh", title = "{SCOTv2}: Single-Cell Multiomic Alignment with Disproportionate Cell-Type Representation", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1213--1228", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0270", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0270; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0270", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 October 2022", } @Article{Li:2022:UTU, author = "Dongshunyi Li and Jun Ding and Ziv Bar-joseph", title = "{UNIFAN}: a Tool for Unsupervised Single-Cell Clustering and Annotation", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1229--1232", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0251", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0251; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0251", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 August 2022", } @Article{Qian:2022:SPI, author = "Kun Qian and Shiwei Fu and Hongwei Li and Wei Vivian Li", title = "The {scINSIGHT} Package for Integrating Single-Cell {RNA-Seq} Data from Different Biological Conditions", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1233--1236", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0244", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0244; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0244", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 August 2022", } @Article{Jain:2022:ACC, author = "Chirag Jain and Daniel Gibney and Sharma V. Thankachan", title = "Algorithms for Colinear Chaining with Overlaps and Gap Costs", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1237--1251", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0266", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0266; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0266", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 November 2022", } @Article{Dias:2022:EMF, author = "Fernando H. C. Dias and Lucia Williams and Brendan Mumey and Alexandru I. Tomescu", title = "Efficient Minimum Flow Decomposition via Integer Linear Programming", journal = j-J-COMPUT-BIOL, volume = "29", number = "11", pages = "1252--1267", month = nov, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0257", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:31 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0257; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0257", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 October 2022", } @Article{Peer:2022:SIRb, author = "Itsik Pe'er", title = "Special Issue: {RECOMB 2022}, Part 2", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1269", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.29076.ip", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.29076.ip", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 December 2022", } @Article{Khan:2022:IRA, author = "Shahbaz Khan and Milla Kortelainen and Manuel C{\'a}ceres and Lucia Williams and Alexandru I. Tomescu", title = "Improving {RNA} Assembly via Safety and Completeness in Flow Decompositions", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1270--1287", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0261", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0261; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0261", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2022", } @Article{Hoang:2022:DLS, author = "Minh Hoang and Hongyu Zheng and Carl Kingsford", title = "Differentiable Learning of Sequence-Specific Minimizer Schemes with {DeepMinimizer}", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1288--1304", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0275", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0275; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0275", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 September 2022", } @Article{Chitra:2022:NPN, author = "Uthsav Chitra and Tae Yoon Park and Benjamin J. Raphael", title = "{NetMix2}: a Principled Network Propagation Algorithm for Identifying Altered Subnetworks", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1305--1323", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0336", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0336; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0336", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 December 2022", } @Article{Ganjdanesh:2022:MGP, author = "Alireza Ganjdanesh and Jipeng Zhang and Sarah Yan and Wei Chen and Heng Huang", title = "Multimodal Genotype and Phenotype Data Integration to Improve Partial Data-Based Longitudinal Prediction", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1324--1345", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0378", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0378; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0378", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 November 2022", } @Article{Guerin:2022:RNO, author = "Nathan Guerin and Teresa Kaserer and Bruce R. Donald", title = "{RESISTOR}: a New {OSPREY} Module to Predict Resistance Mutations", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1346--1352", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0254", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0254; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0254", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 September 2022", } @Article{Wang:2022:KMM, author = "Haohan Wang and Oscar Lopez and Eric P. Xing and Wei Wu", title = "Kernel Mixed Model for Transcriptome Association Study", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1353--1356", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0280", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0280; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0280", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 September 2022", } @Article{Mallawaarachchi:2022:ABM, author = "Vijini Mallawaarachchi and Yu Lin", title = "Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1357--1376", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0262", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0262; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0262", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 November 2022", } @Article{Gibney:2022:HSA, author = "Daniel Gibney and Sharma V. Thankachan and Srinivas Aluru", title = "On the Hardness of Sequence Alignment on {de Bruijn} Graphs", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1377--1396", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0411", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0411; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0411", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 November 2022", } @Article{Saeedi:2022:GTM, author = "Seyran Saeedi and Myrna Serrano and Dennis G. Yang and J. Paul Brooks and Gregory A. Buck and Tomasz Arodz", title = "Group Testing Matrix Design for {PCR} Screening with Real-Valued Measurements", journal = j-J-COMPUT-BIOL, volume = "29", number = "12", pages = "1397--1411", month = dec, year = "2022", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0413", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:33 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0413; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0413", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 November 2022", } @Article{Anonymous:2023:AR, author = "Anonymous", title = "Acknowledgment of Reviewers 2022", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "1--2", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.29078.ack", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.29078.ack", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2022", } @Article{Zaman:2023:VVR, author = "Sumaira Zaman and Samuel Sledzieski and Bonnie Berger and Yi-Chieh Wu and Mukul S. Bansal", title = "{virDTL}: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and {SARS-CoV-2}", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "3--20", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0507", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0507; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0507", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 September 2022", } @Article{Pal:2023:SMG, author = "Soumitra Pal and Brian Oliver and Teresa M. Przytycka", title = "Stochastic Modeling of Gene Expression Evolution Uncovers Tissue- and Sex-Specific Properties of Expression Evolution in the \bioname{Drosophila} Genus", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "21--40", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0121", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0121; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0121", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 August 2022", } @Article{Wang:2023:FAS, author = "Biing-feng Wang", title = "Fast Algorithms for the Simplified Partial Digest Problem", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "41--51", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0641", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0641; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0641", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 May 2022", } @Article{Akman:2023:BMP, author = "Ozgur E. Akman and Kevin Doherty and Benjamin J. Wareham", title = "{BDEtools}: a {MATLAB} Package for {Boolean} Delay Equation Modeling", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "52--69", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0658", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/matlab.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0658; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0658", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 September 2022", } @Article{Goulet:2023:COU, author = "Dennis R. Goulet and Yongqi Yan and Palak Agrawal and Andrew B. Waight and Amanda Nga-sze Mak and Yi Zhu", title = "Codon Optimization Using a Recurrent Neural Network", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "70--81", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0458", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0458; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0458", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 June 2022", } @Article{Yan:2023:MSG, author = "Chaochao Yan and Jinyu Yang and Hehuan Ma and Sheng Wang and Junzhou Huang", title = "Molecule Sequence Generation with Rebalanced Variational Autoencoder Loss", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "82--94", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0063", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0063; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0063", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 August 2022", } @Article{Nambiar:2023:TNN, author = "Ananthan Nambiar and Simon Liu and Maeve Heflin and John Malcolm Forsyth and Sergei Maslov and Mark Hopkins and Anna Ritz", title = "Transformer Neural Networks for Protein Family and Interaction Prediction Tasks", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "95--111", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0132", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0132; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0132", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2022", } @Article{Shao:2023:CGM, author = "Jian Shao and Ziqing Liu and Shaoyun Li and Benrui Wu and Zedong Nie and Yuefei Li and Kaixin Zhou", title = "Continuous Glucose Monitoring Time Series Data Analysis: a Time Series Analysis Package for Continuous Glucose Monitoring Data", journal = j-J-COMPUT-BIOL, volume = "30", number = "1", pages = "112--116", month = jan, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0100", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:35 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0100; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0100", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 August 2022", } @Article{Alzamel:2023:PMS, author = "Mai Alzamel and Christopher Hampson and Costas Iliopoulos and Fatima Vayani", title = "Preface: {MatBio 2021} Special Section", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "117", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.29080.pre", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.29080.pre", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 January 2023", xxnote = "Check downcased author string??", } @Article{Miardan:2023:EPD, author = "Mona Meghdari Miardan and Arash Jamshidpey and David Sankoff", title = "Escape from Parsimony of a Double-Cut-and-Join Genome Evolution Process", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "118--130", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0468", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0468; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0468", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 January 2023", } @Article{Alnasir:2023:IEM, author = "Jamie J. Alnasir and Hugh P. Shanahan", title = "Intra-Exon {Motif} Correlations as a Proxy Measure for Mean Per-Tile Sequence Quality Data in {RNA-Seq}", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "131--148", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0476", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0476; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0476", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 January 2023", } @Article{Golding:2023:CMC, author = "G. Brian Golding and Holly Koponen and Neerja Mhaskar and W. F. Smyth", title = "Computing Maximal Covers for Protein Sequences", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "149--160", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0520", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0520; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0520", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 August 2022", } @Article{Bayzid:2023:IOS, author = "Md. Shamsuzzoha Bayzid", title = "Inferring Optimal Species Trees in the Presence of Gene Duplication and Loss: Beyond Rooted Gene Trees", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "161--175", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0522", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0522; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0522", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 October 2022", } @Article{Yamamoto:2023:PPS, author = "Akito Yamamoto and Tetsuo Shibuya", title = "Privacy-Preserving Statistical Analysis of Genomic Data Using Compressive Mechanism with {Haar} Wavelet Transform", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "176--188", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0246", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0246; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0246", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 November 2022", } @Article{Wang:2023:GWA, author = "Shijia Wang and Shufei Ge and Benjamin Sobkowiak and Liangliang Wang and Louis Grandjean and Caroline Colijn and Lloyd T. Elliott", title = "Genome-Wide Association with Uncertainty in the Genetic Similarity Matrix", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "189--203", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0067", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0067; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0067", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 November 2022", } @Article{Pande:2023:PTC, author = "Akshara Pande and Sumeet Patiyal and Anjali Lathwal and Chakit Arora and Dilraj Kaur and Anjali Dhall and Gaurav Mishra and Harpreet Kaur and Neelam Sharma and Shipra Jain and Salman Sadullah Usmani and Piyush Agrawal and {\textellipsis} See all authors", title = "Pfeature: a Tool for Computing Wide Range of Protein Features and Building Prediction Models", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "204--222", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0241", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0241; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0241", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 October 2022", } @Article{Park:2023:GRN, author = "Heewon Park and Seiya Imoto and Satoru Miyano", title = "Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification", journal = j-J-COMPUT-BIOL, volume = "30", number = "2", pages = "223--243", month = feb, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0181", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:37 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0181; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0181", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 November 2022", } @Article{Nayeem:2023:MFP, author = "Muhammad Ali Nayeem and Naser Anjum Samudro and M. Saifur Rahman and M. Sohel Rahman", title = "{MAMMLE}: a Framework for Phylogeny Estimation Based on Multiobjective Application-aware Multiple Sequence Alignment and Maximum Likelihood Ensemble", journal = j-J-COMPUT-BIOL, volume = "30", number = "3", pages = "245--249", month = mar, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0533", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:39 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0533; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0533", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 January 2023", } @Article{Wilson:2023:ECB, author = "Deangelo Wilson and John D. Rogers", title = "Evaluating Compression-Based Phylogeny Estimation in the Presence of Incomplete Lineage Sorting", journal = j-J-COMPUT-BIOL, volume = "30", number = "3", pages = "250--260", month = mar, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0197", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:39 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0197; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0197", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 February 2023", } @Article{Bogdanowicz:2023:GPM, author = "Damian Bogdanowicz and Krzysztof Giaro", title = "Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages", journal = j-J-COMPUT-BIOL, volume = "30", number = "3", pages = "261--276", month = mar, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0090", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:39 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0090; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0090", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2022", } @Article{Dragomir:2023:PIM, author = "Dakota Dragomir and Elizabeth S. Allman and John A. Rhodes", title = "Parameter Identifiability of a Multitype Pure-Birth Model of Speciation", journal = j-J-COMPUT-BIOL, volume = "30", number = "3", pages = "277--292", month = mar, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0330", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:39 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0330; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0330", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 February 2023", } @Article{Ren:2023:PPT, author = "Jie Ren and Huaimin Yuan and Qimin Zhang", title = "Positivity Preserving Truncated {Euler--Maruyama} Scheme for the Stochastic Age-Structured {HIV\slash AIDS} Model", journal = j-J-COMPUT-BIOL, volume = "30", number = "3", pages = "293--322", month = mar, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0032", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:39 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0032; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0032", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 January 2023", } @Article{Banman:2023:AMA, author = "Andrew Banman and Nikita A. Sakhanenko and James Kunert-graf and David J. Galas", title = "{{\em ApoE\/}} Modifier Alleles for {Alzheimer}'s Disease Discovered by Information Theory Dependency Measures: \pkg{MIST} Software Package", journal = j-J-COMPUT-BIOL, volume = "30", number = "3", pages = "323--336", month = mar, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:39 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0185; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0185", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 November 2022", } @Article{Zhang:2023:ADW, author = "Shilong Zhang and Sufang Wang", title = "{ATAC-DEA}: a {Web}-Based {ATAC-Seq} Data Differential Peak and Annotation Analysis Application", journal = j-J-COMPUT-BIOL, volume = "30", number = "3", pages = "337--345", month = mar, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0033", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:39 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0033; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0033", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 January 2023", } @Article{Ashok:2023:ASO, author = "Malvika Ashok and Abhishek Gupta", title = "Automatic Segmentation of Organs-at-Risk in Thoracic Computed Tomography Images Using Ensembled {U-Net InceptionV3} Model", journal = j-J-COMPUT-BIOL, volume = "30", number = "3", pages = "346--362", month = mar, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0248", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:39 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0248; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0248", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 January 2023", } @Article{Bansal:2023:SII, author = "Mukul S. Bansal and Ion I. M{\u{a}}ndoiu and Marmar Moussa and Murray Patterson and Sanguthevar Rajasekaran and Pavel Skums and Alexander Zelikovsky", title = "Special Issue: {11th International Computational Advances in Bio and Medical Sciences (ICCABS 2021)}", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "363--365", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.29085.msb", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/fpi/10.1089/cmb.2023.29085.msb; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.29085.msb", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 February 2023", } @Article{Mitchell:2023:EUM, author = "Audrey Mitchell and Marco Ruiz and Soua Yang and Chen Wang and Jaime I. Davila", title = "{Excerno}: Using Mutational Signatures in Sequencing Data to Filter False Variants Caused by Clinical Archival", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "366--375", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0394", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0394; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0394", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 November 2022", } @Article{Li:2023:AST, author = "Yi Li and Mandy Chen and Joshy George and Edison T. Liu and R. Krishna Murthy Karuturi", title = "Adaptive Sentinel Testing in Workplace for {COVID-19} Pandemic", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "376--390", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0291", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0291; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0291", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 November 2022", } @Article{Tithi:2023:FNR, author = "Saima Sultana Tithi and Frank O. Aylward and Roderick V. Jensen and Liqing Zhang", title = "{FastViromeExplorer-Novel}: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "391--408", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0397", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0397; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0397", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 January 2023", } @Article{Tan:2023:NNM, author = "Jiahui Tan and Yutong Zhao and Cara C. Burns and Dechao Tian and Kun Zhao", title = "Novel Network Method Major Minor Variation Clustering Enables Identification of Poliovirus Clusters with High-Resolution Linkages", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "409--419", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0292", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0292; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0292", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 September 2022", } @Article{Campo:2023:NIT, author = "David S. Campo and Alexander Mosa and Yury Khudyakov", title = "A Novel Information-Theory-Based Genetic Distance That Approximates Phenotypic Differences", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "420--431", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0395", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0395; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0395", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 January 2023", } @Article{Ali:2023:CSC, author = "Sarwan Ali and Babatunde Bello and Zahra Tayebi and Murray Patterson", title = "Characterizing {SARS-CoV-2} Spike Sequences Based on Geographical Location", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "432--445", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0391", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0391; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0391", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 January 2023", } @Article{Senchyna:2023:DEN, author = "Fiona Senchyna and Rahul Singh", title = "Dynamic Epidemiological Networks: a Data Representation Framework for Modeling and Tracking of {SARS-CoV-2} Variants", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "446--468", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0469", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0469; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0469", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 April 2023", } @Article{Chourasia:2023:REE, author = "Prakash Chourasia and Sarwan Ali and Simone Ciccolella and Gianluca {Della Vedova} and Murray Patterson", title = "{Reads2Vec}: Efficient Embedding of Raw High-Throughput Sequencing Reads Data", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "469--491", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0424", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0424; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0424", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2023", } @Article{Bunimovich:2023:LIC, author = "Leonid Bunimovich and Athulya Ram", title = "Local Immunodeficiency: Combining Cross-Immunoreactivity Networks", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "492--501", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0390", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0390; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0390", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 January 2023", } @Article{Sahoo:2023:IBU, author = "Bikram Sahoo and Zandra Pinnix and Seth Sims and Alex Zelikovsky", title = "Identifying Biomarkers Using Support Vector Machine to Understand the Racial Disparity in Triple-Negative Breast Cancer", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "502--517", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0422", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0422; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0422", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 January 2023", } @Article{Moravec:2023:TPS, author = "Ji{\v{r}}{\'\i} C. Moravec and Robert Lanfear and David L. Spector and Sarah D. Diermeier and Alex Gavryushkin", title = "Testing for Phylogenetic Signal in Single-Cell {RNA-Seq} Data", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "518--537", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0357", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0357; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0357", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 December 2022", } @Article{Seesi:2023:GBT, author = "Sahar {Al Seesi} and Anas Al-okaily and Tatiana V. Shcheglova and Elham Sherafat and Fahad H. Alqahtani and Adam T. Hagymasi and Anupinder Kaur and Pramod K. Srivastava and Ion I. M{\u{a}}ndoiu", title = "{GeNeo}: a Bioinformatics Toolbox for Genomics-Guided Neoepitope Prediction", journal = j-J-COMPUT-BIOL, volume = "30", number = "4", pages = "538--551", month = apr, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0491", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:41 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0491; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0491", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 March 2023", } @Article{Tamura:2023:GDA, author = "Takeyuki Tamura and Ai Muto-fujita and Yukako Tohsato and Tomoyuki Kosaka", title = "Gene Deletion Algorithms for Minimum Reaction Network Design by Mixed-Integer Linear Programming for Metabolite Production in Constraint-Based Models: {gDel\_minRN}", journal = j-J-COMPUT-BIOL, volume = "30", number = "5", pages = "553--568", month = may, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0352", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:44 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0352; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0352", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 February 2023", } @Article{Pacinkova:2023:IBF, author = "Anna Pa{\v{c}}{\'\i}nkov{\'a} and Vlad Popovici", title = "{IntOMICS}: a {Bayesian} Framework for Reconstructing Regulatory Networks Using Multi-Omics Data", journal = j-J-COMPUT-BIOL, volume = "30", number = "5", pages = "569--574", month = may, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:44 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0149; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0149", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2023", } @Article{Li:2023:CTD, author = "Fang-Zhen Li and Xue-Fen Zhang and Hui-Ying Cai and Ling-Qiang Ran and Hai-Yan Zhou and Zhi-E Liu", title = "Chromosome Three-Dimensional Structure Reconstruction: an Iterative {ShRec3D} Algorithm", journal = j-J-COMPUT-BIOL, volume = "30", number = "5", pages = "575--587", month = may, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0179", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:44 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0179; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0179", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 February 2023", } @Article{Chen:2023:NAL, author = "Zhijie Chen and Tianhao Yan and Zhanwen Yang", title = "Numerical Analysis of Linearly Implicit Methods for Discontinuous Nonlinear {Gurtin--MacCamy} Model", journal = j-J-COMPUT-BIOL, volume = "30", number = "5", pages = "588--608", month = may, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0331", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:44 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0331; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0331", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 March 2023", } @Article{Son:2023:EOD, author = "Donghui Son and Jaejik Kim", title = "Estimation of Ordinary Differential Equation Models for Gene Regulatory Networks Through Data Cloning", journal = j-J-COMPUT-BIOL, volume = "30", number = "5", pages = "609--618", month = may, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0201", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:44 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0201; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0201", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 March 2023", } @Article{Mao:2023:GRN, author = "Guo Mao and Zhengbin Pang and Ke Zuo and Jie Liu", title = "Gene Regulatory Network Inference Using Convolutional Neural Networks from {scRNA-seq} Data", journal = j-J-COMPUT-BIOL, volume = "30", number = "5", pages = "619--631", month = may, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0355", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:44 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0355; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0355", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 March 2023", } @Article{Cavattoni:2023:CIM, author = "Margherita Cavattoni and Matteo Comin", title = "{ClassGraph}: Improving Metagenomic Read Classification with Overlap Graphs", journal = j-J-COMPUT-BIOL, volume = "30", number = "6", pages = "633--647", month = jun, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0208", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:45 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0208; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0208", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 April 2023", } @Article{Hasegawa:2023:ECB, author = "Nozomi Hasegawa and Kana Shimizu", title = "Efficient Colored {de Bruijn} Graph for Indexing Reads", journal = j-J-COMPUT-BIOL, volume = "30", number = "6", pages = "648--662", month = jun, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0259", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:45 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0259; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0259", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 April 2023", } @Article{Liu:2023:SJS, author = "Yi Liu and Gang Li", title = "Sure Joint Screening for High Dimensional {Cox}'s Proportional Hazards Model Under the Case-Cohort Design", journal = j-J-COMPUT-BIOL, volume = "30", number = "6", pages = "663--677", month = jun, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0416", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:45 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0416; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0416", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 May 2023", } @Article{Sedaghat:2023:SSA, author = "Nafiseh Sedaghat and Tamon Stephen and Leonid Chindelevitch", title = "Speeding Up the Structural Analysis of Metabolic Network Models Using the {Fredman--Khachiyan} Algorithm {B}", journal = j-J-COMPUT-BIOL, volume = "30", number = "6", pages = "678--694", month = jun, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0319", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:45 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0319; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0319", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 June 2023", } @Article{Wang:2023:PPN, author = "Zong Wang and Qimin Zhang", title = "Positivity-Preserving Numerical Method and Relaxed Control for Stochastic Susceptible--Infected--Vaccinated Epidemic Model with {Markov} Switching", journal = j-J-COMPUT-BIOL, volume = "30", number = "6", pages = "695--725", month = jun, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0388", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:45 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0388; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0388", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 May 2023", } @Article{Manes:2023:ESP, author = "Nathan P. Manes and Jian Song and Aleksandra Nita-lazar", title = "{EnsMOD}: a Software Program for Omics Sample Outlier Detection", journal = j-J-COMPUT-BIOL, volume = "30", number = "6", pages = "726--735", month = jun, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0243", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:45 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0243; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0243", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 April 2023", } @Article{Jeong:2023:SIC, author = "Hyundoo Jeong and Jos{\'e} Lugo-martinez and Anna Ritz and Yijie Wang and Chi Zhang", title = "{{\em Special Issue\/}} Computational Network Biology: Modeling, Analysis, and Control {(CNB-MAC) Workshop (2022)}", journal = j-J-COMPUT-BIOL, volume = "30", number = "7", pages = "737", month = jul, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.29090.hj", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:47 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.29090.hj", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 June 2023", } @Article{Lim:2023:QCT, author = "Hong Seo Lim and Peng Qiu", title = "Quantifying Cell-Type-Specific Differences of Single-Cell Datasets Using Uniform Manifold Approximation and Projection for Dimension Reduction and {Shapley} Additive {exPlanations}", journal = j-J-COMPUT-BIOL, volume = "30", number = "7", pages = "738--750", month = jul, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0366", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:47 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0366; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0366", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 April 2023", } @Article{Niu:2023:SAG, author = "Puhua Niu and Maria J. Soto and Shuai Huang and Byung-jun Yoon and Edward R. Dougherty and Francis J. Alexander and Ian Blaby and Xiaoning Qian", title = "Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction", journal = j-J-COMPUT-BIOL, volume = "30", number = "7", pages = "751--765", month = jul, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0368", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:47 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0368; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0368", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 March 2023", } @Article{Robben:2023:CSW, author = "Michael Robben and Mohammad Sadegh Nasr and Avishek Das and Jai Prakash Veerla and Manfred Huber and Justyn Jaworski and Jon Weidanz and Jacob Luber", title = "Comparison of the Strengths and Weaknesses of Machine Learning Algorithms and Feature Selection on {KEGG} Database Microbial Gene Pathway Annotation and Its Effects on Reconstructed Network Topology", journal = j-J-COMPUT-BIOL, volume = "30", number = "7", pages = "766--782", month = jul, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0370", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:47 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0370; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0370", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 July 2023", } @Article{Tavori:2023:CER, author = "Jhonatan Tavori and Hanoch Levy", title = "On the Convexity of the Effective Reproduction Number", journal = j-J-COMPUT-BIOL, volume = "30", number = "7", pages = "783--795", month = jul, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0371", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:47 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0371; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0371", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 May 2023", } @Article{Ke:2023:GBR, author = "Ziqi Ke and Haris Vikalo", title = "Graph-Based Reconstruction and Analysis of Disease Transmission Networks Using Viral Genomic Data", journal = j-J-COMPUT-BIOL, volume = "30", number = "7", pages = "796--813", month = jul, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0373", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:47 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0373; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0373", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 June 2023", } @Article{Kose:2023:GDA, author = "Tun{\c{c}} Ba{\c{s}}ar K{\"o}se and Jiarong Li and Anna Ritz", title = "Growing Directed Acyclic Graphs: Optimization Functions for Pathway Reconstruction Algorithms", journal = j-J-COMPUT-BIOL, volume = "30", number = "7", pages = "814--828", month = jul, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0376", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:47 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0376; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0376", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 March 2023", } @Article{Cai:2023:SIPa, author = "Zhipeng Cai and Pavel Skums and Alexander Zelikovsky", title = "Special Issue, Part {I}: {18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022)}", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "829--830", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.29095.az", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.29095.az", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 July 2023", } @Article{Srivatsa:2023:CES, author = "Arjun Srivatsa and Haoyun Lei and Russell Schwartz", title = "A Clonal Evolution Simulator for Planning Somatic Evolution Studies", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "831--847", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0086", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0086; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0086", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 May 2023", } @Article{Wang:2023:ASL, author = "Zhen-chang Wang and Jin-xing Liu and Jun-liang Shang and Ling-yun Dai and Chun-hou Zheng and Juan Wang", title = "{ARGLRR}: a Sparse Low-Rank Representation Single-Cell {RNA-Sequencing} Data Clustering Method Combined with a New Graph Regularization", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "848--860", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0077", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0077; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0077", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 July 2023", } @Article{Alexandrino:2023:RTD, author = "Alexsandro Oliveira Alexandrino and Andre Rodrigues Oliveira and G{\'e}raldine Jean and Guillaume Fertin and Ulisses Dias and Zanoni Dias", title = "Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "861--876", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0087", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0087; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0087", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 May 2023", } @Article{Zhu:2023:GCM, author = "Xiaoshu Zhu and Liyuan Pang and Xiaojun Ding and Wei Lan and Shuang Meng and Xiaoqing Peng", title = "A Gene Correlation Measurement Method for Spatial Transcriptome Data Based on Partitioning and Distribution", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "877--888", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0108", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0108; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0108", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 July 2023", } @Article{Qiao:2023:MVE, author = "Qian Qiao and Sha-sha Yuan and Junliang Shang and Jin-xing Liu", title = "Multi-View Enhanced Tensor Nuclear Norm and Local Constraint Model for Cancer Clustering and Feature Gene Selection", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "889--899", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0107", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0107; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0107", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 July 2023", } @Article{Yu:2023:MLP, author = "Ying Yu and Tian Qiu and Junwen Duan and Jianxin Wang", title = "Multigranularity Label Prediction Model for Automatic International Classification of Diseases Coding in Clinical Text", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "900--911", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0096", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0096; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0096", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 July 2023", } @Article{Li:2023:AIC, author = "Xiaobo Li and Yijia Zhang and Xingwang Li and Xianwei Pan and Jian Wang and Mingyu Lu", title = "Automatic International Classification of Diseases Coding via Note-Code Interaction Network with Denoising Mechanism", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "912--925", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0079", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0079; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0079", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 August 2023", } @Article{Shen:2023:IDA, author = "Yi Shen and Ying-lian Gao and Juan Wang and Bo-xin Guan and Jin-xing Liu", title = "Identification of Disease-Associated {MicroRNAs} Via Locality-Constrained Linear Coding-Based Ensemble Learning", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "926--936", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0084", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0084; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0084", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 July 2023", } @Article{Wang:2023:GRA, author = "Ying Wang and Jin-xing Liu and Juan Wang and Junliang Shang and Ying-lian Gao", title = "A Graph Representation Approach Based on Light Gradient Boosting Machine for Predicting Drug--Disease Associations", journal = j-J-COMPUT-BIOL, volume = "30", number = "8", pages = "937--947", month = aug, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0078", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:49 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0078; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0078", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2023", } @Article{Cai:2023:SIPb, author = "Zhipeng Cai and Pavel Skums and Alexander Zeilkovsky", title = "Special Issue, Part 2: {18th International Symposium on Bioinformatics Research and Applications (ISBRA 2022)}", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "949--950", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.29099.az", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.29099.az", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 September 2023", } @Article{Wang:2023:SNS, author = "Zhichao Wang and Xuelei Li and Jianping Fan and Jintao Meng and Zhenli Lin and Yi Pan and Yanjie Wei", title = "{SWsnn}: a Novel Simulator for Spiking Neural Networks", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "951--960", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0098", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0098; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0098", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 August 2023", } @Article{Huang:2023:HDP, author = "An Huang and Xiaolan Xie and Xiaojun Yao and Huanxiang Liu and Xiaoqi Wang and Shaoliang Peng", title = "{HF-DDI}: Predicting Drug--Drug Interaction Events Based on Multimodal Hybrid Fusion", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "961--971", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0068", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0068; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0068", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 August 2023", } @Article{Liu:2023:EMA, author = "Da Liu and Yijia Zhang and Ming Yang and Jianyuan Yuan and Wen Qu", title = "Extracting Mutant-Affected Protein--Protein Interactions via {Gaussian}-Enhanced Representation and Contrastive Learning", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "972--984", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0080", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0080; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0080", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 September 2023", } @Article{Zhou:2023:PCI, author = "Peixuan Zhou and Yijia Zhang and Zeqian Li and Kuo Pang and Di Zhao", title = "Protein Complex Identification Based on Heterogeneous Protein Information Network", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "985--998", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0081", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0081; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0081", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 September 2023", } @Article{Zabel:2023:BIW, author = "Susanne Zabel and Jennifer M{\"u}ller and Friedrich G{\"o}tz and Kay Nieselt", title = "{BLASTphylo}: an Interactive {Web} Tool for Taxonomic and Phylogenetic Analysis of Prokaryotic Genes", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "999--1008", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0156", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0156; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0156", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 August 2023", } @Article{Juyal:2023:RVV, author = "Akshay Juyal and Roya Hosseini and Daniel Novikov and Mark Grinshpon and Alex Zelikovsky", title = "Reconstruction of Viral Variants via {Monte Carlo} Clustering", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "1009--1018", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0154", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0154; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0154", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 September 2023", } @Article{Zhong:2023:DGC, author = "Jiancheng Zhong and Pan Cui and Yihong Zhu and Qiu Xiao and Zuohang Qu", title = "{DAHNGC}: a Graph Convolution Model for Drug--Disease Association Prediction by Using Heterogeneous Network", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "1019--1033", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0135", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0135; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0135", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 September 2023", } @Article{Pan:2023:IFS, author = "Liang Pan and Xia Xiao and Shengyun Liu and Shaoliang Peng", title = "An Integration Framework of Secure Multiparty Computation and Deep Neural Network for Improving Drug--Drug Interaction Predictions", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "1034--1045", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0076", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0076; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0076", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 September 2023", } @Article{Yordanov:2023:RES, author = "Boyan Yordanov and Sara-jane Dunn and Colin Gravill and Himanshu Arora and Hillel Kugler and Christoph M. Wintersteiger", title = "The Reasoning Engine: a Satisfiability Modulo Theories-Based Framework for Reasoning About Discrete Biological Models", journal = j-J-COMPUT-BIOL, volume = "30", number = "9", pages = "1046--1058", month = sep, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0117", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:52 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0117; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0117", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 September 2023", } @Article{Wilson:2023:ISC, author = "Tom Wilson and Duong H. T. Vo and Thomas Thorne", title = "Identifying Subpopulations of Cells in Single-Cell Transcriptomic Data: a {Bayesian} Mixture Modeling Approach to Zero Inflation of Counts", journal = j-J-COMPUT-BIOL, volume = "30", number = "10", pages = "1059--1074", month = oct, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0273", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:54 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0273; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0273", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2023", } @Article{Liang:2023:WSP, author = "Xianglong Liang and Hokeun Sun", title = "Weighted Selection Probability to Prioritize Susceptible Rare Variants in Multi-Phenotype Association Studies with Application to a Soybean Genetic Data Set", journal = j-J-COMPUT-BIOL, volume = "30", number = "10", pages = "1075--1088", month = oct, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0487", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:54 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0487; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0487", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2023", } @Article{Nakajima:2023:CDR, author = "Masaru Nakajima and Andrew D. Smith", title = "Counting Distinguishable {RNA} Secondary Structures", journal = j-J-COMPUT-BIOL, volume = "30", number = "10", pages = "1089--1097", month = oct, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0501", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:54 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0501; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0501", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 October 2023", } @Article{Yang:2023:NAS, author = "Xiaochen Yang and Zhanwen Yang and Chiping Zhang", title = "Numerical Analysis of Split-Step Backward {Euler} Method with Truncated {Wiener} Process for a Stochastic Susceptible-Infected-Susceptible Model", journal = j-J-COMPUT-BIOL, volume = "30", number = "10", pages = "1098--1111", month = oct, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0462", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:54 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0462; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0462", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 October 2023", } @Article{Kanlaya:2023:CDC, author = "Arunothai Kanlaya and Chakkrid Klin-eam", title = "Constructing Double Cyclic Codes over {F2+uF2} for {DNA} Codes", journal = j-J-COMPUT-BIOL, volume = "30", number = "10", pages = "1112--1130", month = oct, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0151", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:54 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0151; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0151", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2023", } @Article{Zou:2023:ILO, author = "Hongliang Zou and Wanting Yu", title = "Integrating Low-Order and High-Order Correlation Information for Identifying Phage Virion Proteins", journal = j-J-COMPUT-BIOL, volume = "30", number = "10", pages = "1131--1143", month = oct, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0237", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:54 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0237; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0237", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 September 2023", } @Article{Tang:2023:PRS, author = "Haixu Tang", title = "Preface: {RECOMB 2023} Special Issue", journal = j-J-COMPUT-BIOL, volume = "30", number = "11", pages = "1145", month = nov, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.29101.ht", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:56 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.29101.ht", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 November 2023", } @Article{Tabatabaee:2023:QSP, author = "Yasamin Tabatabaee and Sebastien Roch and Tandy Warnow", title = "{QR-STAR}: a Polynomial-Time Statistically Consistent Method for Rooting Species Trees Under the Coalescent", journal = j-J-COMPUT-BIOL, volume = "30", number = "11", pages = "1146--1181", month = nov, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0185", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:56 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0185; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0185", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2023", } @Article{Chandra:2023:GSC, author = "Ghanshyam Chandra and Chirag Jain", title = "Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs", journal = j-J-COMPUT-BIOL, volume = "30", number = "11", pages = "1182--1197", month = nov, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0186", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:56 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0186; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0186", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2023", } @Article{Krieger:2023:SHD, author = "Spencer Krieger and John Kececioglu", title = "Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference", journal = j-J-COMPUT-BIOL, volume = "30", number = "11", pages = "1198--1225", month = nov, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0242", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:56 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0242; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0242", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 October 2023", } @Article{Ozcelik:2023:FIG, author = "R{\i}za {\"O}z{\c{c}}elik and Alperen Ba{\u{g}} and Berk Atil and Melih Barsbey and Arzucan {\"O}zg{\"u}r and Elif Ozkirimli", title = "A Framework for Improving the Generalizability of Drug--Target Affinity Prediction Models", journal = j-J-COMPUT-BIOL, volume = "30", number = "11", pages = "1226--1239", month = nov, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0208", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:56 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0208; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0208", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 November 2023", } @Article{Barsbey:2023:CST, author = "Melih Barsbey and R{\i}za {\"O}z{\c{c}}elik and Alperen Ba{\u{g}} and Berk Atil and Arzucan {\"O}zg{\"u}r and Elif Ozkirimli", title = "A Computational Software for Training Robust Drug--Target Affinity Prediction Models: pydebiaseddta", journal = j-J-COMPUT-BIOL, volume = "30", number = "11", pages = "1240--1245", month = nov, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0194", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:56 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0194; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0194", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 November 2023", } @Article{Zhang:2023:PPI, author = "Chihao Zhang and Shihua Zhang and Jingyi Jessica Li", title = "A {Python} Package \pkg{itca} for Information-Theoretic Classification Accuracy: a Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification", journal = j-J-COMPUT-BIOL, volume = "30", number = "11", pages = "1246--1249", month = nov, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0191", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:56 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/python.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0191; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0191", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 November 2023", } @Article{Zheng:2023:CUM, author = "Hongyu Zheng and Guillaume Mar{\c{c}}ais and Carl Kingsford", title = "Creating and Using Minimizer Sketches in Computational Genomics", journal = j-J-COMPUT-BIOL, volume = "30", number = "12", pages = "1251--1276", month = dec, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0094", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:58 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0094; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0094", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 August 2023", } @Article{Silva:2023:BFA, author = "Luiz A. G. Silva and Luis A. B. Kowada and Maria E. M. T. Walter", title = "A Barrier for Further Approximating Sorting by Transpositions", journal = j-J-COMPUT-BIOL, volume = "30", number = "12", pages = "1277--1288", month = dec, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0138", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:58 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0138; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0138", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 October 2023", } @Article{Su:2023:EGE, author = "Rui Su and Jujuan Zhuang and Shuhan Liu and Di Liu and Kexin Feng", title = "{EnILs}: a General Ensemble Computational Approach for Predicting Inducing Peptides of Multiple Interleukins", journal = j-J-COMPUT-BIOL, volume = "30", number = "12", pages = "1289--1304", month = dec, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0002", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:58 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0002; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0002", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 November 2023", } @Article{Jain:2023:HAM, author = "Shipra Jain and Kawal Preet Kaur Malhotra and Sumeet Patiyal and Gajendra Pal Singh Raghava", title = "A Highly Accurate Model for Screening Prostate Cancer Using Propensity Index Panel of Ten Genes", journal = j-J-COMPUT-BIOL, volume = "30", number = "12", pages = "1305--1314", month = dec, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0040", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:58 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/fpi/10.1089/cmb.2023.0040; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0040", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 November 2023", } @Article{Rozas:2023:PDP, author = "Gladys M. Cavero Rozas and Jose M. Cisneros Mandujano and Yomali A. Ferreyra Chombo and Daniela V. Moreno Rencoret and Yerko M. Ortiz Mora and Mart{\'\i}n E. Guti{\'e}rrez Pescarmona and Alberto J. Donayre Torres", title = "\pkg{pyBrick-DNA}: a {Python}-Based Environment for Automated Genetic Component Assembly", journal = j-J-COMPUT-BIOL, volume = "30", number = "12", pages = "1315--1321", month = dec, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0008", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:58 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/python.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0008; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0008", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 November 2023", } @Article{Jastrzebski:2023:IRP, author = "Jan Pawel Jastrzebski and Stefano Pascarella and Aleksandra Lipka and Slawomir Dorocki", title = "\pkg{IncRna}: The {R} Package for Optimizing {lncRNA} Identification Processes", journal = j-J-COMPUT-BIOL, volume = "30", number = "12", pages = "1322--1326", month = dec, year = "2023", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0091", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:00:58 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib; https://www.math.utah.edu/pub/tex/bib/s-plus.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0091; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0091", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 October 2023", } @Article{Anonymous:2024:AR, author = "Anonymous", title = "Acknowledgment of Reviewers 2023", journal = j-J-COMPUT-BIOL, volume = "31", number = "1", pages = "1", month = jan, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.29108.ack", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:01 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.29108.ack", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 December 2023", } @Article{Hoang:2024:DCO, author = "Minh Hoang and Guillaume Mar{\c{c}}ais and Carl Kingsford", title = "Density and Conservation Optimization of the Generalized Masked-Minimizer Sketching Scheme", journal = j-J-COMPUT-BIOL, volume = "31", number = "1", pages = "2--20", month = jan, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0212", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:01 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0212; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0212", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 November 2023", } @Article{Croydon-veleslavov:2024:RDS, author = "Ivan A. Croydon-veleslavov and Michael P. H. Stumpf", title = "Repeated Decision Stumping Distils Simple Rules from Single-Cell Data", journal = j-J-COMPUT-BIOL, volume = "31", number = "1", pages = "21--40", month = jan, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2021.0613", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:01 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2021.0613; https://www.liebertpub.com/doi/reader/10.1089/cmb.2021.0613", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 January 2024", } @Article{Jiang:2024:QMS, author = "Hao Jiang and Jingxin Liu and You Song and Jinzhi Lei", title = "Quantitative Modeling of Stemness in Single-Cell {RNA} Sequencing Data: a Nonlinear One-Class Support Vector Machine Method", journal = j-J-COMPUT-BIOL, volume = "31", number = "1", pages = "41--57", month = jan, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2022.0484", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:01 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2022.0484; https://www.liebertpub.com/doi/reader/10.1089/cmb.2022.0484", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 November 2023", } @Article{Qi:2024:CTU, author = "Yuanyuan Qi and Mohammed El-kebir", title = "Consensus Tree Under the Ancestor--Descendant Distance is {NP-Hard}", journal = j-J-COMPUT-BIOL, volume = "31", number = "1", pages = "58--70", month = jan, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0262", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:01 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0262; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0262", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 November 2023", } @Article{Lee:2024:GSM, author = "Hajoung Lee and Jaejik Kim", title = "A Gene Selection Method Considering Measurement Errors", journal = j-J-COMPUT-BIOL, volume = "31", number = "1", pages = "71--82", month = jan, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0041", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:01 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0041; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0041", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "21 November 2023", } @Article{Mehrzadi:2024:MGM, author = "Arash Mehrzadi and Elham Rezaee and Sajjad Gharaghani and Zeynab Fakhar and Seyed Mohsen Mirhosseini", title = "A Molecular Generative Model of {COVID-19} Main Protease Inhibitors Using Long Short-Term Memory-Based Recurrent Neural Network", journal = j-J-COMPUT-BIOL, volume = "31", number = "1", pages = "83--98", month = jan, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0064", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:01 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0064; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0064", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 December 2023", } @Article{Song:2024:PPI, author = "Junrong Song and Zhiming Song and Jinpeng Zhang and Yuanli Gong", title = "Privacy-Preserving Identification of Cancer Subtype-Specific Driver Genes Based on Multigenomics Data with Privatedriver", journal = j-J-COMPUT-BIOL, volume = "31", number = "2", pages = "99--116", month = feb, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0115", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:03 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0115; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0115", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 January 2024", } @Article{Karlebach:2024:CMB, author = "Guy Karlebach and Peter N. Robinson", title = "Computing Minimal {Boolean} Models of Gene Regulatory Networks", journal = j-J-COMPUT-BIOL, volume = "31", number = "2", pages = "117--127", month = feb, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0122", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:03 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0122; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0122", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 October 2023", } @Article{Wang:2024:CPT, author = "Zihan Wang and Mengxia Xu and Zonglin Yang and Yu Jin and Yong Zhang", title = "Comparing the Performance of Three Computational Methods for Estimating the Effective Reproduction Number", journal = j-J-COMPUT-BIOL, volume = "31", number = "2", pages = "128--146", month = feb, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0065", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:03 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0065; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0065", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 January 2024", } @Article{Xiang:2024:DDL, author = "Xiaoyang Xiang and Jiaxuan Gao and Yanrui Ding", title = "{DeepPPThermo}: a Deep Learning Framework for Predicting Protein Thermostability Combining Protein-Level and Amino Acid-Level Features", journal = j-J-COMPUT-BIOL, volume = "31", number = "2", pages = "147--160", month = feb, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0097", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:03 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0097; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0097", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 December 2023", } @Article{Jia:2024:III, author = "Jianhua Jia and Genqiang Wu and Meifang Li", title = "{iGly-IDN}: Identifying {Lysine} Glycation Sites in Proteins Based on Improved {DenseNet}", journal = j-J-COMPUT-BIOL, volume = "31", number = "2", pages = "161--174", month = feb, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0112", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:03 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0112; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0112", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 November 2023", } @Article{Ogurtsov:2024:MGG, author = "Aleksey Ogurtsov and Gelio Alves and Alex Rubio and Brendan Joyce and Bj{\"o}rn Andersson and Roger Karlsson and Edward R. B. Moore and Yi-Kuo Yu", title = "\pkg{MiCId GUI}: The Graphical User Interface for \pkg{MiCId}, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall", journal = j-J-COMPUT-BIOL, volume = "31", number = "2", pages = "175--178", month = feb, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0149", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:03 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0149; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0149", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 February 2024", } @Article{Gu:2024:DEP, author = "Xinyu Gu and Yuanyuan Qi and Mohammed El-kebir", title = "{DERNA} Enables {Pareto} Optimal {RNA} Design", journal = j-J-COMPUT-BIOL, volume = "31", number = "3", pages = "179--196", month = mar, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0283", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:05 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0283; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0283", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 February 2024", } @Article{Bataa:2024:FHS, author = "Magsarjav Bataa and Siwoo Song and Kunsoo Park and Miran Kim and Jung Hee Cheon and Sun Kim", title = "Finding Highly Similar Regions of Genomic Sequences Through Homomorphic Encryption", journal = j-J-COMPUT-BIOL, volume = "31", number = "3", pages = "197--212", month = mar, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0050", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:05 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0050; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0050", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 March 2024", } @Article{Ma:2024:TRS, author = "Hehuan Ma and Feng Jiang and Yu Rong and Yuzhi Guo and Junzhou Huang", title = "Toward Robust Self-Training Paradigm for Molecular Prediction Tasks", journal = j-J-COMPUT-BIOL, volume = "31", number = "3", pages = "213--228", month = mar, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0187", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:05 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0187; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0187", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 March 2024", } @Article{Baird:2024:GTG, author = "Tarrion Baird and Rahul Roychoudhuri", title = "{GS-TCGA}: Gene Set-Based Analysis of {{\booktitle{The Cancer Genome Atlas}}}", journal = j-J-COMPUT-BIOL, volume = "31", number = "3", pages = "229--240", month = mar, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0278", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:05 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0278; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0278", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 March 2024", } @Article{Yao:2024:PMD, author = "Hai-bin Yao and Zhen-jie Hou and Wen-guang Zhang and Han Li and Yan Chen", title = "Prediction of {MicroRNA-Disease} Potential Association Based on Sparse Learning and Multilayer Random Walks", journal = j-J-COMPUT-BIOL, volume = "31", number = "3", pages = "241--256", month = mar, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0266", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:05 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0266; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0266", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "19 February 2024", } @Article{Park:2024:UGR, author = "Heewon Park", title = "Unveiling Gene Regulatory Networks That Characterize Difference of Molecular Interplays Between Gastric Cancer Drug Sensitive and Resistance Cell Lines", journal = j-J-COMPUT-BIOL, volume = "31", number = "3", pages = "257--274", month = mar, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0215", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:05 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0215; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0215", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 February 2024", } @Article{Editor:2024:RSC, author = "Tomas VinarGuest Editor", title = "{RECOMB} Satellite Conference on Comparative Genomics ({RECOMB-CG 2023})", journal = j-J-COMPUT-BIOL, volume = "31", number = "4", pages = "275--276", month = apr, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.29113.tv", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:07 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.29113.tv", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 April 2024", } @Article{Ouedraogo:2024:OPR, author = "Wend Yam D. D. Ouedraogo and Aida Ouangraoua", title = "Orthology and Paralogy Relationships at Transcript Level", journal = j-J-COMPUT-BIOL, volume = "31", number = "4", pages = "277--293", month = apr, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0400", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:07 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0400; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0400", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 April 2024", } @Article{Bohnenkamper:2024:FLH, author = "Leonard Bohnenk{\"a}mper", title = "The Floor Is Lava: Halving Natural Genomes with Viaducts, Piers, and Pontoons", journal = j-J-COMPUT-BIOL, volume = "31", number = "4", pages = "294--311", month = apr, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0330", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:07 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0330; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0330", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 April 2024", } @Article{Wagle:2024:ACB, author = "Sanket Wagle and Alexey Markin and Pawe{\l} G{\'o}recki and Tavis K. Anderson and Oliver Eulenstein", title = "Asymmetric Cluster-Based Measures for Comparative Phylogenetics", journal = j-J-COMPUT-BIOL, volume = "31", number = "4", pages = "312--327", month = apr, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0338", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:07 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0338; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0338", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 April 2024", } @Article{Khayatian:2024:RFD, author = "Elahe Khayatian and Gabriel Valiente and Louxin Zhang", title = "The $k$-{Robinson--Foulds} Dissimilarity Measures for Comparison of Labeled Trees", journal = j-J-COMPUT-BIOL, volume = "31", number = "4", pages = "328--344", month = apr, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0312", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:07 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0312; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0312", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 January 2024", } @Article{Wu:2024:CBN, author = "Yufeng Wu and Louxin Zhang", title = "Computing the Bounds of the Number of Reticulations in a Tree--Child Network That Displays a Set of Trees", journal = j-J-COMPUT-BIOL, volume = "31", number = "4", pages = "345--359", month = apr, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0309", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:07 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0309; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0309", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 January 2024", } @Article{Landry:2024:FPT, author = "Kaari Landry and Olivier Tremblay-savard and Manuel Lafond", title = "A Fixed-Parameter Tractable Algorithm for Finding Agreement Cherry-Reduced Subnetworks in Level-1 Orchard Networks", journal = j-J-COMPUT-BIOL, volume = "31", number = "4", pages = "360--379", month = apr, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0317", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:07 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0317; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0317", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 December 2023", } @Article{Yu:2024:MCF, author = "Yun William Yu", title = "On Minimizers and Convolutional Filters: Theoretical Connections and Applications to Genome Analysis", journal = j-J-COMPUT-BIOL, volume = "31", number = "5", pages = "381--395", month = may, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0483", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:09 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0483; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0483", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 April 2024", } @Article{Roddur:2024:ETC, author = "Mrinmoy Saha Roddur and Sagi Snir and Mohammed El-Kebir", title = "Enforcing Temporal Consistency in Migration History Inference", journal = j-J-COMPUT-BIOL, volume = "31", number = "5", pages = "396--415", month = may, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0352", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:09 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0352; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0352", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 May 2024", } @Article{Arbib:2024:ILP, author = "Claudio Arbib and Andrea D'ascenzo and Fabrizio Rossi and Daniele Santoni", title = "An Integer Linear Programming Model to Optimize Coding {DNA} Sequences By Joint Control of Transcript Indicators", journal = j-J-COMPUT-BIOL, volume = "31", number = "5", pages = "416--428", month = may, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0166", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:09 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0166; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0166", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 April 2024", } @Article{Ferdous:2024:MFW, author = "Jannatul Ferdous and George Matthew Fricke and Melanie E. Moses", title = "More Is Faster: Why Population Size Matters in Biological Search", journal = j-J-COMPUT-BIOL, volume = "31", number = "5", pages = "429--444", month = may, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0296", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:09 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0296; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0296", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "16 May 2024", } @Article{Xia:2024:BCP, author = "Juan Xia and Yuxia Li and Haotian Zhu and Feiyang Xue and Feng Shi and Nana Li", title = "A {Bayesian} Change Point Model for Dynamic Alternative Transcription Start Site Usage During Cellular Differentiation", journal = j-J-COMPUT-BIOL, volume = "31", number = "5", pages = "445--457", month = may, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0174", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:09 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0174; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0174", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 May 2024", } @Article{Mohammed:2024:SVD, author = "Isra Mohammed and Murtada K. Elbashir and Areeg S. Faggad", title = "Singular Value Decomposition-Based Penalized Multinomial Regression for Classifying Imbalanced Medulloblastoma Subgroups Using Methylation Data", journal = j-J-COMPUT-BIOL, volume = "31", number = "5", pages = "458--471", month = may, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0198", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Tue May 28 16:19:09 MDT 2024", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0198; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0198", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "14 May 2024", } @Article{Patterson:2024:SIP, author = "Murray Patterson", title = "{{\em Special Issue, Part I\/} 19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023)}", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "473--474", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0636", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 June 2024", } @Article{Souza:2024:BBA, author = "Michael Souza and Nilton Maia and R{\^o}mulo S. Marques and Carlile Lavor", title = "A Branch-and-Bound Algorithm for the Molecular Ordered Covering Problem", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "475--485", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0522", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 May 2024", } @Article{Hou:2024:VRG, author = "Xiaodi Hou and Guoming Sang and Zhi Liu and Xiaobo Li and Yijia Zhang", title = "Visual Recalibration and Gating Enhancement Network for Radiology Report Generation", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "486--497", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0514", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "5 June 2024", } @Article{Eriksen:2024:TRI, author = "Casper Asbj{\o}rn Eriksen and Jakob Lykke Andersen and Rolf Fagerberg and Daniel Merkle", title = "Toward the Reconciliation of Inconsistent Molecular Structures from Biochemical Databases", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "498--512", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0520", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 May 2024", } @Article{Bolteau:2024:BNM, author = "Mathieu Bolteau and Lokmane Chebouba and Laurent David and J{\'e}r{\'e}mie Bourdon and Carito Guziolowski", title = "{Boolean} Network Models of Human Preimplantation Development", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "513--523", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0517", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 May 2024", } @Article{Rossignolo:2024:ECM, author = "Enrico Rossignolo and Matteo Comin", title = "Enhanced Compression of $k$-Mer Sets with Counters via {de Bruijn} Graphs", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "524--538", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0530", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 May 2024", } @Article{Bleker:2024:CSG, author = "Carissa Bleker and Stephen K. Grady and Michael A. Langston", title = "A Comparative Study of Gene Co-Expression Thresholding Algorithms", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "539--548", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0509", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 May 2024", } @Article{vonLohneysen:2024:PCP, author = "Sarah von L{\"o}hneysen and Thomas Spicher and Yuliia Varenyk and Hua-Ting Yao and Ronny Lorenz and Ivo Hofacker and Peter F. Stadler", title = "Phylogenetic and Chemical Probing Information as Soft Constraints in {RNA} Secondary Structure Prediction", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "549--563", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0519", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 June 2024", } @Article{Yang:2024:IDC, author = "Zhidong Yang and Hongjia Li and Dawei Zang and Renmin Han and Fa Zhang", title = "Improved Denoising of Cryo-Electron Microscopy Micrographs with Simulation-Aware Pretraining", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "564--575", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0513", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "28 May 2024", } @Article{Qiao:2024:FLM, author = "Tian-jing Qiao and Feng Li and Sha-sha Yuan and Ling-yun Dai and Juan Wang", title = "A Fusion Learning Model Based on Deep Learning for Single-Cell {RNA} Sequencing Data Clustering", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "576--588", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0512", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 May 2024", } @Article{Melkus:2024:THW, author = "Gatis Melkus and Andrejs Sizovs and Peteris Rucevskis and Sandra Silina", title = "Transcriptional Hubs Within Cliques in Ensemble {Hi-C} Chromatin Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "31", number = "6", pages = "589--596", month = jun, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0515", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:23 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 May 2024", } @Article{Marcais:2024:SMS, author = "Guillaume Mar{\c{c}}ais and Dan DeBlasio and Carl Kingsford", title = "Sketching Methods with Small Window Guarantee Using Minimum Decycling Sets", journal = j-J-COMPUT-BIOL, volume = "31", number = "7", pages = "597--615", month = jul, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0544", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:24 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 July 2024", } @Article{Tavakoli:2024:GPR, author = "Neda Tavakoli and Daniel Gibney and Srinivas Aluru", title = "{GraphSlimmer}: Preserving Read Mappability with the Minimum Number of Variants", journal = j-J-COMPUT-BIOL, volume = "31", number = "7", pages = "616--637", month = jul, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0601", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:24 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 July 2024", } @Article{Libeskind-Hadas:2024:PDP, author = "Ran Libeskind-Hadas", title = "Pairwise Distances and the Problem of Multiple Optima", journal = j-J-COMPUT-BIOL, volume = "31", number = "7", pages = "638--650", month = jul, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0382", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:24 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 July 2024", xxnote = "Check downcased author string??", } @Article{P:2024:DVW, author = "Preeti P and Azeen Riyaz and Alakto Choudhury and Priyanka Ray Choudhury and Nischal Pradhan and Abhishek Singh and Mihir Nakul and Chhavi Dudeja and Abhijeet Yadav and {\textellipsis} See all authors", title = "{DNASCANNER v2}: a {Web}-Based Tool to Analyze the Characteristic Properties of Nucleotide Sequences", journal = j-J-COMPUT-BIOL, volume = "31", number = "7", pages = "651--669", month = jul, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0227", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:24 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 April 2024", } @Article{Li:2024:SNM, author = "Juntao Li and Shan Xiang and Xuekun Song", title = "Screening Nonlinear {miRNA} Features of Breast Cancer by Using Ensemble Regularized Polynomial Logistic Regression", journal = j-J-COMPUT-BIOL, volume = "31", number = "7", pages = "670--690", month = jul, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0289", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:24 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 July 2024", xxnote = "Check downcased author string??", } @Article{Jisna:2024:UAU, author = "V. A. Jisna and Abhaysing Pawar Ajay and P. B. Jayaraj", title = "Using {Attention-UNet} Models to Predict Protein Contact Maps", journal = j-J-COMPUT-BIOL, volume = "31", number = "7", pages = "691--702", month = jul, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0102", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:24 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 July 2024", xxnote = "Check downcased author string??", } @Article{Tinh:2024:QEP, author = "Nguyen Huy Tinh and Cuong Cao Dang and Le Sy Vinh", title = "{QMix}: an Efficient Program to Automatically Estimate Multi-Matrix Mixture Models for Amino Acid Substitution Process", journal = j-J-COMPUT-BIOL, volume = "31", number = "8", pages = "703--707", month = aug, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0403", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:26 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0403; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0403", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 June 2024", } @Article{Wang:2024:EHS, author = "Yuexuan Wang and Ritabrata Dutta and Andreas Futschik", title = "Estimating Haplotype Structure and Frequencies: a {Bayesian} Approach to Unknown Design in Pooled Genomic Data", journal = j-J-COMPUT-BIOL, volume = "31", number = "8", pages = "708--726", month = aug, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0211", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:26 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0211; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0211", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 July 2024", } @Article{Benth:2024:NIT, author = "J{\=u}rat{\.E} {\v{S}}altyt{\.E} Benth and Fred Espen Benth and Espen Rostrup Nakstad", title = "Nearly Instantaneous Time-Varying Reproduction Number for Contagious Diseases --- a Direct Approach Based on Nonlinear Regression", journal = j-J-COMPUT-BIOL, volume = "31", number = "8", pages = "727--741", month = aug, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0414", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:26 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0414; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0414", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 June 2024", } @Article{Zhang:2024:NDA, author = "Xin Zhang and Liangwei Zhao and Ziyi Chai and Hao Wu and Wei Yang and Chen Li and Yu Jiang and Quanzhong Liu", title = "{NPI-DCGNN}: an Accurate Tool for Identifying {ncRNA-Protein} Interactions Using a Dual-Channel Graph Neural Network", journal = j-J-COMPUT-BIOL, volume = "31", number = "8", pages = "742--756", month = aug, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0449", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:26 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0449; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0449", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 June 2024", } @Article{Tamilarasi:2024:DSG, author = "M. Tamilarasi and S. Kumarganesh and K. Martin Sagayam and J. Andrew", title = "Detection and Segmentation of Glioma Tumors Utilizing a {UNet} Convolutional Neural Network Approach with Non-Subsampled Shearlet Transform", journal = j-J-COMPUT-BIOL, volume = "31", number = "8", pages = "757--768", month = aug, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0339", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:26 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0339; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0339", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 June 2024", } @Article{Biswas:2024:CCB, author = "Gargi Biswas and Debasish Mukherjee and Sankar Basu", title = "Combining Complementarity and Binding Energetics in the Assessment of Protein Interactions: {EnCPdock} --- a Practical Manual", journal = j-J-COMPUT-BIOL, volume = "31", number = "8", pages = "769--781", month = aug, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0554", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:26 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0554; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0554", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 June 2024", } @Article{Przytycka:2024:RFS, author = "Teresa M. Przytycka", title = "{Rosalind Franklin Society} Proudly Announces the 2023 Award Recipient for {{\booktitle{Journal of Computational Biology}}}", journal = j-J-COMPUT-BIOL, volume = "31", number = "9", pages = "783", month = sep, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.15655.rfs2023", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:27 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 September 2024", } @Article{Ling:2024:SFA, author = "Zhao Ling and Yu Wei Zhang and Shuai Cheng Li", title = "{SuperTAD-Fast}: Accelerating Topologically Associating Domains Detection Through Discretization", journal = j-J-COMPUT-BIOL, volume = "31", number = "9", pages = "784--796", month = sep, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0490", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:27 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 July 2024", } @Article{Gao:2024:PPI, author = "Qian Gao and Chi Zhang and Ming Li and Tianfei Yu", title = "Protein--Protein Interaction Prediction Model Based on {ProtBert-BiGRU-Attention}", journal = j-J-COMPUT-BIOL, volume = "31", number = "9", pages = "797--814", month = sep, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0297", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:27 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "29 July 2024", } @Article{Kalhor:2024:RFC, author = "Reza Kalhor and Guillaume Beslon and Manuel Lafond and Celine Scornavacca", title = "A Rigorous Framework to Classify the Postduplication Fate of Paralogous Genes", journal = j-J-COMPUT-BIOL, volume = "31", number = "9", pages = "815--833", month = sep, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0331", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:27 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "1 August 2024", } @Article{Mei:2024:UCD, author = "Biao Mei and Yu Jiang and Yifan Sun", title = "Unveiling Commonalities and Differences in Genetic Regulations via Two-Way Fusion", journal = j-J-COMPUT-BIOL, volume = "31", number = "9", pages = "834--870", month = sep, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0437", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:27 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 August 2024", } @Article{Ding:2024:SLS, author = "Jiayuan Ding and Lingxiao Li and Qiaolin Lu and Julian Venegas and Yixin Wang and Lidan Wu and Wei Jin and Hongzhi Wen and Renming Liu and Wenzhuo Tang and Xinnan Dai and Zhaoheng Li and {\textellipsis} See all authors", title = "{SpatialCTD}: a Large-Scale Tumor Microenvironment Spatial Transcriptomic Dataset to Evaluate Cell Type Deconvolution for Immuno-Oncology", journal = j-J-COMPUT-BIOL, volume = "31", number = "9", pages = "871--885", month = sep, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0532", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:27 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 August 2024", } @Article{Sun:2024:HHO, author = "Xiao-Yan Sun and Zhen-Jie Hou and Wen-Guang Zhang and Yan Chen and Hai-Bin Yao", title = "{HTFSMMA}: Higher-Order Topological Guided Small Molecule--{MicroRNA} Associations Prediction", journal = j-J-COMPUT-BIOL, volume = "31", number = "9", pages = "886--906", month = sep, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0587", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:27 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 August 2024", } @Article{Ma:2024:RSI, author = "Jian Ma and Mona Singh", title = "{RECOMB 2024} Special Issue", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "907", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0809", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0809", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "20 September 2024", } @Article{Elder:2024:AEO, author = "C. S. Elder and Minh Hoang and Mohsen Ferdosi and Carl Kingsford", title = "Approximate and Exact Optimization Algorithms for the {Beltway} and {Turnpike} Problems with Duplicated, Missing, Partially Labeled, and Uncertain Measurements", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "908--926", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0661", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0661; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0661", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 October 2024", } @Article{Schill:2024:COB, author = "Rudolf Schill and Maren Klever and Andreas L{\"o}sch and Y. Linda Hu and Stefan Vocht and Kevin Rupp and Lars Grasedyck and Rainer Spang and Niko Beerenwinkel", title = "Correcting for Observation Bias in Cancer Progression Modeling", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "927--945", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0666", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0666; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0666", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 October 2024", } @Article{Gafurov:2024:FCA, author = "Askar Gafurov and Tom{\'a}{\v{s}} Vina{\v{R}} and Paul Medvedev and Bro{\v{N}}a Brejov{\'a}", title = "Fast Context-Aware Analysis of Genome Annotation Colocalization", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "946--964", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0667", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0667; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0667", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 October 2024", } @Article{Childs:2024:PDN, author = "Henry Childs and Nathan Guerin and Pei Zhou and Bruce R. Donald", title = "Protocol for Designing {{\em De Novo\/}} Noncanonical Peptide Binders in {OSPREY}", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "965--974", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0669", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0669; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0669", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "4 October 2024", } @Article{Renders:2024:LAP, author = "Luca Renders and Lore Depuydt and Sven Rahmann and Jan Fostier", title = "Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "975--989", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0664", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0664; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0664", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "30 September 2024", } @Article{Devkota:2024:AIS, author = "Kapil Devkota and Anselm Blumer and Xiaozhe Hu and Lenore Cowen", title = "Approximate {IsoRank} for Scalable and Functionally Meaningful Cross-Species Alignments of Protein Interaction Networks", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "990--1007", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0673", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0673; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0673", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "24 September 2024", } @Article{Du:2024:IMH, author = "Yuxuan Du and Wenxuan Zuo and Fengzhu Sun", title = "Imputing Metagenomic {Hi-C} Contacts Facilitates the Integrative Contig Binning Through Constrained Random Walk with Restart", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "1008--1021", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0663", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0663; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0663", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2024", } @Article{Campanelli:2024:WPR, author = "Alessio Campanelli and Giulio Ermanno Pibiri and Jason Fan and Rob Patro", title = "Where the Patterns Are: Repetition-Aware Compression for Colored {de Bruijn} Graphs", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "1022--1044", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0714", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0714; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0714", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 October 2024", } @Article{Krieger:2024:ROM, author = "Spencer Krieger and John Kececioglu", title = "Robust Optimal Metabolic Factories", journal = j-J-COMPUT-BIOL, volume = "31", number = "10", pages = "1045--1086", month = oct, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0748", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:29 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0748; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0748", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 September 2024", } @Article{Zhu:2024:NKD, author = "Hao Zhu and Donna Slonim", title = "From Noise to Knowledge: Diffusion Probabilistic Model-Based Neural Inference of Gene Regulatory Networks", journal = j-J-COMPUT-BIOL, volume = "31", number = "11", pages = "1087--1103", month = nov, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0607", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:31 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0607; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0607", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 October 2024", } @Article{Chakraborty:2024:PPA, author = "Amit K. Chakraborty and Hao Wang and Pouria Ramazi", title = "From Policy to Prediction: Assessing Forecasting Accuracy in an Integrated Framework with Machine Learning and Disease Models", journal = j-J-COMPUT-BIOL, volume = "31", number = "11", pages = "1104--1117", month = nov, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0377", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:31 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0377; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0377", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 August 2024", } @Article{Khanghahi:2024:BHO, author = "Maryam Jafari Khanghahi and Reza Khoshsiar Ghaziani", title = "Bifurcations and Homoclinic Orbits of a Model Consisting of Vegetation--Prey--Predator Populations", journal = j-J-COMPUT-BIOL, volume = "31", number = "11", pages = "1118--1145", month = nov, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0485", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:31 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0485; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0485", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 September 2024", } @Article{Quesado:2024:HGA, author = "Pedro Quesado and Luis H. M. Torres and Bernardete Ribeiro and Joel P. Arrais", title = "A Hybrid {GNN} Approach for Improved Molecular Property Prediction", journal = j-J-COMPUT-BIOL, volume = "31", number = "11", pages = "1146--1157", month = nov, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0452", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:31 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0452; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0452", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "31 July 2024", } @Article{Park:2024:NCE, author = "Heewon Park and Satoru Miyano", title = "Network-Constrained Eigen-Single-Cell Profile Estimation for Uncovering Crucial Immunogene Regulatory Systems in Human Bone Marrow", journal = j-J-COMPUT-BIOL, volume = "31", number = "11", pages = "1158--1178", month = nov, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0539", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:31 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0539; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0539", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 September 2024", } @Article{Sukpol:2024:CSC, author = "Wimonnat Sukpol and Teeraphan Laomettachit and Anuwat Tangthanawatsakul", title = "A Cancer Subpopulation Competition Model Reveals Optimal Levels of Immune Response that Minimize Tumor Size", journal = j-J-COMPUT-BIOL, volume = "31", number = "11", pages = "1179--1194", month = nov, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0618", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:31 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0618; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0618", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 September 2024", } @Article{Spouge:2024:SPS, author = "John L. Spouge and Pijush Das and Ye Chen and Martin Frith", title = "The Statistics of Parametrized Syncmers in a Simple Mutation Process Without Spurious Matches", journal = j-J-COMPUT-BIOL, volume = "31", number = "12", pages = "1195--1210", month = dec, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0508", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:32 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0508; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0508", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "12 November 2024", } @Article{Yu:2024:MRG, author = "Boyuan Yu and Hao Zhang and Cong Pian and Yuanyuan Chen", title = "{MMG4}: Recognition of {G4}-Forming Sequences Based on {Markov} Model", journal = j-J-COMPUT-BIOL, volume = "31", number = "12", pages = "1211--1223", month = dec, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0523", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:32 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0523; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0523", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "17 October 2024", } @Article{Zhang:2024:HAP, author = "Lin Zhang and Jigen Peng and Yongbin Ge and Haiyang Li and Yuchao Tang", title = "High-Accuracy Positivity-Preserving Finite Difference Approximations of the Chemotaxis Model for Tumor Invasion", journal = j-J-COMPUT-BIOL, volume = "31", number = "12", pages = "1224--1258", month = dec, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0316", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:32 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0316; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0316", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "7 October 2024", } @Article{Ma:2024:PBP, author = "Han Ma and Yanyan Du and Zong Wang and Qimin Zhang", title = "Positivity and Boundedness Preserving Numerical Scheme for a Stochastic Multigroup Susceptible-Infected-Recovering Epidemic Model with Age Structure", journal = j-J-COMPUT-BIOL, volume = "31", number = "12", pages = "1259--1290", month = dec, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0443", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:32 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0443; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0443", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 September 2024", } @Article{Yang:2024:SAD, author = "Jing Yang and Shaojuan Ma and Juan Ma and Jinhua Ran and Xinyu Bai", title = "Stochastic Analysis for the Dual Virus Parallel Transmission Model with Immunity Delay", journal = j-J-COMPUT-BIOL, volume = "31", number = "12", pages = "1291--1304", month = dec, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0662", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:32 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0662; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0662", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 October 2024", } @Article{Ascolani:2024:RPN, author = "Filippo Ascolani and Stefano Damato and Matteo Ruggiero", title = "An {R} Package for Nonparametric Inference on Dynamic Populations with Infinitely Many Types", journal = j-J-COMPUT-BIOL, volume = "31", number = "12", pages = "1305--1311", month = dec, year = "2024", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0600", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:32 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/s-plus.bib; https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0600; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0600", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "22 October 2024", } @Article{Anonymous:2025:AR, author = "Anonymous", title = "Acknowledgment of Reviewers 2024", journal = j-J-COMPUT-BIOL, volume = "32", number = "1", pages = "1--2", month = jan, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.10852.revack", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:34 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.10852.revack", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 January 2025", } @Article{Warnow:2025:AEL, author = "Tandy Warnow and Yasamin Tabatabaee and Steven N. Evans", title = "Advances in Estimating Level-1 Phylogenetic Networks from Unrooted {SNPs}", journal = j-J-COMPUT-BIOL, volume = "32", number = "1", pages = "3--27", month = jan, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0710", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:34 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0710; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0710", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 November 2024", } @Article{Biane:2025:EPM, author = "C{\'e}lia Biane and Greg Hampikian and Sergey Kirgizov and Khaydar Nurligareev", title = "Endhered Patterns in Matchings and {RNA}", journal = j-J-COMPUT-BIOL, volume = "32", number = "1", pages = "28--46", month = jan, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0658", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:34 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0658; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0658", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 December 2024", } @Article{Zhu:2025:CHN, author = "Rong Zhu and Yong Wang and Ling-Yun Dai", title = "{CLHGNNMDA}: Hypergraph Neural Network Model Enhanced by Contrastive Learning for {miRNA}--Disease Association Prediction", journal = j-J-COMPUT-BIOL, volume = "32", number = "1", pages = "47--63", month = jan, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0720", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:34 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0720; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0720", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 November 2024", } @Article{Bai:2025:OMP, author = "Lidan Bai and Jun Sun and Vasile Palade and Chao Li and Hengyang Lu and Cong Gao", title = "Optimizing Metabolite Production with Neighborhood-Based Binary Quantum-Behaved Particle Swarm Optimization and Flux Balance Analysis", journal = j-J-COMPUT-BIOL, volume = "32", number = "1", pages = "64--88", month = jan, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0538", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:34 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0538; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0538", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "10 December 2024", } @Article{DeVoe:2025:AAC, author = "Elias DeVoe and Honey V. Reddi and Bradley W. Taylor and Samantha Stachowiak and Jennifer L. Geurts and Ben George and Reza Shaker and Raul Urrutia and Michael T. Zimmermann", title = "An Analytical Approach that Combines Knowledge from Germline and Somatic Mutations Enhances Tumor Genomic Reanalyses in Precision Oncology", journal = j-J-COMPUT-BIOL, volume = "32", number = "1", pages = "89--103", month = jan, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0461", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:34 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0461; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0461", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "11 December 2024", } @Article{Sanchez:2025:TGI, author = "Juan Felipe S{\'a}nchez and Salah Ramtani and Abdelkader Boucetta and Marco Antonio Velasco and Juan Jairo Vaca-Gonz{\'a}lez and Carlos A. Duque-Daza and Diego A. Garz{\'o}n-Alvarado", title = "Is Tumor Growth Influenced by the Bone Remodeling Process?", journal = j-J-COMPUT-BIOL, volume = "32", number = "1", pages = "104--124", month = jan, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0390", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:34 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0390; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0390", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "26 December 2024", } @Article{Patterson:2025:SIP, author = "Murray Patterson", title = "{{\em Special Issue, Part 2\/} 19th International Symposium on Bioinformatics Research and Applications (ISBRA 2023)}", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "125--126", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0905", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0905", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 December 2024", } @Article{Qingge:2025:GAM, author = "Letu Qingge and Kushal Badal and Richard Annan and Jordan Sturtz and Xiaowen Liu and Binhai Zhu", title = "Generative {AI} Models for the Protein Scaffold Filling Problem", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "127--142", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0510", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0510; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0510", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "23 October 2024", } @Article{Yang:2025:PPD, author = "Wanyi Yang and Qingsong Du and Xunyu Zhou and Chuanfang Wu and Jinku Bao", title = "{PDFll}: Predictors of Disorder and Function of Proteins from the Language of Life", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "143--155", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0506", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0506; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0506", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 September 2024", } @Article{Zhang:2025:AAF, author = "Yan Zhang and Xin Liu and Panrui Tang and Zuping Zhang", title = "{AFMDD}: Analyzing Functional Connectivity Feature of Major Depressive Disorder by Graph Neural Network-Based Model", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "156--163", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0505", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0505; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0505", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 February 2025", } @Article{Andersen:2025:PRC, author = "Jakob L. Andersen and Sissel Banke and Rolf Fagerberg and Christoph Flamm and Daniel Merkle and Peter F. Stadler", title = "Pathway Realizability in Chemical Networks", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "164--187", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0521", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0521; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0521", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "3 February 2025", } @Article{Rondel:2025:EEE, author = "Filipp Martin Rondel and Hafsa Farooq and Roya Hosseini and Akshay Juyal and Sergey Knyazev and Serghei Mangul and Artem S. Rogovskyy and Alexander Zelikovsky", title = "Estimating Enzyme Expression and Metabolic Pathway Activity in \bioname{Borreliella}-Infected and Uninfected Mice", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "188--197", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0564", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0564; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0564", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "27 June 2024", } @Article{Wang:2025:BDD, author = "GuiShen Wang and Hui Feng and Chen Cao", title = "{BiRNN-DDI}: a Drug-Drug Interaction Event Type Prediction Model Based on Bidirectional Recurrent Neural Network and {Graph2Seq} Representation", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "198--211", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0476", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0476; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0476", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "25 July 2024", } @Article{Lv:2025:CCM, author = "Ya Lv and Jin Liu and Xu Tian and Pei Yang and Yi Pan", title = "{CFINet}: Cross-Modality {MRI} Feature Interaction Network for Pseudoprogression Prediction of Glioblastoma", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "212--224", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0518", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0518; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0518", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "8 July 2024", } @Article{Niyogisubizo:2025:AGR, author = "Jovial Niyogisubizo and Keliang Zhao and Jintao Meng and Yi Pan and Rosiyadi Didi and Yanjie Wei", title = "Attention-Guided Residual {U}-Net with {SE} Connection and {ASPP} for Watershed-Based Cell Segmentation in Microscopy Images", journal = j-J-COMPUT-BIOL, volume = "32", number = "2", pages = "225--237", month = feb, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0446", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:35 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0446; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0446", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "18 October 2024", } @Article{Wu:2025:GBM, author = "Ziqian Wu and Jiyoon Park and Paul R. Steiner and Bo Zhu and John X. J. Zhang", title = "A Graph-Based Machine-Learning Approach Combined with Optical Measurements to Understand Beating Dynamics of Cardiomyocytes", journal = j-J-COMPUT-BIOL, volume = "32", number = "3", pages = "239--252", month = mar, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0491", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:37 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0491; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0491", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 December 2024", } @Article{Chen:2025:FBI, author = "Xiang Chen and Yibing Ma and Yongle Shi and Bai Zhang and Hanwen Wu and Jie Gao", title = "Fuzzy-Based Identification of Transition Cells to Infer Cell Trajectory for Single-Cell Transcriptomics", journal = j-J-COMPUT-BIOL, volume = "32", number = "3", pages = "253--273", month = mar, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0432", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:37 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0432; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0432", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "13 December 2024", } @Article{Pang:2025:EMD, author = "Fengqian Pang and Chunyue Lei and Hongfei Zhao and Zhiqiang Xing", title = "An Earth Mover's Distance-Based Self-Supervised Framework for Cellular Dynamic Grading in Live-Cell Imaging", journal = j-J-COMPUT-BIOL, volume = "32", number = "3", pages = "274--297", month = mar, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0672", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:37 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0672; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0672", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "2 December 2024", } @Article{Hu:2025:AAC, author = "Yingxin Hu and Yanjun Liu and Yuefei Yang", title = "Adaptive Arithmetic Coding-Based Encoding Method Toward High-Density {DNA} Storage", journal = j-J-COMPUT-BIOL, volume = "32", number = "3", pages = "298--315", month = mar, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0697", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:37 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0697; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0697", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "15 November 2024", } @Article{Abbasi:2025:DRU, author = "Hanieh Abbasi and Amir Lakizadeh", title = "Drug Repurposing Using Hypergraph Embedding Based on Common Therapeutic Targets of a Drug", journal = j-J-COMPUT-BIOL, volume = "32", number = "3", pages = "316--329", month = mar, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2023.0427", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:37 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2023.0427; https://www.liebertpub.com/doi/reader/10.1089/cmb.2023.0427", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "9 December 2024", } @Article{Sefer:2025:DPD, author = "Emre Sefer", title = "{DRGAT}: Predicting Drug Responses Via Diffusion-Based Graph Attention Network", journal = j-J-COMPUT-BIOL, volume = "32", number = "3", pages = "330--350", month = mar, year = "2025", CODEN = "JCOBEM", DOI = "https://doi.org/10.1089/cmb.2024.0807", ISSN = "1066-5277 (print), 1557-8666 (electronic)", ISSN-L = "1066-5277", bibdate = "Sat Apr 5 08:52:37 MDT 2025", bibsource = "https://www.math.utah.edu/pub/tex/bib/jcomputbiol.bib", URL = "https://www.liebertpub.com/doi/abs/10.1089/cmb.2024.0807; https://www.liebertpub.com/doi/reader/10.1089/cmb.2024.0807", acknowledgement = ack-nhfb, ajournal = "J. Comput. Biol.", fjournal = "Journal of Computational Biology", journal-URL = "https://www.liebertpub.com/loi/cmb/", onlinedate = "6 December 2024", }