Table of contents for issues of Journal of Computational Biology

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Volume 1, Number 1, January, 1994
Volume 1, Number 2, January, 1994
Volume 1, Number 3, January, 1994
Volume 1, Number 4, January, 1994
Volume 2, Number 1, January, 1995
Volume 2, Number 2, January, 1995
Volume 2, Number 3, January, 1995
Volume 2, Number 4, January, 1995
Volume 3, Number 1, January, 1996
Volume 3, Number 2, January, 1996
Volume 3, Number 3, January, 1996
Volume 3, Number 4, January, 1996
Volume 4, Number 1, January, 1997
Volume 4, Number 2, January, 1997
Volume 4, Number 3, January, 1997
Volume 4, Number 4, January, 1997
Volume 5, Number 1, January, 1998
Volume 5, Number 2, January, 1998
Volume 5, Number 3, January, 1998
Volume 5, Number 4, January, 1998
Volume 6, Number 1, January, 1999
Volume 6, Number 2, January, 1999
Volume 6, Number 3--4, October, 1999
Volume 7, Number 1--2, February, 2000
Volume 7, Number 3--4, August, 2000
Volume 7, Number 5, October, 2000
Volume 7, Number 6, December, 2000
Volume 8, Number 1, February, 2001
Volume 8, Number 2, April, 2001
Volume 8, Number 3, June, 2001
Volume 8, Number 4, September, 2001
Volume 8, Number 5, October, 2001
Volume 8, Number 6, November, 2001
Volume 9, Number 1, January, 2002
Volume 9, Number 2, April, 2002
Volume 9, Number 3, June, 2002
Volume 9, Number 4, August, 2002
Volume 9, Number 5, October, 2002
Volume 9, Number 6, December, 2002
Volume 10, Number 1, February, 2003
Volume 10, Number 2, April, 2003
Volume 10, Number 3--4, June, 2003
Volume 10, Number 5, October, 2003
Volume 10, Number 6, December, 2003
Volume 11, Number 1, January, 2004
Volume 11, Number 2--3, March, 2004
Volume 11, Number 4, August, 2004
Volume 11, Number 5, October, 2004
Volume 11, Number 6, December, 2004
Volume 12, Number 1, February, 2005
Volume 12, Number 2, March, 2005
Volume 12, Number 3, April, 2005
Volume 12, Number 4, May, 2005
Volume 12, Number 5, June, 2005
Volume 12, Number 6, July, 2005
Volume 12, Number 7, September, 2005
Volume 12, Number 8, October, 2005
Volume 12, Number 9, November, 2005
Volume 12, Number 10, December, 2005
Volume 13, Number 1, January, 2006
Volume 13, Number 2, March, 2006
Volume 13, Number 3, April, 2006
Volume 13, Number 4, May, 2006
Volume 13, Number 5, June, 2006
Volume 13, Number 6, July, 2006
Volume 13, Number 7, September, 2006
Volume 13, Number 8, October, 2006
Volume 13, Number 9, November, 2006
Volume 13, Number 10, December, 2006
Volume 14, Number 1, January, 2007
Volume 14, Number 2, March, 2007
Volume 14, Number 3, April, 2007
Volume 14, Number 4, May, 2007
Volume 14, Number 5, June, 2007
Volume 14, Number 6, July, 2007
Volume 14, Number 7, September, 2007
Volume 14, Number 8, October, 2007
Volume 14, Number 9, November, 2007
Volume 14, Number 10, December, 2007
Volume 15, Number 1, January, 2008
Volume 15, Number 2, March, 2008
Volume 15, Number 3, April, 2008
Volume 15, Number 4, May, 2008
Volume 15, Number 5, June, 2008
Volume 15, Number 6, July, 2008
Volume 15, Number 7, September, 2008
Volume 15, Number 8, October, 2008
Volume 15, Number 9, November, 2008
Volume 15, Number 10, December, 2008
Volume 16, Number 1, January, 2009
Volume 16, Number 2, February, 2009
Volume 16, Number 3, March, 2009
Volume 16, Number 4, April, 2009
Volume 16, Number 5, May, 2009
Volume 16, Number 6, June, 2009
Volume 16, Number 7, July, 2009
Volume 16, Number 8, August, 2009
Volume 16, Number 9, September, 2009
Volume 16, Number 10, October, 2009
Volume 16, Number 11, November, 2009
Volume 16, Number 12, December, 2009
Volume 17, Number 1, January, 2010
Volume 17, Number 2, February, 2010
Volume 17, Number 3, March, 2010
Volume 17, Number 4, April, 2010
Volume 17, Number 5, May, 2010
Volume 17, Number 6, June, 2010
Volume 17, Number 7, July, 2010
Volume 17, Number 8, August, 2010
Volume 17, Number 9, September, 2010
Volume 17, Number 10, October, 2010
Volume 17, Number 11, November, 2010
Volume 17, Number 12, December, 2010
Volume 18, Number 1, January, 2011
Volume 18, Number 2, February, 2011
Volume 18, Number 3, March, 2011
Volume 18, Number 4, April, 2011
Volume 18, Number 5, May, 2011
Volume 18, Number 6, June, 2011
Volume 18, Number 7, July, 2011
Volume 18, Number 8, August, 2011
Volume 18, Number 9, September, 2011
Volume 18, Number 10, October, 2011
Volume 18, Number 11, November, 2011
Volume 18, Number 12, December, 2011
Volume 19, Number 1, January, 2012
Volume 19, Number 2, February, 2012
Volume 19, Number 3, March, 2012
Volume 19, Number 4, April, 2012
Volume 19, Number 5, May, 2012
Volume 19, Number 6, June, 2012
Volume 19, Number 7, July, 2012
Volume 19, Number 8, August, 2012
Volume 19, Number 9, September, 2012
Volume 19, Number 10, October, 2012
Volume 19, Number 11, November, 2012
Volume 19, Number 12, December, 2012
Volume 20, Number 1, January, 2013
Volume 20, Number 2, February, 2013
Volume 20, Number 3, March, 2013
Volume 20, Number 4, April, 2013
Volume 20, Number 5, May, 2013
Volume 20, Number 6, June, 2013
Volume 20, Number 7, July, 2013
Volume 20, Number 8, August, 2013
Volume 20, Number 9, September, 2013
Volume 20, Number 10, October, 2013
Volume 20, Number 11, November, 2013
Volume 20, Number 12, December, 2013
Volume 21, Number 1, January, 2014
Volume 21, Number 2, February, 2014
Volume 21, Number 3, March, 2014
Volume 21, Number 4, April, 2014
Volume 21, Number 5, May, 2014
Volume 21, Number 6, June, 2014
Volume 21, Number 7, July, 2014
Volume 21, Number 8, August, 2014
Volume 21, Number 9, September, 2014
Volume 21, Number 10, October, 2014
Volume 21, Number 11, November, 2014
Volume 21, Number 12, December, 2014
Volume 22, Number 1, January, 2015
Volume 22, Number 2, February, 2015
Volume 22, Number 3, March, 2015
Volume 22, Number 4, April, 2015
Volume 22, Number 5, May, 2015
Volume 22, Number 6, June, 2015
Volume 22, Number 7, July, 2015
Volume 22, Number 8, August, 2015
Volume 22, Number 9, September, 2015
Volume 22, Number 10, October, 2015
Volume 22, Number 11, November, 2015
Volume 22, Number 12, December, 2015
Volume 23, Number 1, January, 2016
Volume 23, Number 2, February, 2016
Volume 23, Number 3, March, 2016
Volume 23, Number 4, April, 2016
Volume 23, Number 5, May, 2016
Volume 23, Number 6, June, 2016
Volume 23, Number 7, July, 2016
Volume 23, Number 8, August, 2016
Volume 23, Number 9, September, 2016
Volume 23, Number 10, October, 2016
Volume 23, Number 11, November, 2016
Volume 23, Number 12, December, 2016
Volume 24, Number 1, January, 2017
Volume 24, Number 2, February, 2017
Volume 24, Number 3, March, 2017
Volume 24, Number 4, April, 2017
Volume 24, Number 5, May, 2017
Volume 24, Number 6, June, 2017
Volume 24, Number 7, July, 2017
Volume 24, Number 8, August, 2017
Volume 24, Number 9, September, 2017
Volume 24, Number 10, October, 2017
Volume 24, Number 11, November, 2017
Volume 24, Number 12, December, 2017
Volume 25, Number 1, January, 2018
Volume 25, Number 2, February, 2018
Volume 25, Number 3, March, 2018
Volume 25, Number 4, April, 2018
Volume 25, Number 5, May, 2018
Volume 25, Number 6, June, 2018
Volume 25, Number 7, July, 2018
Volume 25, Number 8, August, 2018
Volume 25, Number 9, September, 2018
Volume 25, Number 10, October, 2018
Volume 25, Number 11, November, 2018
Volume 25, Number 12, December, 2018
Volume 26, Number 1, January, 2019
Volume 26, Number 2, February, 2019
Volume 26, Number 3, March, 2019
Volume 26, Number 4, April, 2019
Volume 26, Number 5, May, 2019
Volume 26, Number 6, June, 2019
Volume 26, Number 7, July, 2019
Volume 26, Number 8, August, 2019
Volume 26, Number 9, September, 2019
Volume 26, Number 10, October, 2019
Volume 26, Number 11, November, 2019
Volume 26, Number 12, December, 2019
Volume 27, Number 1, January, 2020
Volume 27, Number 2, February, 2020
Volume 27, Number 3, March, 2020
Volume 27, Number 4, April, 2020
Volume 27, Number 5, May, 2020
Volume 27, Number 6, June, 2020
Volume 27, Number 7, July, 2020
Volume 27, Number 8, August, 2020
Volume 27, Number 9, September, 2020
Volume 27, Number 10, October, 2020
Volume 27, Number 11, November, 2020
Volume 27, Number 12, December, 2020
Volume 28, Number 1, January, 2021
Volume 28, Number 2, February, 2021
Volume 28, Number 3, March, 2021
Volume 28, Number 4, April, 2021
Volume 28, Number 5, May, 2021
Volume 28, Number 6, June, 2021
Volume 28, Number 7, July, 2021
Volume 28, Number 8, August, 2021
Volume 28, Number 9, September, 2021
Volume 28, Number 10, October, 2021
Volume 28, Number 11, November, 2021
Volume 28, Number 12, December, 2021
Volume 29, Number 1, January, 2022
Volume 29, Number 2, February, 2022
Volume 29, Number 3, March, 2022
Volume 29, Number 4, April, 2022
Volume 29, Number 5, May, 2022
Volume 29, Number 6, June, 2022
Volume 29, Number 7, July, 2022
Volume 29, Number 8, August, 2022
Volume 29, Number 9, September, 2022
Volume 29, Number 10, October, 2022
Volume 29, Number 11, November, 2022
Volume 29, Number 12, December, 2022
Volume 30, Number 1, January, 2023
Volume 30, Number 2, February, 2023
Volume 30, Number 3, March, 2023
Volume 30, Number 4, April, 2023
Volume 30, Number 5, May, 2023
Volume 30, Number 6, June, 2023
Volume 30, Number 7, July, 2023
Volume 30, Number 8, August, 2023
Volume 30, Number 9, September, 2023
Volume 30, Number 10, October, 2023
Volume 30, Number 11, November, 2023
Volume 30, Number 12, December, 2023
Volume 31, Number 1, January, 2024
Volume 31, Number 2, February, 2024
Volume 31, Number 3, March, 2024
Volume 31, Number 4, April, 2024
Volume 31, Number 5, May, 2024


Journal of Computational Biology
Volume 1, Number 1, January, 1994

                      Anonymous   Editorial: Whither Computational Biology 1--2
       G. Christian Overton and   
        Jeffrey S. Aaronson and   
               Juergen Haas and   
                    Julie Adams   QGB: a System for Querying Sequence
                                  Database Fields and Features . . . . . . 3--14
        Kimberly E. Forsten and   
       Douglas A. Lauffenburger   Probability of Autocrine Ligand Capture
                                  by Cell-Surface Receptors: Implications
                                  for Ligand Secretion Measurements  . . . 15--23
                  Bing Leng and   
          Bruce G. Buchanan and   
               Hugh B. Nicholas   Protein Secondary Structure Prediction
                                  Using Two-Level Case-Based Reasoning . . 25--38
            David J. States and   
                    Warren Gish   QGB: Combined Use of Sequence Similarity
                                  and Codon Bias for Coding Region
                                  Identification . . . . . . . . . . . . . 39--50
                Webb Miller and   
               Mark Boguski and   
        Balaji Raghavachari and   
                Zheng Zhang and   
               Ross C. Hardison   Constructing Aligned Sequence Blocks . . 51--64
                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   A Conceptual Database Model for Genomic
                                  Research . . . . . . . . . . . . . . . . 65--76
                V. Ferretti and   
                 B. F. Lang and   
                     D. Sankoff   Skewed Base Compositions, Asymmetric
                                  Transition Matrices, and Phylogenetic
                                  Invariants . . . . . . . . . . . . . . . 77--92

Journal of Computational Biology
Volume 1, Number 2, January, 1994

            Larry Goldstein and   
            Michael S. Waterman   Approximations to Profile Score
                                  Distributions  . . . . . . . . . . . . . 93--104
                Martin Dyer and   
                Alan Frieze and   
                   Stephen Suen   The Probability of Unique Solutions of
                                  Sequencing by Hybridization  . . . . . . 105--110
               G. A. Rohrer and   
              D. W. Behrens and   
                    J. W. Keele   A Simplified Procedure for Entry of Raw
                                  Genotypic Data . . . . . . . . . . . . . 111--119
              Mauro Rustici and   
                 Arthur M. Lesk   Three-Dimensional Searching for
                                  Recurrent Structural Motifs in Data
                                  Bases of Protein Structures  . . . . . . 121--132
      Michael A. Charleston and   
           Michael D. Hendy and   
                    David Penny   The Effects of Sequence Length, Tree
                                  Topology, and Number of Taxa on the
                                  Performance of Phylogenetic Methods  . . 133--151
                M. A. Steel and   
       L. A. Székely and   
                    M. D. Hendy   Reconstructing Trees When Sequence Sites
                                  Evolve at Variable Rates . . . . . . . . 153--163
              Kenneth H. Fasman   Restructuring the Genome Data Base: a
                                  Model for a Federation of Biological
                                  Databases  . . . . . . . . . . . . . . . 165--171

Journal of Computational Biology
Volume 1, Number 3, January, 1994

              Robert J. Robbins   Genome Informatics I: Community
                                  Databases  . . . . . . . . . . . . . . . 173--190
            R. Knüppel and   
                  P. Dietze and   
                W. Lehnberg and   
                   K. Frech and   
                   E. Wingender   TRANSFAC Retrieval Program: a Network
                                  Model Database of Eukaryotic
                                  Transcription Regulating Sequences and
                                  Proteins . . . . . . . . . . . . . . . . 191--198
               Winston Hide and   
                 John Burke and   
             Daniel B. Da Vison   Biological Evaluation of d$^2$, an
                                  Algorithm for High-Performance Sequence
                                  Comparison . . . . . . . . . . . . . . . 199--215
                Zheng Zhang and   
        Balaji Raghavachari and   
           Ross C. Hardison and   
                    Webb Miller   Chaining Multiple-Alignment Blocks . . . 217--226
                       Chi Wang   A Subgraph Problem from Restriction Maps
                                  of DNA . . . . . . . . . . . . . . . . . 227--234
                    Zheng Zhang   An Exponential Example for a Partial
                                  Digest Mapping Algorithm . . . . . . . . 235--239
              Daniela R. Martin   Equivalence Classes for the
                                  Double-Digest Problem with Coincident
                                  Cut Sites  . . . . . . . . . . . . . . . 241--253

Journal of Computational Biology
Volume 1, Number 4, January, 1994

              Dan Gustfield and   
               David Shmoys and   
          Jan Karel Lenstra and   
                   Tandy Warnow   In Memoriam Eugene L. Lawler . . . . . . 255--256
             Mark J. Miller and   
                 John I. Powell   A Quantitative Comparison of DNA
                                  Sequence Assembly Programs . . . . . . . 257--269
               Kun-Mao Chao and   
           Ross C. Hardison and   
                    Webb Miller   Recent Developments in Linear-Space
                                  Alignment Methods: a Survey  . . . . . . 271--291
            Pierre A. Rioux and   
         William A. Gilbert and   
          Timothy G. Littlejohn   A Portable Search Engine and Browser for
                                  the Entrez Database  . . . . . . . . . . 293--295
              William R. Taylor   Motif-Biased Protein Sequence Alignment  297--310
               Pierre Baldi and   
                   Yves Chauvin   Hidden Markov Models of the
                                  G-Protein-Coupled Receptor Family  . . . 311--336
               Lusheng Wang and   
                      Tao Jiang   On the Complexity of Multiple Sequence
                                  Alignment  . . . . . . . . . . . . . . . 337--348
                 Dalit Naor and   
             Douglas L. Brutlag   On Near-Optimal Alignments of Biological
                                  Sequences  . . . . . . . . . . . . . . . 349--366


Journal of Computational Biology
Volume 2, Number 1, January, 1995

                  Donald Beaver   Computing with DNA . . . . . . . . . . . 1--7
               Sean R. Eddy and   
           Graeme Mitchison and   
                 Richard Durbin   Maximum Discrimination Hidden Markov
                                  Models of Sequence Consensus . . . . . . 9--23
            Roger F. Sewell and   
                 Richard Durbin   Method for Calculation of Probability of
                                  Matching a Bounded Regular Expression in
                                  a Random Data String . . . . . . . . . . 25--31
                Mudita Jain and   
                Eugene W. Myers   A Note on Scoring Clones Given a Probe
                                  Ordering . . . . . . . . . . . . . . . . 33--37
                M. A. Steel and   
                       Y. X. Fu   Classifying and Counting Linear
                                  Phylogenetic Invariants for the
                                  Jukes--Cantor Model  . . . . . . . . . . 39--47
               Gunter Weiss and   
             Arndt Von Haeseler   Modeling the Polymerase Chain Reaction   49--61
                    Fengzhu Sun   The Polymerase Chain Reaction and
                                  Branching Processes  . . . . . . . . . . 63--86
                  M. S. Gelfand   Prediction of Function in DNA Sequence
                                  Analysis . . . . . . . . . . . . . . . . 87--115
               James W. Fickett   ORFs and Genes: How Strong a Connection? 117--123
                  Bonnie Berger   Algorithms for Protein Structural Motif
                                  Recognition  . . . . . . . . . . . . . . 125--138
           Paul W. Goldberg and   
         Martin C. Golumbic and   
                Haim Kaplan and   
                     Ron Shamir   Four Strikes Against Physical Mapping of
                                  DNA  . . . . . . . . . . . . . . . . . . 139--152

Journal of Computational Biology
Volume 2, Number 2, January, 1995

               Pavel A. Pevzner   Combinatorial Methods for DNA Mapping
                                  and Sequencing . . . . . . . . . . . . . 153--158
             Farid Alizadeh and   
            Richard M. Karp and   
         Deborah K. Weisser and   
                 Geoffrey Zweig   Physical Mapping of Chromosomes Using
                                  Unique Probes  . . . . . . . . . . . . . 159--184
               Will Gillett and   
                  Jim Daues and   
                  Liz Hanks and   
                      Rob Capra   Fragment Collapsing and Splitting While
                                  Assembling High-Resolution Restriction
                                  Maps . . . . . . . . . . . . . . . . . . 185--205
                Martin Dyer and   
                Alan Frieze and   
                   Stephen Suen   Ordering Clone Libraries in
                                  Computational Biology  . . . . . . . . . 207--218
         David S. Greenberg and   
                  Sorin Istrail   Physical Mapping by STS Hybridization:
                                  Algorithmic Strategies and the Challenge
                                  of Software Evaluation . . . . . . . . . 219--273
                Eugene W. Myers   Toward Simplifying and Accurately
                                  Formulating Fragment Assembly  . . . . . 275--290
            Ramana M. Idury and   
            Michael S. Waterman   A New Algorithm for DNA Sequence
                                  Assembly . . . . . . . . . . . . . . . . 291--306
                Chris Armen and   
                 Clifford Stein   Short Superstrings and the Structure of
                                  Overlapping Strings  . . . . . . . . . . 307--332
           Steven S. Skiena and   
        Gopalakrishnan Sundaram   Reconstructing Strings from Substrings   333--353
     Aleksandar Milosavljevi\'c   DNA Sequence Recognition by
                                  Hybridization to Short Oligomers . . . . 355--370
              A. R. Rubinov and   
                  M. S. Gelfand   Reconstruction of a String from
                                  Substring Precedence Data  . . . . . . . 371--381
            Oleg Razgulyaev and   
            Anatoly Rubinov and   
            Mikhail Gelfand and   
            Alexander Chetverin   Sequencing Potential of Nested Strand
                                  Hybridization  . . . . . . . . . . . . . 383--395

Journal of Computational Biology
Volume 2, Number 3, January, 1995

             Richa Agarwala and   
David Fernández-Baca and   
                  Giora Slutzki   Fast Algorithms for Inferring
                                  Evolutionary Trees . . . . . . . . . . . 397--407
                   Jian Sun and   
              Wen-Yuan Song and   
               Li-Huang Zhu and   
                 Run-Sheng Chen   Analysis of tRNA Gene Sequences by
                                  Neural Network . . . . . . . . . . . . . 409--416
             Sophie Schbath and   
               Bernard Prum and   
         Elisabeth De Turckheim   Exceptional Motifs in Different Markov
                                  Chain Models for a Statistical Analysis
                                  of DNA Sequences . . . . . . . . . . . . 417--437
               M. A. Charleston   Toward a Characterization of Landscapes
                                  of Combinatorial Optimization Problems,
                                  with Special Attention to the Phylogeny
                                  Problem  . . . . . . . . . . . . . . . . 439--450
               K. C. Worley and   
                 K. Y. King and   
                    S. Chua and   
            E. R. B. Mccabe and   
                    R. F. Smith   Identification of New Members of a
                                  Carbohydrate Kinase-Encoding Gene Family 451--458
           Sandeep K. Gupta and   
         John D. Kececioglu and   
     Alejandro A. Schäffer   Improving the Practical Space and Time
                                  Efficiency of the Shortest-Paths
                                  Approach to Sum-of-Pairs Multiple
                                  Sequence Alignment . . . . . . . . . . . 459--472
                Steven Salzberg   Locating Protein Coding Regions in Human
                                  DNA Using a Decision Tree Algorithm  . . 473--485
                   Pierre Baldi   Substitution Matrices and Hidden Markov
                                  Models . . . . . . . . . . . . . . . . . 487--491

Journal of Computational Biology
Volume 2, Number 4, January, 1995

               Boris Mirkin and   
               Ilya Muchnik and   
                Temple F. Smith   A Biologically Consistent Model for
                                  Comparing Molecular Phylogenies  . . . . 493--507
                H. Todd Wareham   A Simplified Proof of the NP- and MAX
                                  SNP-Hardness of Multiple Sequence Tree
                                  Alignment  . . . . . . . . . . . . . . . 509--514
               Craig Benham and   
             Sampath Kannan and   
           Michael Paterson and   
                   Tandy Warnow   Hen's Teeth and Whale's Feet:
                                  Generalized Characters and Their
                                  Compatibility  . . . . . . . . . . . . . 515--525
              Boris A. Reva and   
         Dmitrii S. Rykunov and   
            Arthur J. Olson and   
          Alexei V. Finkelstein   Constructing Lattice Models of Protein
                                  Chains with Side Groups  . . . . . . . . 527--535
            Victor M. Markowitz   Heterogeneous Molecular Biology
                                  Databases  . . . . . . . . . . . . . . . 537--538
               Stanley Letovsky   Beyond the Information Maze  . . . . . . 539--546
        Victor M. Markowitz and   
                    Otto Ritter   Characterizing Heterogeneous Molecular
                                  Biology Database Systems . . . . . . . . 547--556
             S. B. Davidson and   
                 C. Overton and   
                     P. Buneman   Challenges in Integrating Biological
                                  Data Sources . . . . . . . . . . . . . . 557--572
                  Peter D. Karp   A Strategy for Database Interoperation   573--586


Journal of Computational Biology
Volume 3, Number 1, January, 1996

             Pankaj Agarwal and   
                David J. States   A Bayesian Evolutionary Distance for
                                  Parametrically Aligned Sequences . . . . 1--17
           Michael D. Hendy and   
                    David Penny   Complete Families of Linear Invariants
                                  for Some Stochastic Models of Sequence
                                  Evolution, with and without the
                                  Molecular Clock Assumption . . . . . . . 19--31
                Eugene W. Myers   Approximate Matching of Network
                                  Expressions with Spacers . . . . . . . . 33--51
            William E. Hart and   
               Sorin C. Istrail   Fast Protein Folding in the
                                  Hydrophobic--Hydrophilic Model within
                                  Three-Eighths of Optimal . . . . . . . . 53--96
            Yoshikane Takahashi   A Mathematical Solution to a Network
                                  Designing Problem  . . . . . . . . . . . 97--141
            Rajani R. Joshi and   
                 K. Krishnanand   Probabilistic Learning in Immune
                                  Network: Weighted Tree Matching Model    143--162
  Sòren Kamaric Riis and   
                   Anders Krogh   Improving Prediction of Protein
                                  Secondary Structure Using Structured
                                  Neural Networks and Multiple Sequence
                                  Alignments . . . . . . . . . . . . . . . 163--183
                Simon Tsang and   
           Milton H. Saier, Jr.   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 . . . . . . . . . . . 185--190
              Peter D. Karp and   
                  Suzanne Paley   Integrated Access to Metabolic and
                                  Genomic Data . . . . . . . . . . . . . . 191--212

Journal of Computational Biology
Volume 3, Number 2, January, 1996

               Raj K. Singh and   
          Alexander Tropsha and   
               Iosif I. Vaisman   Delaunay Tessellation of Proteins: Four
                                  Body Nearest-Neighbor Propensities of
                                  Amino Acid Residues  . . . . . . . . . . 213--221
              M. S. Gelfand and   
             L. I. Podolsky and   
            T. V. Astakhova and   
                 M. A. Roytberg   Recognition of Genes in Human DNA
                                  Sequences  . . . . . . . . . . . . . . . 223--234
          Bernd Schierwater and   
               Dirk Metzler and   
          Katja Krüger and   
                   Bruno Streit   The Effects of Nested Primer Binding
                                  Sites on the Reproducibility of PCR:
                                  Mathematical Modeling and Computer
                                  Simulation Studies . . . . . . . . . . . 235--251
          Martijn A. Huynen and   
              Alan Perelson and   
            Wayne A. Vieira and   
               Peter F. Stadler   Base Pairing Probabilities in a Complete
                                  HIV-1 RNA  . . . . . . . . . . . . . . . 253--274
                   David Bryant   Hunting for Trees in Binary Character
                                  Sets: Efficient Algorithms for
                                  Extraction, Enumeration, and
                                  Optimization . . . . . . . . . . . . . . 275--288
                   Ina Koch and   
            Thomas Lengauer and   
                     Egon Wanke   An Algorithm for Finding Maximal Common
                                  Subtopologies in a Set of Protein
                                  Structures . . . . . . . . . . . . . . . 289--306
              Colleen Kelly and   
              Gary A. Churchill   Biases in Amino Acid Replacement
                                  Matrices and Alignment Scores Due to
                                  Rate Heterogeneity . . . . . . . . . . . 307--318
           Prakash Nadkarni and   
             Kei-Hoi Cheung and   
        Carmela Castiglione and   
               Perry Miller and   
                   Kenneth Kidd   DNA Workbench: a Database Package to
                                  Manage Regional Physical Mapping . . . . 319--329
                Martin Dyer and   
                Alan Frieze and   
                   Stephen Suen   Corrigendum to \booktitleProbability of
                                  Unique Solutions of Sequencing by
                                  Hybridization  . . . . . . . . . . . . . 331--331

Journal of Computational Biology
Volume 3, Number 3, January, 1996

                    Ying Xu and   
           Richard J. Mural and   
           Edward C. Uberbacher   An Iterative Algorithm for Correcting
                                  Sequencing Errors in DNA Coding Regions  333--344
            Ming-Ying Leung and   
         Genevieve M. Marsh and   
               Terence P. Speed   Over- and Underrepresentation of Short
                                  DNA Words in Herpesvirus Genomes . . . . 345--360
              Hiroshi Mamitsuka   A Learning Method of Hidden Markov
                                  Models for Sequence Discrimination . . . 361--373
                   Thomas D. Wu   A Segment-Based Dynamic Programming
                                  Algorithm for Predicting Gene Structure  375--394
                   E. Knill and   
                 A. Schliep and   
                   D. C. Torney   Interpretation of Pooling Experiments
                                  Using the Markov Chain Monte Carlo
                                  Method . . . . . . . . . . . . . . . . . 395--406
               Hugh Salamon and   
               Jorma Tarhio and   
   Kjersti Rònningen and   
                 Glenys Thomson   On Distinguishing Unique Combinations in
                                  Biological Sequences . . . . . . . . . . 407--423
            Richard Arratia and   
             Daniela Martin and   
             Gesine Reinert and   
            Michael S. Waterman   Poisson Process Approximation for
                                  Sequence Repeats, and Sequencing by
                                  Hybridization  . . . . . . . . . . . . . 425--463
              Robert J. Robbins   Bioinformatics: Essential Infrastructure
                                  for Global Biology$^1$ . . . . . . . . . 465--478

Journal of Computational Biology
Volume 3, Number 4, January, 1996

            R. C. Griffiths and   
                    P. Marjoram   Ancestral Inference from Samples of DNA
                                  Sequences with Recombination . . . . . . 479--502
    Suchendra M. Bhandarkar and   
         Sridhar Chirravuri and   
                Jonathan Arnold   Parallel Computing of Physical Maps ---
                                  a Comparative Study in SIMD and MIMD
                                  Parallelism  . . . . . . . . . . . . . . 503--528
                Rajani R. Joshi   A Self-Organizing Cognitive Network of
                                  Antibody Repertoire Development  . . . . 529--545
                Cathy H. Wu and   
                 Sheng Zhao and   
                  Hsi-Lien Chen   A Protein Class Database Organized with
                                  ProSite Protein Groups and PIR
                                  Superfamilies  . . . . . . . . . . . . . 547--561
                 Gene Myers and   
           Sanford Selznick and   
                Zheng Zhang and   
                    Webb Miller   Progressive Multiple Alignment with
                                  Constraints  . . . . . . . . . . . . . . 563--572
          Michael Teitelman and   
               Frank H. Eeckman   Principal Component Analysis and
                                  Large-Scale Correlations in Non-Coding
                                  Sequences of Human DNA . . . . . . . . . 573--576


Journal of Computational Biology
Volume 4, Number 1, January, 1997

            William E. Hart and   
                  Sorin Istrail   Robust Proofs of NP-Hardness for Protein
                                  Folding: General Lattices and Energy
                                  Potentials . . . . . . . . . . . . . . . 1--22
             Martin Vingron and   
             Arndt Von Haeseler   Towards Integration of Multiple
                                  Alignment and Phylogenetic Tree
                                  Construction . . . . . . . . . . . . . . 23--34
       Miroslav S. Tanushev and   
                Richard Arratia   Central Limit Theorem for Renewal Theory
                                  for Several Patterns . . . . . . . . . . 35--44
          Timothy L. Bailey and   
               Michael Gribskov   Score Distributions for Simultaneous
                                  Matching to Multiple Motifs  . . . . . . 45--59
                 Sophie Schbath   Coverage Processes in Physical Mapping
                                  by Anchoring Random Clones . . . . . . . 61--82
     Michael P. Ponomarenko and   
         Anna N. Kolchanova and   
           Nikolay A. Kolchanov   Generating Programs for Predicting the
                                  Activity of Functional Sites . . . . . . 83--90

Journal of Computational Biology
Volume 4, Number 2, January, 1997

     Thomas S. Anantharaman and   
                 Bud Mishra and   
              David C. Schwartz   Genomics via Optical Mapping II: Ordered
                                  Restriction Maps . . . . . . . . . . . . 91--118
      Vlado Dan\vcík and   
        Sridhar Hannenhalli and   
               S. Muthukrishnan   Hardness of Flip-Cut Problems from
                                  Optical Mapping  . . . . . . . . . . . . 119--125
             John Henderson and   
            Steven Salzberg and   
              Kenneth H. Fasman   Finding Genes in DNA with a Hidden
                                  Markov Model . . . . . . . . . . . . . . 127--141
                Paul E. Kearney   A Six-Point Condition for Ordinal
                                  Matrices . . . . . . . . . . . . . . . . 143--156
                  Martin Farach   Recognizing Circular Decomposable
                                  Metrics  . . . . . . . . . . . . . . . . 157--162
          Dorit S. Hochbaum and   
                    Anu Pathria   Path Costs in Evolutionary Tree
                                  Reconstruction . . . . . . . . . . . . . 163--175
                   Louxin Zhang   On a Mirkin--Muchnik--Smith Conjecture
                                  for Comparing Molecular Phylogenies  . . 177--187
                 Sophie Schbath   An Efficient Statistic to Detect Over-
                                  and Under-represented Words in DNA
                                  Sequences  . . . . . . . . . . . . . . . 189--192
          Jacob Z. Dalgaard and   
           Michael J. Moser and   
             Richard Hughey and   
                  I. Saira Mian   Statistical Modeling, Phylogenetic
                                  Analysis and Structure Prediction of a
                                  Protein Splicing Domain Common to
                                  Inteins and Hedgehog Proteins  . . . . . 193--214

Journal of Computational Biology
Volume 4, Number 3, January, 1997

        Michael S. Waterman and   
              Sorin Istrail and   
               Pavel A. Pevzner   Preface: Special RECOMB'97 Issues  . . . 215--215
            Temple F. Smith and   
          Loredana Lo Conte and   
         Jadwiga Bienkowska and   
       Chrysanthe Gaitatzes and   
      Robert G. Rogers, Jr. and   
                Richard Lathrop   Current Limitations to Protein Threading
                                  Approaches . . . . . . . . . . . . . . . 217--225
                 K. A. Dill and   
             A. T. Phillips and   
                    J. B. Rosen   Protein Structure and Energy Landscape
                                  Dependence on Sequence Using a
                                  Continuous Energy Function . . . . . . . 227--239
            William E. Hart and   
                  Sorin Istrail   Lattice and Off-Lattice Side Chain
                                  Models of Protein Folding: Linear Time
                                  Structure Prediction Better than 86% of
                                  Optimal  . . . . . . . . . . . . . . . . 241--259
              Bonnie Berger and   
                     Mona Singh   An Iterative Method for Improved Protein
                                  Structural Motif Recognition . . . . . . 261--273
             Richa Agarwala and   
          Serafim Batzoglou and   
      Vlado Dan\vcík and   
           Scott E. Decatur and   
        Sridhar Hannenhalli and   
              Martin Farach and   
           S. Muthukrishnan and   
                  Steven Skiena   Local Rules for Protein Folding on a
                                  Triangular Lattice and Generalized
                                  Hydrophobicity in the HP Model . . . . . 275--296
               Sing-Hoi Sze and   
               Pavel A. Pevzner   Las Vegas Algorithms for Gene
                                  Recognition: Suboptimal and
                                  Error-Tolerant Spliced Alignment . . . . 297--309
            Martin G. Reese and   
           Frank H. Eeckman and   
                 David Kulp and   
                 David Haussler   Improved Splice Site Detection in Genie  311--323
                    Ying Xu and   
           Edward C. Uberbacher   Automated Gene Identification in
                                  Large-Scale Genomic Sequences$^1$  . . . 325--338
                Zheng Zhang and   
         William R. Pearson and   
                    Webb Miller   Aligning a DNA Sequence with a Protein
                                  Sequence . . . . . . . . . . . . . . . . 339--349
                    Gary Benson   Sequence Alignment with Tandem
                                  Duplication  . . . . . . . . . . . . . . 351--367
              Eric L. Anson and   
                Eugene W. Myers   ReAligner: a Program for Refining DNA
                                  Sequence Multi-Alignments  . . . . . . . 369--383
             Tetsuo Shibuya and   
                   Hiroshi Imai   New Flexible Approaches for Multiple
                                  Sequence Alignment . . . . . . . . . . . 385--413
          Benno Schwikowski and   
                 Martin Vingron   The Deferred Path Heuristic for the
                                  Generalized Tree Alignment Problem . . . 415--431

Journal of Computational Biology
Volume 4, Number 4, January, 1997

            Thomas Christof and   
        Michael Jünger and   
            John Kececioglu and   
               Petra Mutzel and   
                Gerhard Reinelt   A Branch-and-Cut Approach to Physical
                                  Mapping of Chromosomes by Unique
                                  End-Probes . . . . . . . . . . . . . . . 433--447
                Mudita Jain and   
                Eugene W. Myers   Algorithms for Computing and Integrating
                                  Physical Maps Using Unique Probes  . . . 449--466
                Fengzhu Sun and   
                Gary Benson and   
               Norm Arnheim and   
               Michael Waterman   Pooling Strategies for Establishing
                                  Physical Genome Maps Using FISH  . . . . 467--486
               Donna Slonim and   
            Leonid Kruglyak and   
              Lincoln Stein and   
                    Eric Lander   Building Human Genome Maps with
                                  Radiation Hybrids  . . . . . . . . . . . 487--504
                    S. C. Heath   Markov Chain Monte Carlo Methods for
                                  Radiation Hybrid Mapping . . . . . . . . 505--515
               Amir Ben-Dor and   
                     Benny Chor   On Constructing Radiation Hybrid Maps    517--533
                  Shili Lin and   
               Terence P. Speed   An Algorithm for Haplotype Analysis  . . 535--546
                Jaime Cohen and   
                  Martin Farach   Numerical Taxonomy on Data: Experimental
                                  Results  . . . . . . . . . . . . . . . . 547--558
              David Sankoff and   
           Vincent Ferretti and   
               Joseph H. Nadeau   Conserved Segment Identification . . . . 559--565


Journal of Computational Biology
Volume 5, Number 1, January, 1998

            Leonid Kruglyak and   
                 Eric S. Lander   Faster Multipoint Linkage Analysis Using
                                  Fourier Transforms . . . . . . . . . . . 1--7
            S. Rao Kosaraju and   
 Alejandro A. Schäffer and   
            Leslie G. Biesecker   Approximation Algorithms for a Genetic
                                  Diagnostics Problem  . . . . . . . . . . 9--26
              Bonnie Berger and   
                   Tom Leighton   Protein Folding in the
                                  Hydrophobic--Hydrophilic (\em HP) Model
                                  is NP-Complete . . . . . . . . . . . . . 27--40
           Vincent Escalier and   
        Joél Pothier and   
              Henri Soldano and   
                    Alain Viari   Pairwise and Multiple Identification of
                                  Three-Dimensional Common Substructures
                                  in Proteins  . . . . . . . . . . . . . . 41--56
              I. Saira Mian and   
           Michael J. Moser and   
          William R. Holley and   
               Aloke Chatterjee   Statistical Modelling and Phylogenetic
                                  Analysis of a Deaminase Domain . . . . . 57--72
               Daniel E. Bentil   Modelling and Simulation of Motility in
                                  Actomyosin Systems . . . . . . . . . . . 73--86
                Gary Benson and   
                    Xiaoping Su   On the Distribution of $K$-tuple Matches
                                  for Sequence Homology: a Constant Time
                                  Exact Calculation of the Variance  . . . 87--100
           Andrew F. Siegel and   
             Jared C. Roach and   
               Ger Van Den Engh   Expectation and Variance of True and
                                  False Fragment Matches in DNA
                                  Restriction Mapping  . . . . . . . . . . 101--111
           Andrew F. Siegel and   
             Jared C. Roach and   
            Charles Magness and   
                  Ed Thayer and   
               Ger Van Den Engh   Optimization of Restriction Fragment DNA
                                  Mapping  . . . . . . . . . . . . . . . . 113--126
               Lusheng Wang and   
                   Dan Gusfield   Constructing Additive Trees When the
                                  Error Is Small . . . . . . . . . . . . . 127--133
              O. Eulenstein and   
                  B. Mirkin and   
                     M. Vingron   Duplication-Based Measures of Difference
                                  Between Gene and Species Trees . . . . . 135--148
         Arndt Von Haeseler and   
         Michael Schöniger   Evolution of DNA or Amino Acid Sequences
                                  with Dependent Sites . . . . . . . . . . 149--163
                Semyon Kruglyak   Multistage Sequencing by Hybridization   165--171

Journal of Computational Biology
Volume 5, Number 2, January, 1998

         Alberto Apostolico and   
             Raffaele Giancarlo   Sequence Alignment in Molecular Biology  173--196
                Zheng Zhang and   
               Piotr Berman and   
                    Webb Miller   Alignments Without Low-Scoring Regions   197--210
          Timothy L. Bailey and   
               Michael Gribskov   Methods and Statistics for Combining
                                  Motif Match Scores . . . . . . . . . . . 211--221
             Gesine Reinert and   
                 Sophie Schbath   Compound Poisson and Poisson Process
                                  Approximations for Occurrences of
                                  Multiple Words in Markov Chains  . . . . 223--253
             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   A Surface-Based Approach to DNA
                                  Computation  . . . . . . . . . . . . . . 255--267
                Qinghua Liu and   
          Anthony G. Frutos and   
            Andrew J. Thiel and   
             Robert M. Corn and   
                 Lloyd M. Smith   DNA Computing on Surfaces: Encoding
                                  Information at the Single Base Level . . 269--278
               Alvis Brazma and   
              Inge Jonassen and   
           Ingvar Eidhammer and   
                  David Gilbert   Approaches to the Automatic Discovery of
                                  Patterns in Biosequences . . . . . . . . 279--305
            Michael T. Laub and   
               Douglas W. Smith   Finding Intron/Exon Splice Junctions
                                  Using INFO, INterruption Finder and
                                  Organizer  . . . . . . . . . . . . . . . 307--321
                Sharon Browning   Relationship Information Contained in
                                  Gamete Identity by Descent Data  . . . . 323--334
            Teresa M. Przytycka   Transforming Rooted Agreement into
                                  Unrooted Agreement . . . . . . . . . . . 335--349
          Nora Benhabil\`es and   
              Xavier Gallet and   
    Annick Thomas-Soumarmon and   
                Robert Brasseur   A Descriptive Analysis of Populations of
                                  Three-Dimensional Structures Calculated
                                  from Primary Sequences of Proteins by
                                  OSIRIS . . . . . . . . . . . . . . . . . 351--366

Journal of Computational Biology
Volume 5, Number 3, January, 1998

               Pavel A. Pevzner   Preface  . . . . . . . . . . . . . . . . 367--367
        Azat Ya Badretdinov and   
          Alexei V. Finkelstein   How Homologs Can Help to Predict Protein
                                  Folds Even Though They Cannot Be
                                  Predicted for Individual Sequences . . . 369--376
               Amir Ben-Dor and   
                 Benny Chor and   
                  Dan Graur and   
                  Ron Ophir and   
                     Dan Pelleg   Constructing Phylogenies from Quartets:
                                  Elucidation of Eutherian Superordinal
                                  Relationships  . . . . . . . . . . . . . 377--390
                Maria Bonet and   
                 Mike Steel and   
               Tandy Warnow and   
                  Shibu Yooseph   Better Methods for Solving Parsimony and
                                  Compatibility  . . . . . . . . . . . . . 391--407
             Cheng Che Chen and   
       Jas Winder Pal Singh and   
                 Russ B. Altman   Hierarchical Organization of Molecular
                                  Structure Computations . . . . . . . . . 409--422
        Pierluigi Crescenzi and   
            Deborah Goldman and   
     Christos Papadimitriou and   
         Antonio Piccolboni and   
             Mihalis Yannakakis   On the Complexity of Protein Folding . . 423--465
             Israel Gelfand and   
           Alexander Kister and   
         Casimir Kulikowski and   
                Ognyan Stoyanov   Algorithmic Determination of Core
                                  Positions in the $ V_L $ and $ V_H $
                                  Domains of Immunoglobulin Molecules  . . 467--477
           William Noble Grundy   Homology Detection via Family Pairwise
                                  Search . . . . . . . . . . . . . . . . . 479--491
                 Ian Holmes and   
                 Richard Durbin   Dynamic Programming Alignment Accuracy   493--504
                 Jae K. Lee and   
      Vlado Dan\vcík and   
            Michael S. Waterman   Estimation for Restriction Sites
                                  Observed by Optical Mapping Using
                                  Reversible-Jump Markov Chain Monte Carlo 505--515
          Hans-Peter Lenhof and   
               Knut Reinert and   
                 Martin Vingron   A Polyhedral Approach to RNA Sequence
                                  Structure Alignment  . . . . . . . . . . 517--530
              Boris A. Reva and   
              D. S. Rykunov and   
      Alexei V. Finkelstein and   
               Jeffrey Skolnick   Optimization of Protein Structure on
                                  Lattices Using a Self-Consistent Field
                                  Approach . . . . . . . . . . . . . . . . 531--538
         Marie-France Sagot and   
                Eugene W. Myers   Identifying Satellites and Periodic
                                  Repetitions in Biological Sequences  . . 539--553
              David Sankoff and   
             Mathieu Blanchette   Multiple Genome Rearrangement and
                                  Breakpoint Phylogeny . . . . . . . . . . 555--570
             Wynn L. Walker and   
          David S. Goodsell and   
               Elliot M. Landaw   An Analysis of a Class of DNA Sequence
                                  Reading Molecules  . . . . . . . . . . . 571--583
               Thomas D. Wu and   
         Scott C. Schmidler and   
              Trevor Hastie and   
             Douglas L. Brutlag   Regression Analysis of Multiple Protein
                                  Structures . . . . . . . . . . . . . . . 585--595
                    Ying Xu and   
                    Dong Xu and   
           Edward C. Uberbacher   An Efficient Computational Method for
                                  Globally Optimal Threading1  . . . . . . 597--614

Journal of Computational Biology
Volume 5, Number 4, January, 1998

                 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   A Sticker-Based Model for DNA
                                  Computation  . . . . . . . . . . . . . . 615--629
               Bilha Sandak and   
              Ruth Nussinov and   
                Haim J. Wolfson   A Method for Biomolecular Structural
                                  Recognition and Docking Allowing
                                  Conformational Flexibility . . . . . . . 631--654
             Wing Hung Wong and   
                    Yan Cui and   
                 Run Sheng Chen   Torsional Relaxation for Biopolymers . . 655--665
            Steven Salzberg and   
          Arthur L. Delcher and   
          Kenneth H. Fasman and   
                 John Henderson   A Decision Tree System for Finding Genes
                                  in DNA . . . . . . . . . . . . . . . . . 667--680
           Roderic Guigó   Assembling Genes from Predicted Exons in
                                  Linear Time with Dynamic Programming . . 681--702
               Ronna R. Mallios   Iterative Stepwise Discriminant
                                  Analysis: a Meta-Algorithm for Detecting
                                  Quantitative Sequence Motifs . . . . . . 703--711
            Steven N. Evans and   
                   Xiaowen Zhou   Constructing and Counting Phylogenetic
                                  Invariants . . . . . . . . . . . . . . . 713--724
                   Laxmi Parida   A Uniform Framework for Ordered
                                  Restriction Map Problems . . . . . . . . 725--739
                  Nicholas Tran   An Easy Case of Sorting by Reversals . . 741--746
      Takako Takai-Igarashi and   
               Yoko Nadaoka and   
            Tsuguchika Kaminuma   A Database for Cell Signaling Networks   747--754


Journal of Computational Biology
Volume 6, Number 1, January, 1999

              Bonnie Berger and   
            Gunnar W. Hoest and   
           James R. Paulson and   
                  Peter W. Shor   On the Structure of the Scaffolding Core
                                  of Bacteriophage T4  . . . . . . . . . . 1--12
               Ashwin Nayak and   
          Alistair Sinclair and   
                      Uri Zwick   Spatial Codes and the Hardness of String
                                  Folding Problems . . . . . . . . . . . . 13--36
             Richard Desper and   
                 Feng Jiang and   
        Olli-P. Kallioniemi and   
                Holger Moch and   
  Christos H. Papadimitriou and   
     Alejandro A. Schäffer   Inferring Tree Models for Oncogenesis
                                  from Comparative Genome Hybridization
                                  Data . . . . . . . . . . . . . . . . . . 37--51
         Leonard M. Adleman and   
       Paul W. K. Rothemund and   
                 Sam Roweis and   
                   Erik Winfree   On Applying Molecular Computation to the
                                  Data Encryption Standard . . . . . . . . 53--63
                 Sam Roweis and   
                   Erik Winfree   On the Reduction of Errors in DNA
                                  Computation  . . . . . . . . . . . . . . 65--75
                    Fengzhu Sun   Modeling DNA Shuffling . . . . . . . . . 77--90
               Richard Mott and   
                    Roger Tribe   Approximate Statistics of Gapped
                                  Alignments . . . . . . . . . . . . . . . 91--112
            J. B\la\.zewicz and   
             P. Formanowicz and   
                M. Kasprzak and   
           W. T. Markiewicz and   
                   J. W\ceglarz   DNA Sequencing With Positive and
                                  Negative Errors  . . . . . . . . . . . . 113--123
          David Loewenstern and   
              Peter N. Yianilos   Significantly Lower Entropy Estimates
                                  for Natural DNA Sequences  . . . . . . . 125--142

Journal of Computational Biology
Volume 6, Number 2, January, 1999

                 S. Istrail and   
                R. Schwartz and   
                        J. King   Lattice Simulations of Aggregation
                                  Funnels for Protein Folding  . . . . . . 143--162
                    Sun Kim and   
            Alberto Maria Segre   AMASS: a Structured Pattern Matching
                                  Approach to Shotgun Sequence Assembly    163--186
                 Dan Fasulo and   
                  Tao Jiang and   
            Richard M. Karp and   
       Reuben J. Settergren and   
                      Ed Thayer   An Algorithmic Approach to Multiple
                                  Complete Digest Mapping  . . . . . . . . 187--207
           Jason T. L. Wang and   
                Steve Rozen and   
           Bruce A. Shapiro and   
              Dennis Shasha and   
               Zhiyuan Wang and   
                   Maisheng Yin   New Techniques for DNA Sequence
                                  Classification . . . . . . . . . . . . . 209--218
               Thomas D. Wu and   
    Craig G. Nevill-Manning and   
             Douglas L. Brutlag   Minimal-Risk Scoring Matrices for
                                  Sequence Analysis  . . . . . . . . . . . 219--235
                 Guy Mayraz and   
                     Ron Shamir   Construction of Physical Maps from
                                  Oligonucleotide Fingerprints Data  . . . 237--252
                   Lihua Yu and   
                Temple F. Smith   Positional Statistical Significance in
                                  Sequence Alignment . . . . . . . . . . . 253--259
          Gary A. Churchill and   
                 Betty Lazareva   Bayesian Restoration of a Hidden Markov
                                  Chain with Applications to DNA
                                  Sequencing . . . . . . . . . . . . . . . 261--277

Journal of Computational Biology
Volume 6, Number 3--4, October, 1999

                  Sorin Istrail   Special RECOMB'99 Issue  . . . . . . . . 279--279
               Amir Ben-Dor and   
                 Ron Shamir and   
                  Zohar Yakhini   Clustering Gene Expression Patterns  . . 281--297
    Jadwiga R. Bie\'nkowska and   
      Robert G. Rogers, Jr. and   
                Temple F. Smith   Performance of Threading Scoring
                                  Functions Designed Using New
                                  Optimization Method  . . . . . . . . . . 299--311
               L. Paul Chew and   
           Dan Huttenlocher and   
                Klara Kedem and   
                  Jon Kleinberg   Fast Detection of Common Geometric
                                  Substructure in Proteins . . . . . . . . 313--325
      Vlado Dan\vcík and   
          Theresa A. Addona and   
            Karl R. Clauser and   
              James E. Vath and   
               Pavel A. Pevzner   \em De Novo Peptide Sequencing via
                                  Tandem Mass Spectrometry . . . . . . . . 327--342
         Christian V. Forst and   
                 Klaus Schulten   Evolution of Metabolisms: a New Method
                                  for the Comparison of Metabolic Pathways
                                  Using Genomics Information . . . . . . . 343--360
             Alan M. Frieze and   
        Franco P. Preparata and   
                      Eli Upfal   Optimal Reconstruction of a Sequence
                                  from its Probes  . . . . . . . . . . . . 361--368
            Daniel H. Huson and   
           Scott M. Nettles and   
                Tandy J. Warnow   Disk-Covering, a Fast-Converging Method
                                  for Phylogenetic Tree Reconstruction . . 369--386
               Jon M. Kleinberg   Efficient Algorithms for Protein
                                  Sequence Design and the Analysis of
                                  Certain Evolutionary Fitness Landscapes  387--404
             Richard H. Lathrop   An Anytime Local-to-Global Optimization
                                  Algorithm for Protein Threading in
                                  O(m$^2$ ñ$^2$ ) Space . . . . . . . . . . 405--418
               Lior Pachter and   
          Serafim Batzoglou and   
     Valentin I. Spitkovsky and   
                 Eric Banks and   
             Eric S. Lander and   
         Daniel J. Kleitman and   
                  Bonnie Berger   A Dictionary-Based Approach for Gene
                                  Annotation . . . . . . . . . . . . . . . 419--430
              David Sankoff and   
             Mathieu Blanchette   Phylogenetic Invariants for Genome
                                  Rearrangements . . . . . . . . . . . . . 431--445
                  Peter Willett   Dissimilarity-Based Algorithms for
                                  Selecting Structurally Diverse Sets of
                                  Compounds  . . . . . . . . . . . . . . . 447--457
                 John C. Wooley   Trends in Computational Biology: a
                                  Summary Based on a RECOMB Plenary
                                  Lecture, 1999  . . . . . . . . . . . . . 459--474


Journal of Computational Biology
Volume 7, Number 1--2, February, 2000

             Gesine Reinert and   
             Sophie Schbath and   
            Michael S. Waterman   Probabilistic and Statistical Properties
                                  of Words: An Overview  . . . . . . . . . 1--46
             Sophie Schbath and   
           Nathalie Bossard and   
            Simon Tavaré   The Effect of Nonhomogeneous Clone
                                  Length Distribution on the Progress of
                                  an STS Mapping Project . . . . . . . . . 47--57
               Vineet Bafna and   
        Sridhar Hannenhalli and   
                   Ken Rice and   
                    Lisa Vawter   Ligand-Receptor Pairing Via Tree
                                  Comparison . . . . . . . . . . . . . . . 59--70
         Alberto Apostolico and   
            Mary Ellen Bock and   
            Stefano Lonardi and   
                       Xuyan Xu   Efficient Detection of Unusual Words . . 71--94
             Tommi Jaakkola and   
              Mark Diekhans and   
                 David Haussler   A Discriminative Framework for Detecting
                                  Remote Protein Homologies  . . . . . . . 95--114
                Dirk Drasdo and   
                Terence Hwa and   
            Michael Lässig   Scaling Laws and Similarity Detection in
                                  Sequence Alignment with Gaps . . . . . . 115--141
                   Dai Wang and   
                 Cheng Zhao and   
                 Rong Cheng and   
                    Fengzhu Sun   Estimation of the Mutation Rate During
                                  Error-prone Polymerase Chain Reaction    143--158
     Gráinne McGuire and   
               Frank Wright and   
            Michael J. Prentice   A Bayesian Model for Detecting Past
                                  Recombination Events in DNA Multiple
                                  Alignments . . . . . . . . . . . . . . . 159--170
              Martin Fekete and   
            Ivo L. Hofacker and   
               Peter F. Stadler   Prediction of RNA Base Pairing
                                  Probabilities on Massively Parallel
                                  Computers  . . . . . . . . . . . . . . . 171--182
         Igor N. Berezovsky and   
         Natalia G. Esipova and   
           Vladimir G. Tumanyan   Hierarchy of Regions of Amino Acid
                                  Sequence with Respect to Their Role in
                                  the Protein Spatial Structure  . . . . . 183--192
                 Sophie Schbath   An Overview on the Distribution of Word
                                  Counts in Markov Chains  . . . . . . . . 193--201
                Zheng Zhang and   
             Scott Schwartz and   
               Lukas Wagner and   
                    Webb Miller   A Greedy Algorithm for Aligning DNA
                                  Sequences  . . . . . . . . . . . . . . . 203--214
             V. E. Ramensky and   
              V. Ju. Makeev and   
             M. A. Roytberg and   
                 V. G. Tumanyan   DNA Segmentation Through the Bayesian
                                  Approach . . . . . . . . . . . . . . . . 215--231
         Scott C. Schmidler and   
                 Jun S. Liu and   
             Douglas L. Brutlag   Bayesian Segmentation of Protein
                                  Secondary Structure  . . . . . . . . . . 233--248
   François Rodolphe and   
         Catherine Mathé   Translation Conditional Models for
                                  Protein Coding Sequences . . . . . . . . 249--260
           Gaston H. Gonnet and   
        Chantal Korostensky and   
                   Steve Benner   Evaluation Measures of Multiple Sequence
                                  Alignments . . . . . . . . . . . . . . . 261--276
            Vincent Moulton and   
              Michael Zuker and   
              Michael Steel and   
              Robin Pointon and   
                    David Penny   Metrics on RNA Secondary Structures  . . 277--292
               Piotr Berman and   
                Zheng Zhang and   
               Yuri I. Wolf and   
           Eugene V. Koonin and   
                    Webb Miller   Winnowing Sequences from a Database
                                  Search . . . . . . . . . . . . . . . . . 293--302
            Richard M. Karp and   
                     Ron Shamir   Algorithms for Optical Mapping . . . . . 303--316
           Edward C. Thayer and   
             Chris Bystroff and   
                    David Baker   Detection of Protein Coding Sequences
                                  Using a Mixture Model for Local Protein
                                  Amino Acid Sequence  . . . . . . . . . . 317--327

Journal of Computational Biology
Volume 7, Number 3--4, August, 2000

                     Ron Shamir   Preface: Special RECOMB 2000 Issue . . . 329--330
             Tatsuya Akutsu and   
              Satoru Miyano and   
                  Satoru Kuhara   Algorithms for Identifying Boolean
                                  Networks and Related Biological Networks
                                  Based on Matrix Multiplication and
                                  Fingerprint Function . . . . . . . . . . 331--343
             Laurent Marsan and   
             Marie-France Sagot   Algorithms for Extracting Structured
                                  Motifs Using a Suffix Tree with an
                                  Application to Promoter and Regulatory
                                  Site Consensus Identification  . . . . . 345--362
           Y. Zenmei Ohkubo and   
              Gordon M. Crippen   Potential Energy Function for Continuous
                                  State Models of Globular Proteins  . . . 363--379
         Alberto Apostolico and   
                  Gill Bejerano   Optimal Amnesic Probabilistic Automata
                                  or How to Learn and Classify Proteins in
                                  Linear Time and Space  . . . . . . . . . 381--393
              Steffen Heber and   
                 Jens Stoye and   
              Marcus Frohme and   
         Jörg Hoheisel and   
                 Martin Vingron   Contig Selection in Physical Mapping . . 395--408
      Rune B. Lyngsò and   
       Christian N. S. Pedersen   RNA Pseudoknot Prediction in
                                  Energy-Based Models  . . . . . . . . . . 409--427
                 Kevin Chen and   
              Dannie Durand and   
           Martin Farach-Colton   NOTUNG: a Program for Dating Gene
                                  Duplications and Optimizing Gene Family
                                  Trees  . . . . . . . . . . . . . . . . . 429--447
                    Ying Xu and   
                    Dong Xu and   
         Oakley H. Crawford and   
              J. Ralph Einstein   A Computational Method for
                                  NMR-Constrained Protein Threading  . . . 449--467
            Jon M. Sorenson and   
             Teresa Head-Gordon   Matching Simulation and Experiment: a
                                  New Simplified Model for Simulating
                                  Protein Folding  . . . . . . . . . . . . 469--481
             Alexander Zien and   
                Ralf Zimmer and   
                Thomas Lengauer   A Simple Iterative Approach to Parameter
                                  Optimization . . . . . . . . . . . . . . 483--501
               Amir Ben-Dor and   
               Richard Karp and   
          Benno Schwikowski and   
                  Zohar Yakhini   Universal DNA Tag Systems: a
                                  Combinatorial Design Scheme  . . . . . . 503--519
              David Sankoff and   
               David Bryant and   
    Mélanie Deneault and   
              B. Franz Lang and   
                Gertraud Burger   Early Eukaryote Evolution Based on
                                  Mitochondrial Gene Order Breakpoints . . 521--535
       Chris Bailey-Kellogg and   
                 Alik Widge and   
             John J. Kelley and   
         Marcelo J. Berardi and   
         John H. Bushweller and   
           Bruce Randall Donald   The NOESY Jigsaw: Automated Protein
                                  Secondary Structure and Main-Chain
                                  Assignment from Sparse, Unassigned NMR
                                  Data . . . . . . . . . . . . . . . . . . 537--558
               Amir Ben-Dor and   
             Laurakay Bruhn and   
               Nir Friedman and   
             Iftach Nachman and   
          Mich\`el Schummer and   
                  Zohar Yakhini   Tissue Classification with Gene
                                  Expression Profiles  . . . . . . . . . . 559--583
              Reece K. Hart and   
            Ajay K. Royyuru and   
        Gustavo Stolovitzky and   
                Andrea Califano   Systematic and Fully Automated
                                  Identification of Protein Sequence
                                  Patterns . . . . . . . . . . . . . . . . 585--600
               Nir Friedman and   
              Michal Linial and   
             Iftach Nachman and   
                     Dana Pe'er   Using Bayesian Networks to Analyze
                                  Expression Data  . . . . . . . . . . . . 601--620
        Franco P. Preparata and   
                      Eli Upfal   Sequencing-by-Hybridization at the
                                  Information-Theory Bound: an Optimal
                                  Algorithm  . . . . . . . . . . . . . . . 621--630
                      Anonymous   Abstracts from TIGR's Fourth Annual
                                  Conference on Computational Genomics
                                  November 16--19, 2000 Baltimore, MD  . . 631--651

Journal of Computational Biology
Volume 7, Number 5, October, 2000

              Martin Lermen and   
                   Knut Reinert   The Practical Use of the $ A* $
                                  Algorithm for Exact Multiple Sequence
                                  Alignment  . . . . . . . . . . . . . . . 655--671
            Ognyan Stoyanov and   
           Alexander Kister and   
             Israel Gelfand and   
         Casimir Kulikowski and   
                  Cyrus Chothia   Geometric Invariant Core for the $ C_L $
                                  and $C$$_{H 1}$ Domains of
                                  Immunoglobulin Molecules . . . . . . . . 673--684
           Ingvar Eidhammer and   
              Inge Jonassen and   
              William R. Taylor   Structure Comparison and Structure
                                  Patterns . . . . . . . . . . . . . . . . 685--716
            Simon E. Cawley and   
               Terence P. Speed   DNA Sequencing with Transposons  . . . . 717--729
        Vladimir Makarenkov and   
                  Bruno Leclerc   Comparison of Additive Trees Using
                                  Circular Orders  . . . . . . . . . . . . 731--744
            Richard M. Karp and   
                Itsik Pe'er and   
                     Ron Shamir   An Algorithm Combining Discrete and
                                  Continuous Methods for Optical Mapping   745--760

Journal of Computational Biology
Volume 7, Number 6, December, 2000

         Tobias Müller and   
                 Martin Vingron   Modeling Amino Acid Replacement  . . . . 761--776
           Pavel A. Pevzner and   
      Vlado Dan\vcík and   
                  Chris L. Tang   Mutation-Tolerant Protein Identification
                                  by Mass Spectrometry . . . . . . . . . . 777--787
             Richard Desper and   
                 Feng Jiang and   
        Olli-P. Kallioniemi and   
                Holger Moch and   
  Christos H. Papadimitriou and   
     Alejandro A. Schäffer   Distance-Based Reconstruction of Tree
                                  Models for Oncogenesis . . . . . . . . . 789--803
                Trey Ideker and   
          Vesteinn Thorsson and   
           Andrew F. Siegel and   
                  Leroy E. Hood   Testing for Differentially-Expressed
                                  Genes by Maximum-Likelihood Analysis of
                                  Microarray Data  . . . . . . . . . . . . 805--817
           M. Kathleen Kerr and   
            Mitchell Martin and   
              Gary A. Churchill   Analysis of Variance for Gene Expression
                                  Microarray Data  . . . . . . . . . . . . 819--837
            Dirk Faulhammer and   
          Richard J. Lipton and   
             Laura F. Landweber   Fidelity of Enzymatic Ligation for DNA
                                  Computing  . . . . . . . . . . . . . . . 839--848
                 I. S. Mian and   
                     I. Dubchak   Representing and Reasoning about Protein
                                  Families Using Generative and
                                  Discriminative Methods . . . . . . . . . 849--862


Journal of Computational Biology
Volume 8, Number 1, February, 2001

              Gad M. Landau and   
        Jeanette P. Schmidt and   
                     Dina Sokol   An Algorithm for Approximate Tandem
                                  Repeats  . . . . . . . . . . . . . . . . 1--18
       Chris Bailey-Kellogg and   
          John J. Kelleyiii and   
                Cliff Stein and   
           Bruce Randall Donald   Reducing Mass Degeneracy in SAR by MS by
                                  Stable Isotopic Labeling . . . . . . . . 19--36
               M. A. Newton and   
          C. M. Kendziorski and   
             C. S. Richmond and   
             F. R. Blattner and   
                     K. W. Tsui   On Differential Variability of
                                  Expression Ratios: Improving Statistical
                                  Inference about Gene Expression Changes
                                  from Microarray Data . . . . . . . . . . 37--52
             David Liben-Nowell   On the Structure of Syntenic Distance    53--67
               Lusheng Wang and   
             Kaizhong Zhang and   
                   Louxin Zhang   Perfect Phylogenetic Networks with
                                  Recombination  . . . . . . . . . . . . . 69--78
          Michael A. Charleston   Hitch-Hiking: a Parallel Heuristic
                                  Search Strategy, Applied to the
                                  Phylogeny Problem  . . . . . . . . . . . 79--91

Journal of Computational Biology
Volume 8, Number 2, April, 2001

        Nathaniel Leibowitz and   
              Ruth Nussinov and   
                Haim J. Wolfson   MUSTA --- a General, Efficient,
                                  Automated Method for Multiple Structure
                                  Alignment and Detection of Common
                                  Motifs: Application to Proteins  . . . . 93--121
           Peter B. Gilbert and   
       Vladimir A. Novitsky and   
           Monty A. Montano and   
                      Max Essex   An Efficient Test for Comparing Sequence
                                  Diversity between Two Populations  . . . 123--139
                   Earl Hubbell   Multiplex Sequencing by Hybridization    141--149
                     Jeff Elhai   Determination of Bias in the Relative
                                  Abundance of Oligonucleotides in DNA
                                  Sequences  . . . . . . . . . . . . . . . 151--175
               T. Gregory Dewey   A Sequence Alignment Algorithm with an
                                  Arbitrary Gap Penalty Function . . . . . 177--190
                Hongyu Zhao and   
                     Feng Liang   On Relationship Inference Using Gamete
                                  Identity by Descent Data . . . . . . . . 191--200

Journal of Computational Biology
Volume 8, Number 3, June, 2001

               Amit Marathe and   
             Anne E. Condon and   
                 Robert M. Corn   On Combinatorial DNA Word Design . . . . 201--219
                         Xun Gu   Mathematical Modeling for Functional
                                  Divergence after Gene Duplication  . . . 221--234
              Pierre Nicod\`eme   Fast Approximate Motif Statistics  . . . 235--248
                  Yi-Kuo Yu and   
                    Terence Hwa   Statistical Significance of
                                  Probabilistic Sequence Alignment and
                                  Related Local Hidden Markov Models . . . 249--282
                    Paul Horton   Tsukuba BB: a Branch and Bound Algorithm
                                  for Local Multiple Alignment of DNA and
                                  Protein Sequences  . . . . . . . . . . . 283--303
                   Dan Gusfield   Inference of Haplotypes from Samples of
                                  Diploid Populations: Complexity and
                                  Algorithms . . . . . . . . . . . . . . . 305--323
                  Ting Chen and   
              Ming-Yang Kao and   
              Matthew Tepel and   
                  John Rush and   
               George M. Church   A Dynamic Programming Approach to De
                                  Novo Peptide Sequencing via Tandem Mass
                                  Spectrometry . . . . . . . . . . . . . . 325--337
                David B. Searls   From Jabberwocky to Genome: Lewis
                                  Carroll and Computational Biology  . . . 339--348

Journal of Computational Biology
Volume 8, Number 4, September, 2001

      Stéphane Robin and   
                 Sophie Schbath   Numerical Comparison of Several
                                  Approximations of the Word Count
                                  Distribution in Random Sequences . . . . 349--359
                 A. Ben-Dor and   
                   I. Pe'er and   
                  R. Shamir and   
                      R. Sharan   On the Complexity of Positional
                                  Sequencing by Hybridization  . . . . . . 361--371
                 S. Mercier and   
                   J. J. Daudin   Exact Distribution for the Local Score
                                  of One i.i.d. Random Sequence  . . . . . 373--380
             C. Devauchelle and   
               A. Grossmann and   
           A. Hénaut and   
            M. Holschneider and   
                M. Monnerot and   
               J. L. Risler and   
            B. Torrésani   Rate Matrices for Analyzing Large
                                  Families of Protein Sequences  . . . . . 381--399
              Dirk Husmeier and   
                   Frank Wright   Detection of Recombination in DNA
                                  Multiple Alignments with Hidden Markov
                                  Models . . . . . . . . . . . . . . . . . 401--427
              Mattias Wahde and   
                     John Hertz   Modeling Genetic Regulatory Dynamics in
                                  Neural Development . . . . . . . . . . . 429--442
        Andrew B. Goryachev and   
       Pascale F. Macgregor and   
                Aled M. Edwards   Unfolding of Microarray Data . . . . . . 443--461

Journal of Computational Biology
Volume 8, Number 5, October, 2001

            Semyon Kruglyak and   
                     Haixu Tang   A New Estimator of Significance of
                                  Correlation in Time Series Data  . . . . 463--470
                  Kuang Lin and   
             Alex C. W. May and   
              William R. Taylor   Amino Acid Substitution Matrices from an
                                  Artificial Neural Network Model  . . . . 471--481
             David A. Bader and   
        Bernard M. E. Moret and   
                         Mi Yan   A Linear-Time Algorithm for Computing
                                  Inversion Distance between Signed
                                  Permutations with an Experimental Study  483--491
            S. H. Muggleton and   
               C. H. Bryant and   
              A. Srinivasan and   
               A. Whittaker and   
                    S. Topp and   
                    C. Rawlings   Are Grammatical Representations Useful
                                  for Learning from Biological Sequence
                                  Data? --- a Case Study . . . . . . . . . 493--521
          Glenn A. Williams and   
          Jonathan M. Dugan and   
                 Russ B. Altman   Constrained Global Optimization for
                                  Estimating Molecular Structure from
                                  Atomic Distances . . . . . . . . . . . . 523--547
             John D. Storey and   
                 David Siegmund   Approximate $P$-Values for Local
                                  Sequence Alignments: Numerical Studies   549--556

Journal of Computational Biology
Volume 8, Number 6, November, 2001

             David M. Rocke and   
                  Blythe Durbin   A Model for Measurement Error for Gene
                                  Expression Arrays  . . . . . . . . . . . 557--569
                  Ting Chen and   
             Jacob D. Jaffe and   
               George M. Church   Algorithms for Identifying Protein
                                  Cross-Links via Tandem Mass Spectrometry 571--583
         Joachim Theilhaber and   
            Steven Bushnell and   
             Amanda Jackson and   
                   Rainer Fuchs   Bayesian Estimation of Fold-Changes in
                                  the Analysis of Gene Expression: The
                                  PFOLD Algorithm  . . . . . . . . . . . . 585--614
                  Winfried Just   Computational Complexity of Multiple
                                  Sequence Alignment with SP-Score . . . . 615--623
       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   Assessing Gene Significance from cDNA
                                  Microarray Expression Data via Mixed
                                  Models . . . . . . . . . . . . . . . . . 625--637
          Keith A. Baggerly and   
           Kevin R. Coombes and   
            Kenneth R. Hess and   
           David N. Stivers and   
           Lynne V. Abruzzo and   
                      Wei Zhang   Identifying Differentially Expressed
                                  Genes in cDNA Microarray Experiments . . 639--659


Journal of Computational Biology
Volume 9, Number 1, January, 2002

             Rimli Sengupta and   
                   Martin Tompa   Quality Control in Manufacturing Oligo
                                  Arrays: a Combinatorial Design Approach  1--22
             S. Rajasekaran and   
                     X. Jin and   
                   J. L. Spouge   The Efficient Computation of
                                  Position-Specific Match Scores with the
                                  Fast Fourier Transform . . . . . . . . . 23--33
            Jon M. Sorenson and   
             Teresa Head-Gordon   Protein Engineering Study of Protein L
                                  by Simulation  . . . . . . . . . . . . . 35--54
         Charles Kooperberg and   
           Thomas G. Fazzio and   
          Jeffrey J. Delrow and   
               Toshio Tsukiyama   Improved Background Correction for
                                  Spotted DNA Microarrays  . . . . . . . . 55--66
                  Hidde de Jong   Modeling and Simulation of Genetic
                                  Regulatory Systems: a Literature Review  67--103
        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   Inference from Clustering with
                                  Application to Gene-Expression
                                  Microarrays  . . . . . . . . . . . . . . 105--126
              Seungchan Kim and   
        Edward R. Dougherty and   
             Junior Barrera and   
                Yidong Chen and   
         Michael L. Bittner and   
               Jeffrey M. Trent   Strong Feature Sets from Small Samples   127--146

Journal of Computational Biology
Volume 9, Number 2, April, 2002

                Thomas Lengauer   Preface: Special RECOMB 2001 Issue . . . 147--148
             Nancy M. Amato and   
                     Guang Song   Using Motion Planning to Study Protein
                                  Folding Pathways . . . . . . . . . . . . 149--168
              Yoseph Barash and   
                   Nir Friedman   Context-Specific Bayesian Clustering for
                                  Gene Expression Data . . . . . . . . . . 169--191
               Yonatan Bilu and   
                  Michal Linial   The Advantage of Functional Prediction
                                  Based on Clustering of Yeast Genes and
                                  Its Correlation with Non-Sequence Based
                                  Classifications  . . . . . . . . . . . . 193--210
         Mathieu Blanchette and   
          Benno Schwikowski and   
                   Martin Tompa   Algorithms for Phylogenetic Footprinting 211--223
              Jeremy Buhler and   
                   Martin Tompa   Finding Motifs Using Random Projections  225--242
                 Ralf Bundschuh   Rapid Significance Estimation in Local
                                  Sequence Alignment with Gaps . . . . . . 243--260
               Lenore Cowen and   
               Phil Bradley and   
              Matthew Menke and   
              Jonathan King and   
                  Bonnie Berger   Predicting the Beta-Helix Fold from
                                  Protein Sequence Data  . . . . . . . . . 261--276
      Miklós Csurös   Fast Recovery of Evolutionary Trees with
                                  Thousands of Nodes . . . . . . . . . . . 277--297
                 Alon Efrat and   
             Frank Hoffmann and   
              Klaus Kriegel and   
           Christof Schultz and   
                    Carola Wenk   Geometric Algorithms for the Analysis of
                                  $2$D-Electrophoresis Gels  . . . . . . . 299--315
            Vladimir Filkov and   
              Steven Skiena and   
                       Jizu Zhi   Analysis Techniques for Microarray
                                  Time-Series Data . . . . . . . . . . . . 317--330
               Nir Friedman and   
                Matan Ninio and   
                Itsik Pe'er and   
                      Tal Pupko   A Structural EM Algorithm for
                                  Phylogenetic Inference . . . . . . . . . 331--353
             Alan M. Frieze and   
   Bjarni V. Halldórsson   Optimal Sequencing by Hybridization in
                                  Rounds . . . . . . . . . . . . . . . . . 355--369
                  Tao Jiang and   
                 Guohui Lin and   
                     Bin Ma and   
                 Kaizhong Zhang   A General Edit Distance between RNA
                                  Structures . . . . . . . . . . . . . . . 371--388
               Lior Pachter and   
       Marina Alexandersson and   
                   Simon Cawley   Applications of Generalized Pair Hidden
                                  Markov Models to Alignment and Gene
                                  Finding Problems . . . . . . . . . . . . 389--399
              Paul Pavlidis and   
               Jason Weston and   
                Jinsong Cai and   
         William Stafford Noble   Learning Gene Functional Classifications
                                  from Multiple Data Types . . . . . . . . 401--411
                 Ron Shamir and   
                     Dekel Tsur   Large Scale Sequencing by Hybridization  413--428
             Mengxiang Tang and   
           Michael Waterman and   
                  Shibu Yooseph   Zinc Finger Gene Clusters and Tandem
                                  Gene Duplication . . . . . . . . . . . . 429--446
                 Gert Thijs and   
           Kathleen Marchal and   
              Magali Lescot and   
          Stephane Rombauts and   
               Bart De Moor and   
        Pierre Rouzé and   
                    Yves Moreau   A Gibbs Sampling Method to Detect
                                  Overrepresented Motifs in the Upstream
                                  Regions of Coexpressed Genes . . . . . . 447--464

Journal of Computational Biology
Volume 9, Number 3, June, 2002

            Natalia Berloff and   
              Markus Perola and   
                  Kenneth Lange   Spline Methods for the Comparison of
                                  Physical and Genetic Maps  . . . . . . . 465--475
                Shi-Yi Shen and   
                   Jun Yang and   
                   Adam Yao and   
                  Pei-Ing Hwang   Super Pairwise Alignment (SPA): an
                                  Efficient Approach to Global Alignment
                                  for Homologous Sequences . . . . . . . . 477--486
                     Jian Zhang   Analysis of Information Content for
                                  Biological Sequences . . . . . . . . . . 487--503
       Michael D. Radmacher and   
            Lisa M. McShane and   
                  Richard Simon   A Paradigm for Class Prediction Using
                                  Gene Expression Profiles . . . . . . . . 505--511
                Terry Clark and   
                Sanggyu Lee and   
           L. Ridgway Scott and   
                  San Ming Wang   Computational Analysis of Gene
                                  Identification with SAGE . . . . . . . . 513--526
             Myong-Hee Sung and   
              Yingdong Zhao and   
              Roland Martin and   
                  Richard Simon   T-Cell Epitope Prediction with
                                  Combinatorial Peptide Libraries  . . . . 527--539
                Markus E. Nebel   Combinatorial Properties of RNA
                                  Secondary Structures . . . . . . . . . . 541--573
          Timothy L. Bailey and   
               Michael Gribskov   Estimating and Evaluating the Statistics
                                  of Gapped Local-Alignment Scores . . . . 575--593
                      Anonymous   Correction . . . . . . . . . . . . . . . 594--595

Journal of Computational Biology
Volume 9, Number 4, August, 2002

              Ernst Althaus and   
          Oliver Kohlbacher and   
          Hans-Peter Lenhof and   
              Peter Müller   A Combinatorial Approach to Protein
                                  Docking with Flexible Side Chains  . . . 597--612
           Berrin Yanikoglu and   
                    Burak Erman   Minimum Energy Configurations of the
                                  $2$-Dimensional HP-Model of Proteins by
                                  Self-Organizing Networks . . . . . . . . 613--620
          Jorng-Tzong Horng and   
             Hsien-Da Huang and   
               Ming-Hui Jin and   
                Li-Cheng Wu and   
                  Shir-Ly Huang   The Repetitive Sequence Database and
                                  Mining Putative Regulatory Elements in
                                  Gene Promoter Regions  . . . . . . . . . 621--640
         Alberto Mercatanti and   
          Giuseppe Rainaldi and   
              Laura Mariani and   
          Roberto Marangoni and   
                  Lorenzo Citti   A Method for Prediction of Accessible
                                  Sites on an mRNA Sequence for Target
                                  Selection of Hammerhead Ribozymes  . . . 641--653
           Kevin R. Coombes and   
        W. Edward Highsmith and   
          Tammy A. Krogmann and   
          Keith A. Baggerly and   
           David N. Stivers and   
               Lynne V. Abruzzo   Identifying and Quantifying Sources of
                                  Variation in Microarray Data Using
                                  High-Density cDNA Membrane Arrays  . . . 655--669
        Philippe Broët and   
          Sylvia Richardson and   
       François Radvanyi   Bayesian Hierarchical Model for
                                  Identifying Changes in Gene Expression
                                  from Microarray Experiments  . . . . . . 671--683
                      Anonymous   Correction . . . . . . . . . . . . . . . 685--685

Journal of Computational Biology
Volume 9, Number 5, October, 2002

             Richard Desper and   
                Olivier Gascuel   Fast and Accurate Phylogeny
                                  Reconstruction Algorithms Based on the
                                  Minimum-Evolution Principle  . . . . . . 687--705
            Giri Narasimhan and   
               Changsong Bu and   
                   Yuan Gao and   
                Xuning Wang and   
                    Ning Xu and   
                   Kalai Mathee   Mining Protein Sequences for Motifs  . . 707--720
               James Aspnes and   
             Julia Hartling and   
              Ming-Yang Kao and   
               Junhyong Kim and   
                     Gauri Shah   A Combinatorial Toolbox for Protein
                                  Sequence Design and Landscape Analysis
                                  in the Grand Canonical Model . . . . . . 721--741
       João Meidanis and   
         Maria M. T. Walter and   
                    Zanoni Dias   A Lower Bound on the Reversal and
                                  Transposition Diameter . . . . . . . . . 743--745
               Rainer Spang and   
            Marc Rehmsmeier and   
                     Jens Stoye   A Novel Approach to Remote Homology
                                  Detection: Jumping Alignments  . . . . . 747--760

Journal of Computational Biology
Volume 9, Number 6, December, 2002

                   S. Robin and   
               J.-J. Daudin and   
                 H. Richard and   
                M.-F. Sagot and   
                     S. Schbath   Occurrence Probability of Structured
                                  Motifs in Random Sequences . . . . . . . 761--773
              Eleazar Eskin and   
     William Stafford Noble and   
                   Yoram Singer   Using Substitution Matrices to Estimate
                                  Probability Distributions for Biological
                                  Sequences  . . . . . . . . . . . . . . . 775--791
            Kajsa Ljungberg and   
           Sverker Holmgren and   
            Örjan Carlborg   Efficient Algorithms for Quantitative
                                  Trait Loci Mapping Problems  . . . . . . 793--804
             Thomas L. York and   
            Richard Durrett and   
                 Rasmus Nielsen   Bayesian Estimation of the Number of
                                  Inversions in the History of Two
                                  Chromosomes  . . . . . . . . . . . . . . 805--818
                 D. V. Raje and   
              H. J. Purohit and   
                    R. N. Singh   Distinguishing Features of 16S rDNA Gene
                                  for Five Dominating Bacterial Genus
                                  Observed in Bioremediation . . . . . . . 819--829
                    Didier Piau   Mutation--Replication Statistics of
                                  Polymerase Chain Reactions . . . . . . . 831--847
              Scott Doniger and   
             Thomas Hofmann and   
                     Joanne Yeh   Predicting CNS Permeability of Drug
                                  Molecules: Comparison of Neural Network
                                  and Support Vector Machine Algorithms    849--864


Journal of Computational Biology
Volume 10, Number 1, February, 2003

                 Bingwen Lu and   
                      Ting Chen   A Suboptimal Algorithm for \em De Novo
                                  Peptide Sequencing via Tandem Mass
                                  Spectrometry . . . . . . . . . . . . . . 1--12
           Russell Schwartz and   
Bjarni V. Halldórsson and   
               Vineet Bafna and   
            Andrew G. Clark and   
                  Sorin Istrail   Robustness of Inference of Haplotype
                                  Block Structure  . . . . . . . . . . . . 13--19
              Agatha H. Liu and   
                Andrea Califano   CASTOR: Clustering Algorithm for
                                  Sequence Taxonomical Organization and
                                  Relationships  . . . . . . . . . . . . . 21--45
                Xueliang Li and   
                   Zimao Li and   
                   Lusheng Wang   The Inverse Problems for Some
                                  Topological Indices in Combinatorial
                                  Chemistry  . . . . . . . . . . . . . . . 47--55
         Joseph S. Oliveira and   
            Colin G. Bailey and   
    Janet B. Jones-Oliveira and   
             David A. Dixon and   
               Dean W. Gull and   
               Mary L. Chandler   A Computational Model for the
                                  Identification of Biochemical Pathways
                                  in the Krebs Cycle . . . . . . . . . . . 57--82
        Sujay Chattopadhyay and   
          Jayprokas Chakrabarti   Temporal Changes in Phosphoglycerate
                                  Kinase Coding Sequences: a Quantitative
                                  Measure  . . . . . . . . . . . . . . . . 83--93
           Magnus Åstrand   Contrast Normalization of
                                  Oligonucleotide Arrays . . . . . . . . . 95--102

Journal of Computational Biology
Volume 10, Number 2, April, 2003

                 Gene Myers and   
                 Richard Durbin   A Table-Driven, Full-Sensitivity
                                  Similarity Search Algorithm  . . . . . . 103--117
            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   Estimating Dataset Size Requirements for
                                  Classifying DNA Microarray Data  . . . . 119--142
                Yinglei Lai and   
             Deepali Shinde and   
             Norman Arnheim and   
                    Fengzhu Sun   The Mutation Process of Microsatellites
                                  During the Polymerase Chain Reaction . . 143--155
                Yaning Yang and   
              Josephine Hoh and   
             Clemens Broger and   
                Martin Neeb and   
            Joanne Edington and   
         Klaus Lindpaintner and   
                       Jurg Ott   Statistical Methods for Analyzing
                                  Microarray Feature Data with
                                  Replications . . . . . . . . . . . . . . 157--169
                Honghui Wan and   
                  Lugang Li and   
             Scott Federhen and   
                John C. Wootton   Discovering Simple Regions in Biological
                                  Sequences Associated with Scoring
                                  Schemes  . . . . . . . . . . . . . . . . 171--185
              Eleazar Eskin and   
     William Stafford Noble and   
                   Yoram Singer   Protein Family Classification Using
                                  Sparse Markov Transducers  . . . . . . . 187--213
          Robert Penchovsky and   
            Jörg Ackermann   DNA Library Design for Molecular
                                  Computation  . . . . . . . . . . . . . . 215--229
                F. K. Hwang and   
                      Y. C. Liu   Error-Tolerant Pooling Designs with
                                  Inhibitors . . . . . . . . . . . . . . . 231--236

Journal of Computational Biology
Volume 10, Number 3--4, June, 2003

                Eugene W. Myers   Special RECOMB 2002 Issue  . . . . . . . 237--237
             Nancy M. Amato and   
                Ken A. Dill and   
                     Guang Song   Using Motion Planning to Map Protein
                                  Folding Landscapes and Analyze Folding
                                  Kinetics of Known Native Structures  . . 239--255
      Mehmet Serkan Apaydin and   
         Douglas L. Brutlag and   
            Carlos Guestrin and   
                  David Hsu and   
        Jean-Claude Latombe and   
                    Chris Varma   Stochastic Roadmap Simulation: an
                                  Efficient Representation and Algorithm
                                  for Analyzing Molecular Motion . . . . . 257--281
         Alberto Apostolico and   
            Mary Ellen Bock and   
                Stefano Lonardi   Monotony of Surprise and Large-Scale
                                  Quest for Unusual Words  . . . . . . . . 283--311
             Peter F. Arndt and   
       Christopher B. Burge and   
                    Terence Hwa   DNA Sequence Evolution with
                                  Neighbor-Dependent Mutation  . . . . . . 313--322
               Vineet Bafna and   
               Dan Gusfield and   
            Giuseppe Lancia and   
                  Shibu Yooseph   Haplotyping as Perfect Phylogeny: a
                                  Direct Approach  . . . . . . . . . . . . 323--340
             Ziv Bar-Joseph and   
            Georg K. Gerber and   
           David K. Gifford and   
          Tommi S. Jaakkola and   
                   Itamar Simon   Continuous Representations of
                                  Time-Series Gene Expression Data . . . . 341--356
   S\`everine Bérard and   
                    Eric Rivals   Comparison of Minisatellites . . . . . . 357--372
               Amir Ben-Dor and   
                 Benny Chor and   
               Richard Karp and   
                  Zohar Yakhini   Discovering Local Structure in Gene
                                  Expression Data: The Order-Preserving
                                  Submatrix Problem  . . . . . . . . . . . 373--384
               Amir Ben-Dor and   
            Richard M. Karp and   
          Benno Schwikowski and   
                     Ron Shamir   The Restriction Scaffold Problem . . . . 385--398
                  Jeremy Buhler   Provably Sensitive Indexing Strategies
                                  for Biosequence Similarity Search  . . . 399--417
                Barry Cohen and   
                  Steven Skiena   Natural Selection and Algorithmic Design
                                  of mRNA  . . . . . . . . . . . . . . . . 419--432
                Ron O. Dror and   
        Jonathan G. Murnick and   
          Nicola J. Rinaldi and   
      Voichita D. Marinescu and   
             Ryan M. Rifkin and   
               Richard A. Young   Bayesian Estimation of Transcript Levels
                                  Using a General Model of Array
                                  Measurement Noise  . . . . . . . . . . . 433--452
              Dannie Durand and   
                  David Sankoff   Tests for Gene Clustering  . . . . . . . 453--482
              Eran Halperin and   
              Shay Halperin and   
             Tzvika Hartman and   
                     Ron Shamir   Handling Long Targets and Errors in
                                  Sequencing by Hybridization  . . . . . . 483--497
            Samuel A. Heath and   
        Franco P. Preparata and   
                     Joel Young   Sequencing by Hybridization by
                                  Cooperating Direct and Reverse Spectra   499--508
                  Fumei Lam and   
       Marina Alexandersson and   
                   Lior Pachter   Picking Alignments from (Steiner) Trees  509--520
 Christopher James Langmead and   
             Anthony K. Yan and   
       C. Robertson McClung and   
           Bruce Randall Donald   Phase-Independent Rhythmic Analysis of
                                  Genome-Wide Expression Patterns  . . . . 521--536
                     Jia Li and   
                    Webb Miller   Significance of Interspecies Matches
                                  when Evolutionary Rate Varies  . . . . . 537--554
           Brendan M. Mumey and   
            Brian W. Bailey and   
         Bonnie Kirkpatrick and   
       Algirdas J. Jesaitis and   
               Thomas Angel and   
                Edward A. Dratz   A New Method for Mapping Discontinuous
                                  Antibody Epitopes to Reveal Structural
                                  Features of Proteins . . . . . . . . . . 555--567
                   Jurg Ott and   
                  Josephine Hoh   Set Association Analysis of SNP
                                  Case-Control and Microarray Data . . . . 569--574
                 Adam C. Siepel   An Algorithm to Enumerate Sorting
                                  Reversals for Signed Permutations  . . . 575--597
                  Saurabh Sinha   Discriminative Motifs  . . . . . . . . . 599--615
          Miguel L. Teodoro and   
    George N. Phillips, Jr. and   
               Lydia E. Kavraki   Understanding Protein Flexibility
                                  through Dimensionality Reduction . . . . 617--634
            Andy Wildenberg and   
              Steven Skiena and   
                  Pavel Sumazin   Deconvolving Sequence Variation in Mixed
                                  DNA Populations  . . . . . . . . . . . . 635--652
             Alexander Zien and   
              Juliane Fluck and   
                Ralf Zimmer and   
                Thomas Lengauer   Microarrays: How Many Do You Need? . . . 653--667

Journal of Computational Biology
Volume 10, Number 5, October, 2003

                Elchanan Mossel   On the Impossibility of Reconstructing
                                  Ancestral Data and Phylogenies . . . . . 669--676
                  Fan Chung and   
                 Linyuan Lu and   
           T. Gregory Dewey and   
                 David J. Galas   Duplication Models for Biological
                                  Networks . . . . . . . . . . . . . . . . 677--687
         George Michailidis and   
                  Kerby Shedden   The Application of Rule-Based Methods to
                                  Class Prediction Problems in Genomics    689--698
              Yonghong Wang and   
                  Hongyu Ou and   
                   Fengbiao Guo   Recognition of Translation Initiation
                                  Sites of Eukaryotic Genes Based on an EM
                                  Algorithm  . . . . . . . . . . . . . . . 699--708
                  Wei-Fu Lu and   
                   Wen-Lian Hsu   A Test for the Consecutive Ones Property
                                  on Noisy Data --- Application to
                                  Physical Mapping and Sequence Assembly   709--735
        Henrik Jönsson and   
              Bo Söderberg   An Approximate Maximum Likelihood
                                  Approach, Applied to Phylogenetic Trees  737--749
                  D. Faller and   
                 H. U. Voss and   
                  J. Timmer and   
                      U. Hobohm   Normalization of DNA-Microarray Data by
                                  Nonlinear Correlation Maximization . . . 751--762
         Antonio Piccolboni and   
                   Dan Gusfield   On the Complexity of Fundamental
                                  Computational Problems in Pedigree
                                  Analysis . . . . . . . . . . . . . . . . 763--773
           Lenwood S. Heath and   
           John Paul C. Vergara   Sorting by Short Swaps . . . . . . . . . 775--789
                 N. Pisanti and   
               R. Marangoni and   
               P. Ferragina and   
               A. Frangioni and   
                  A. Savona and   
               C. Pisanelli and   
                      F. Luccio   PaTre: a Method for Paralogy Trees
                                  Construction . . . . . . . . . . . . . . 791--802

Journal of Computational Biology
Volume 10, Number 6, December, 2003

                   Yu Zhang and   
            Michael S. Waterman   An Eulerian Path Approach to Global
                                  Multiple Alignment for DNA Sequences . . 803--819
              Hagit Shatkay and   
                  Ronen Feldman   Mining the Biomedical Literature in the
                                  Genomic Era: An Overview . . . . . . . . 821--855
                    Li Liao and   
         William Stafford Noble   Combining Pairwise Sequence Similarity
                                  and Support Vector Machines for
                                  Detecting Remote Protein Evolutionary
                                  and Structural Relationships . . . . . . 857--868
               G. A. Lunter and   
           I. Miklós and   
                 Y. S. Song and   
                        J. Hein   An Efficient Algorithm for Statistical
                                  Multiple Alignment on Arbitrary
                                  Phylogenetic Trees . . . . . . . . . . . 869--889
               M. Kathleen Kerr   Linear Models for Microarray Data
                                  Analysis: Hidden Similarities and
                                  Differences  . . . . . . . . . . . . . . 891--901
            Gonzalo Navarro and   
               Mathieu Raffinot   Fast and Simple Character Classes and
                                  Bounded Gaps Pattern Matching, with
                                  Applications to Protein Searching  . . . 903--923
             Ryan H. Lilien and   
                 Hany Farid and   
                Bruce R. Donald   Probabilistic Disease Classification of
                                  Expression-Dependent Proteomic Data from
                                  Mass Spectrometry of Human Serum . . . . 925--946
               Minghua Deng and   
                  Kui Zhang and   
               Shipra Mehta and   
                  Ting Chen and   
                    Fengzhu Sun   Prediction of Protein Function Using
                                  Protein--Protein Interaction Data  . . . 947--960
              Mark R. Segal and   
           Kam D. Dahlquist and   
               Bruce R. Conklin   Regression Approaches for Microarray
                                  Data Analysis  . . . . . . . . . . . . . 961--980
               Samuel Ieong and   
              Ming-Yang Kao and   
                Tak-Wah Lam and   
              Wing-Kin Sung and   
                   Siu-Ming Yiu   Predicting RNA Secondary Structures with
                                  Arbitrary Pseudoknots by Maximizing the
                                  Number of Stacking Pairs . . . . . . . . 981--995
         Shalini Veerassamy and   
               Andrew Smith and   
        Elisabeth R. M. Tillier   A Transition Probability Model for Amino
                                  Acid Substitutions from Blocks . . . . . 997--1010


Journal of Computational Biology
Volume 11, Number 1, January, 2004

               Haiyan Huang and   
           Ming-Chih J. Kao and   
             Xianghong Zhou and   
                 Jun S. Liu and   
                   Wing H. Wong   Determination of Local Statistical
                                  Significance of Patterns in Markov
                                  Sequences with Application to Promoter
                                  Element Identification . . . . . . . . . 1--14
         Alberto Apostolico and   
                   Laxmi Parida   Incremental Paradigms of Motif Discovery 15--25
            Alberto Caprara and   
                Robert Carr and   
              Sorin Istrail and   
            Giuseppe Lancia and   
                   Brian Walenz   1001 Optimal PDB Structure Alignments:
                                  Integer Programming Methods for Finding
                                  the Maximum Contact Map Overlap  . . . . 27--52
                 Andreas Wagner   Reconstructing Pathways in Large Genetic
                                  Networks from Genetic Perturbations  . . 53--60
             Peter A. Spiro and   
                  Natasa Macura   A Local Alignment Metric for
                                  Accelerating Biosequence Database Search 61--82
              Maxim Shatsky and   
              Ruth Nussinov and   
                Haim J. Wolfson   FlexProt: Alignment of Flexible Protein
                                  Structures Without a Predefinition of
                                  Hinge Regions  . . . . . . . . . . . . . 83--106
            Leo Wang-Kit Cheung   Use of Runs Statistics for Pattern
                                  Recognition in Genomic DNA Sequences . . 107--124
             Myong-Hee Sung and   
                  Richard Simon   Genomewide Conserved Epitope Profiles of
                                  HIV-1 Predicted by Biophysical
                                  Properties of MHC Binding Peptides . . . 125--145
                Xiaobo Zhou and   
              Xiaodong Wang and   
        Edward R. Dougherty and   
                Daniel Russ and   
                     Edward Suh   Gene Clustering Based on Clusterwide
                                  Mutual Information . . . . . . . . . . . 147--161
              R. W. Adamiak and   
               J. Blazewicz and   
             P. Formanowicz and   
                 Z. Gdaniec and   
                M. Kasprzak and   
                 M. Popenda and   
                   M. Szachniuk   An Algorithm for an Automatic NOE
                                  Pathways Analysis of $2$D NMR Spectra of
                                  RNA Duplexes . . . . . . . . . . . . . . 163--179
            Markus Wistrand and   
          Erik L. L. Sonnhammer   Transition Priors for Protein Hidden
                                  Markov Models: An Empirical Study
                                  towards Maximum Discrimination . . . . . 181--193
        Vladimir Makarenkov and   
                Pierre Legendre   From a Phylogenetic Tree to a
                                  Reticulated Network  . . . . . . . . . . 195--212

Journal of Computational Biology
Volume 11, Number 2--3, March, 2004

                Webb Miller and   
                 Martin Vingron   Special RECOMB 2003 Issue  . . . . . . . 213--213
                 Wentian Li and   
                Fengzhu Sun and   
                     Ivo Grosse   Extreme Value Distribution Based Gene
                                  Selection Criteria for Discriminant
                                  Microarray Data Analysis Using Logistic
                                  Regression . . . . . . . . . . . . . . . 215--226
        Balaji Krishnapuram and   
             Lawrence Carin and   
         Alexander J. Hartemink   Joint Classifier and Feature
                                  Optimization for Comprehensive Cancer
                                  Diagnosis Using Gene Expression Data . . 227--242
          Chen-Hsiang Yeang and   
                Trey Ideker and   
                 Tommi Jaakkola   Physical Network Models  . . . . . . . . 243--262
           Maayan Fishelson and   
                     Dan Geiger   Optimizing Exact Genetic Linkage
                                  Computations . . . . . . . . . . . . . . 263--275
 Christopher James Langmead and   
                Anthony Yan and   
                Ryan Lilien and   
               Lincong Wang and   
           Bruce Randall Donald   A Polynomial-Time Nuclear Vector
                                  Replacement Algorithm for Automated NMR
                                  Resonance Assignments  . . . . . . . . . 277--298
                 Itay Lotan and   
               Fabian Schwarzer   Approximation of Protein Structure for
                                  Fast Similarity Measures . . . . . . . . 299--317
             Manolis Kellis and   
             Nick Patterson and   
               Bruce Birren and   
              Bonnie Berger and   
                 Eric S. Lander   Methods in Comparative Genomics: Genome
                                  Correspondence, Gene Identification and
                                  Regulatory Motif Discovery . . . . . . . 319--355
                 Amos Tanay and   
                     Ron Shamir   Multilevel Modeling and Inference of
                                  Transcription Regulation . . . . . . . . 357--375
                   Gene Yeo and   
           Christopher B. Burge   Maximum Entropy Modeling of Short
                                  Sequence Motifs with Applications to RNA
                                  Splicing Signals . . . . . . . . . . . . 377--394
          Krishna M. Roskin and   
              Mark Diekhans and   
                 David Haussler   Score Functions for Determining Regional
                                  Conservation in Two-Species Local
                                  Alignments . . . . . . . . . . . . . . . 395--411
                Adam Siepel and   
                 David Haussler   Combining Phylogenetic and Hidden Markov
                                  Models in Biosequence Analysis . . . . . 413--428
            Andrew B. Kahng and   
           Ion I. M\uandoiu and   
           Pavel A. Pevzner and   
               Sherief Reda and   
        Alexander Z. Zelikovsky   Scalable Heuristics for Design of DNA
                                  Probe Arrays . . . . . . . . . . . . . . 429--447
                 Tatsuya Akutsu   Efficient Extraction of Mapping Rules of
                                  Atoms from Enzymatic Reaction Data . . . 449--462
               Minghua Deng and   
                  Ting Chen and   
                    Fengzhu Sun   An Integrated Probabilistic Model for
                                  Functional Prediction of Proteins  . . . 463--475
               Amir Ben-Dor and   
             Tzvika Hartman and   
            Richard M. Karp and   
          Benno Schwikowski and   
               Roded Sharan and   
                  Zohar Yakhini   Towards Optimally Multiplexed
                                  Applications of Universal Arrays . . . . 476--492
           Gideon Greenspan and   
                     Dan Geiger   Model-Based Inference of Haplotype Block
                                  Variation  . . . . . . . . . . . . . . . 493--504
                  Lei M. Li and   
              Jong Hyun Kim and   
            Michael S. Waterman   Haplotype Reconstruction from SNP
                                  Alignment  . . . . . . . . . . . . . . . 505--516

Journal of Computational Biology
Volume 11, Number 4, August, 2004

            Craig J. Benham and   
                   Chengpeng Bi   The Analysis of Stress-Induced Duplex
                                  Destabilization in Long Genomic DNA
                                  Sequences  . . . . . . . . . . . . . . . 519--543
             Kevin A. Janes and   
             Jason R. Kelly and   
             Suzanne Gaudet and   
             John G. Albeck and   
            Peter K. Sorger and   
       Douglas A. Lauffenburger   Cue-Signal-Response Analysis of
                                  TNF-Induced Apoptosis by Partial Least
                                  Squares Regression of Dynamic
                                  Multivariate Data  . . . . . . . . . . . 544--561
                Rongling Wu and   
              Chang-Xing Ma and   
                 George Casella   A Mixed Polyploid Model for Linkage
                                  Analysis in Outcrossing Tetraploids
                                  Using a Pseudo-Test Backcross Design . . 562--580
                Paul Helman and   
              Robert Veroff and   
             Susan R. Atlas and   
                 Cheryl Willman   A Bayesian Network Classification
                                  Methodology for Gene Expression Data . . 581--615
            Hilary S. Booth and   
         John H. Maindonald and   
            Susan R. Wilson and   
                 Jill E. Gready   An Efficient $Z$-Score Algorithm for
                                  Assessing Sequence Alignments  . . . . . 616--625
                   Dan Levy and   
             Mariel Vazquez and   
          Michael Cornforth and   
            Bradford Loucas and   
            Rainer K. Sachs and   
                 Javier Arsuaga   Comparing DNA Damage-Processing Pathways
                                  by Computer Analysis of Chromosome
                                  Painting Data  . . . . . . . . . . . . . 626--641
                   Jason Ku and   
            Xiao-Jiang Feng and   
                Herschel Rabitz   Closed-Loop Learning Control of
                                  Bio-Networks . . . . . . . . . . . . . . 642--659
Ciprian Doru Giurc\uarneanu and   
             Ioan T\uabu\cs and   
              Jaakko Astola and   
                Juha Ollila and   
                  Mauno Vihinen   Fast Iterative Gene Clustering Based on
                                  Information Theoretic Criteria for
                                  Selecting the Cluster Structure  . . . . 660--682
                 Lin Zhihua and   
                 Wu Yuzhang and   
                     Zhu Bo and   
                    Ni Bing and   
                        Wang Li   Toward the Quantitative Prediction of
                                  T-Cell Epitopes: QSAR Studies on
                                  Peptides Having Affinity with the Class
                                  I MHC Molecular HLA-A*0201 . . . . . . . 683--694
            T. L. Bergemann and   
                 R. J. Laws and   
                 F. Quiaoit and   
                     L. P. Zhao   A Statistically Driven Approach for
                                  Image Segmentation and Signal Extraction
                                  in cDNA Microarrays  . . . . . . . . . . 695--713
              Sue-Jane Wang and   
                  James J. Chen   Sample Size for Identifying
                                  Differentially Expressed Genes in
                                  Microarray Experiments . . . . . . . . . 714--726
                 N. Galtier and   
                  A. Jean-Marie   Markov-Modulated Markov Chains and the
                                  Covarion Process of Molecular Evolution  727--733
            Michael Roberts and   
              Brian R. Hunt and   
             James A. Yorke and   
         Randall A. Bolanos and   
              Arthur L. Delcher   A Preprocessor for Shotgun Assembly of
                                  Large Genomes  . . . . . . . . . . . . . 734--752
        Franco P. Preparata and   
                 John S. Oliver   DNA Sequencing by Hybridization Using
                                  Semi-Degenerate Bases  . . . . . . . . . 753--765
               Piotr Berman and   
               Paul Bertone and   
           Bhaskar Dasgupta and   
              Mark Gerstein and   
              Ming-Yang Kao and   
                 Michael Snyder   Fast Optimal Genome Tiling with
                                  Applications to Microarray Design and
                                  Homology Search  . . . . . . . . . . . . 766--785

Journal of Computational Biology
Volume 11, Number 5, October, 2004

                 Yuting Jia and   
           T. Gregory Dewey and   
         Ilya N. Shindyalov and   
               Philip E. Bourne   A New Scoring Function and Associated
                                  Statistical Significance for Structure
                                  Alignment by CE  . . . . . . . . . . . . 787--799
              Hagit Shatkay and   
               Jason Miller and   
              Clark Mobarry and   
           Michael Flanigan and   
              Shibu Yooseph and   
                 Granger Sutton   ThurGood: Evaluating
                                  Assembly-to-Assembly Mapping . . . . . . 800--811
         Joseph S. Oliveira and   
    Janet B. Jones-Oliveira and   
             David A. Dixon and   
            Colin G. Bailey and   
                   Dean W. Gull   Hyperdigraph-Theoretic Analysis of the
                                  EGFR Signaling Network: Initial Steps
                                  Leading to GTP:Ras Complex Formation . . 812--842
              Andreas Heger and   
              Michael Lappe and   
                     Liisa Holm   Accurate Detection of Very Sparse
                                  Sequence Motifs  . . . . . . . . . . . . 843--857
               Vineet Bafna and   
               Dan Gusfield and   
        Sridhar Hannenhalli and   
                  Shibu Yooseph   A Note on Efficient Computation of
                                  Haplotypes via Perfect Phylogeny . . . . 858--866
              Gill Bejerano and   
               Nir Friedman and   
                 Naftali Tishby   Efficient Exact $p$-Value Computation
                                  for Small Sample, Sparse, and Surprising
                                  Categorical Data . . . . . . . . . . . . 867--886
            Andres Figueroa and   
             James Borneman and   
                      Tao Jiang   Clustering Binary Fingerprint Vectors
                                  with Missing Values for DNA Array Data
                                  Analysis . . . . . . . . . . . . . . . . 887--901
                 Itay Lotan and   
           Fabian Schwarzer and   
               Dan Halperin and   
            Jean-Claude Latombe   Algorithm and Data Structures for
                                  Efficient Energy Maintenance during
                                  Monte Carlo Simulation of Proteins . . . 902--932
                  Can Alkan and   
            Evan E. Eichler and   
          Jeffrey A. Bailey and   
         S. Cenk \cSahinalp and   
           Eray Tüzün   The Role of Unequal Crossover in
                                  Alpha-Satellite DNA Evolution: a
                                  Computational Analysis . . . . . . . . . 933--944
              Kaleigh Smith and   
                   Mike Hallett   Towards Quality Control for DNA
                                  Microarrays  . . . . . . . . . . . . . . 945--970
                  S. D. Bay and   
                L. Chrisman and   
               A. Pohorille and   
                     J. Shrager   Temporal Aggregation Bias and Inference
                                  of Causal Regulatory Networks  . . . . . 971--985
                 Jieping Ye and   
                  Ravi Janardan   Approximate Multiple Protein Structure
                                  Alignment Using the Sum-of-Pairs
                                  Distance . . . . . . . . . . . . . . . . 986--1000
Miklós Csürös and   
       Aleksandar Milosavljevic   Pooled Genomic Indexing (PGI): Analysis
                                  and Design of Experiments  . . . . . . . 1001--1021

Journal of Computational Biology
Volume 11, Number 6, December, 2004

                        G. Nuel   LD-SPatt: Large Deviations Statistics
                                  for Patterns on Markov Chains  . . . . . 1023--1033
              Irit Gat-Viks and   
                 Amos Tanay and   
                     Ron Shamir   Modeling and Analysis of Heterogeneous
                                  Regulation in Biological Networks  . . . 1034--1049
               Revital Eres and   
              Gad M. Landau and   
                   Laxmi Parida   Permutation Pattern Discovery in
                                  Biosequences . . . . . . . . . . . . . . 1050--1060
               Matteo Comin and   
          Concettina Guerra and   
               Giuseppe Zanotti   PROuST: a Comparison Method of
                                  Three-Dimensional Structures of Proteins
                                  Using Indexing Techniques  . . . . . . . 1061--1072
           C. Bhattacharyya and   
                L. R. Grate and   
               M. I. Jordan and   
               L. El Ghaoui and   
                     I. S. Mian   Robust Sparse Hyperplane Classifiers:
                                  Application to Uncertain Molecular
                                  Profiling Data . . . . . . . . . . . . . 1073--1089
              P. Chiappetta and   
              M. C. Roubaud and   
            B. Torrésani   Blind Source Separation and the Analysis
                                  of Microarray Data . . . . . . . . . . . 1090--1109
          Sebastian Böcker   Sequencing from Compomers: Using Mass
                                  Spectrometry for DNA \em de novo
                                  Sequencing of 200+ nt  . . . . . . . . . 1110--1134
        Mathäus Dejori and   
                 Martin Stetter   Identifying Interventional and
                                  Pathogenic Mechanisms by Generative
                                  Inverse Modeling of Gene Expression
                                  Profiles . . . . . . . . . . . . . . . . 1135--1148
            Ahmet Palazoglu and   
              Attila Gursoy and   
                Yaman Arkun and   
                    Burak Erman   Folding Dynamics of Proteins from
                                  Denatured to Native State: Principal
                                  Component Analysis . . . . . . . . . . . 1149--1168
                   Danny Barash   Spectral Decomposition for the Search
                                  and Analysis of RNA Secondary Structure  1169--1174
                Nanxiang Ge and   
             Charles B. Epstein   An Empirical Bayesian Significance Test
                                  of cDNA Library Data . . . . . . . . . . 1175--1188
                Darrell Conklin   Recognition of the Helical Cytokine Fold 1189--1200


Journal of Computational Biology
Volume 12, Number 1, February, 2005

               Andrei Rodin and   
      Thomas H. Mosley, Jr. and   
            Andrew G. Clark and   
            Charles F. Sing and   
                Eric Boerwinkle   Mining Genetic Epidemiology Data with
                                  Bayesian Networks Application to \em
                                  APOE Gene Variation and Plasma Lipid
                                  Levels . . . . . . . . . . . . . . . . . 1--11
                 Golan Yona and   
                    Klara Kedem   The URMS-RMS Hybrid Algorithm for Fast
                                  and Sensitive Local Protein Structure
                                  Alignment  . . . . . . . . . . . . . . . 12--32
Elodie Nédélec and   
             Thomas Moncion and   
          Elisabeth Gassiat and   
              Bruno Bossard and   
Guillemette Duchateau-Nguyen and   
               Alain Denise and   
                 Michel Termier   A Pairwise Alignment Algorithm Which
                                  Favors Clusters of Blocks  . . . . . . . 33--47
            Jason W. Zwolak and   
              John J. Tyson and   
                Layne T. Watson   Parameter Estimation for a Mathematical
                                  Model of the Cell Cycle in Frog Eggs . . 48--63
        Konstantinos Blekas and   
      Dimitrios I. Fotiadis and   
                Aristidis Likas   Motif-Based Protein Sequence
                                  Classification Using Neural Networks . . 64--82
                       P. Clote   An Efficient Algorithm to Compute the
                                  Landscape of Locally Optimal RNA
                                  Secondary Structures with Respect to the
                                  Nussinov--Jacobson Energy Model  . . . . 83--101
              Ying Chih Lin and   
               Chin Lung Lu and   
             Hwan-You Chang and   
                  Chuan Yi Tang   An Efficient Algorithm for Sorting by
                                  Block-Interchanges and Its Application
                                  to the Evolution of Vibrio Species . . . 102--112

Journal of Computational Biology
Volume 12, Number 2, March, 2005

      Joël R. Pradines and   
             Victor Farutin and   
               Steve Rowley and   
          Vlado Dan\vcík   Analyzing Protein Lists with Large
                                  Networks: Edge-Count Probabilities in
                                  Random Graphs with Given Expected
                                  Degrees  . . . . . . . . . . . . . . . . 113--128
             Zhi-Zhong Chen and   
                 Guohui Lin and   
                Romeo Rizzi and   
                Jianjun Wen and   
                    Dong Xu and   
                    Ying Xu and   
                      Tao Jiang   More Reliable Protein NMR Peak
                                  Assignment via Improved $2$-Interval
                                  Scheduling . . . . . . . . . . . . . . . 129--146
                Yun S. Song and   
                     Jotun Hein   Constructing Minimal Ancestral
                                  Recombination Graphs . . . . . . . . . . 147--169
                  Lei M. Li and   
           Henry Horng-Shing Lu   Explore Biological Pathways from Noisy
                                  Array Data by Directed Acyclic Boolean
                                  Networks . . . . . . . . . . . . . . . . 170--185
              Asger Hobolth and   
              Jens Ledet Jensen   Applications of Hidden Markov Models for
                                  Characterization of Homologous DNA
                                  Sequences with a Common Gene . . . . . . 186--203
            Bernd Sturmfels and   
                 Seth Sullivant   Toric Ideals of Phylogenetic Invariants  204--228
                  Biao Xing and   
           Mark J. van der Laan   A Statistical Method for Constructing
                                  Transcriptional Regulatory Networks
                                  Using Gene Expression and Sequence Data  229--246
                  Yuval Nov and   
               Lawrence M. Wein   Modeling and Analysis of Protein Design
                                  under Resource Constraints . . . . . . . 247--282

Journal of Computational Biology
Volume 12, Number 3, April, 2005

               Michael C. Wendl   Probabilistic Assessment of Clone
                                  Overlaps in DNA Fingerprint Mapping via
                                  a Priori Models  . . . . . . . . . . . . 283--297
                 Yuting Jia and   
               T. Gregory Dewey   A Random Polymer Model of the
                                  Statistical Significance of Structure
                                  Alignment  . . . . . . . . . . . . . . . 298--313
             Libi Hertzberg and   
                     Or Zuk and   
                   Gad Getz and   
                   Eytan Domany   Finding Motifs in Promoter Regions . . . 314--330
            Ming-Ying Leung and   
              Kwok Pui Choi and   
                  Aihua Xia and   
               Louis H. Y. Chen   Nonrandom Clusters of Palindromes in
                                  Herpesvirus Genomes  . . . . . . . . . . 331--354
             Michael Wagner and   
            Rafa\l Adamczak and   
            Aleksey Porollo and   
               Jaros\law Meller   Linear Regression Models for Solvent
                                  Accessibility Prediction in Proteins . . 355--369
                    Lang Li and   
                Huidong Shi and   
     Constantin Yiannoutsos and   
         Tim Hui-Ming Huang and   
              Kenneth P. Nephew   Epigenetic Hypothesis Tests for
                                  Methylation and Acetylation in a Triple
                                  Microarray System  . . . . . . . . . . . 370--390

Journal of Computational Biology
Volume 12, Number 4, May, 2005

                Dabao Zhang and   
            Martin T. Wells and   
         Christine D. Smart and   
                 William E. Fry   Bayesian Normalization and
                                  Identification for Differential Gene
                                  Expression Data  . . . . . . . . . . . . 391--406
                Ross A. Lippert   Space-Efficient Whole Genome Comparisons
                                  with Burrows--Wheeler Transforms . . . . 407--415
                      Uri Keich   sFFT: a Faster Accurate Computation of
                                  the $p$-Value of the Entropy Score . . . 416--430
              Chaim Linhart and   
                     Ron Shamir   The Degenerate Primer Design Problem:
                                  Theory and Applications  . . . . . . . . 431--456
            Bernd Sturmfels and   
                 Seth Sullivant   Toric Ideals of Phylogenetic Invariants  457--481
                Stan Pounds and   
                    Cheng Cheng   Statistical Development and Evaluation
                                  of Microarray Gene Expression Data
                                  Filters  . . . . . . . . . . . . . . . . 482--495

Journal of Computational Biology
Volume 12, Number 5, June, 2005

                 Ian M. Dew and   
               Brian Walenz and   
                 Granger Sutton   A Tool for Analyzing Mate Pairs in
                                  Assemblies (TAMPA) . . . . . . . . . . . 497--513
               Roded Sharan and   
                 Jens Gramm and   
              Zohar Yakhini and   
                   Amir Ben-Dor   Multiplexing Schemes for Generic SNP
                                  Genotyping Assays  . . . . . . . . . . . 514--533
              Daniel Berrar and   
             Brian Sturgeon and   
               Ian Bradbury and   
          C. Stephen Downes and   
                Werner Dubitzky   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  534--544
             Manuel Dehnert and   
            Rainer Plaumann and   
             Werner E. Helm and   
             Marc-Th. Hütt   Genome Phylogeny Based on Short-Range
                                  Correlations in DNA Sequences  . . . . . 545--553
        Martijn J. Schuemie and   
                Jan A. Kors and   
                    Barend Mons   Word Sense Disambiguation in the
                                  Biomedical Domain: An Overview . . . . . 554--565

Journal of Computational Biology
Volume 12, Number 6, July, 2005

                   Dan Gusfield   Preface: Special RECOMB 2004 Issue . . . 567--568
       Chris Bailey-Kellogg and   
           Sheetal Chainraj and   
              Gopal Pandurangan   A Random Graph Approach to NMR
                                  Sequential Assignment  . . . . . . . . . 569--583
          Niko Beerenwinkel and   
Jörg Rahnenführer and   
         Martin Däumer and   
            Daniel Hoffmann and   
                Rolf Kaiser and   
             Joachim Selbig and   
                Thomas Lengauer   Learning Multiple Evolutionary Pathways
                                  from Cross-Sectional Data  . . . . . . . 584--598
           Sourav Chatterji and   
                   Lior Pachter   Large Multiple Organism Gene Finding by
                                  Collapsed Gibbs Sampling . . . . . . . . 599--608
             Michael A. Erdmann   Protein Similarity from Knot Theory:
                                  Geometric Convolution and Line Weavings  609--637
                     Xin He and   
          Michael H. Goldwasser   Identifying Conserved Gene Clusters in
                                  the Presence of Homology Families  . . . 638--656
                   Jun Huan and   
       Deepak Bandyopadhyay and   
                   Wei Wang and   
              Jack Snoeyink and   
                  Jan Prins and   
              Alexander Tropsha   Comparing Graph Representations of
                                  Protein Structure for Mining
                                  Family-Specific Residue-Based Packing
                                  Motifs . . . . . . . . . . . . . . . . . 657--671
             Sabrina Ledent and   
          Stéphane Robin   Checking Homogeneity of Motifs'
                                  Distribution in Heterogeneous Sequences  672--685
          Henry C. M. Leung and   
         Francis Y. L. Chin and   
                  S. M. Yiu and   
             Roni Rosenfeld and   
                    W. W. Tsang   Finding Motifs with Insufficient Number
                                  of Strong Binding Sites  . . . . . . . . 686--701
                 Haifeng Li and   
                      Tao Jiang   A Class of Edit Kernels for SVMs to
                                  Predict Translation Initiation Sites in
                                  Eukaryotic mRNAs . . . . . . . . . . . . 702--718
                    Jing Li and   
                      Tao Jiang   Computing the Minimum Recombinant
                                  Haplotype Configuration from Incomplete
                                  Genotype Data on a Pedigree by Integer
                                  Linear Programming . . . . . . . . . . . 719--739
             Ryan H. Lilien and   
           Brian W. Stevens and   
            Amy C. Anderson and   
                Bruce R. Donald   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 . . . . . . . . . . . . . . . . . 740--761
            Ross A. Lippert and   
               Xiaoyue Zhao and   
             Liliana Florea and   
              Clark Mobarry and   
                  Sorin Istrail   Finding Anchors for Genomic Sequence
                                  Comparison . . . . . . . . . . . . . . . 762--776
              Matthew Menke and   
              Jonathan King and   
              Bonnie Berger and   
                   Lenore Cowen   Wrap-and-Pack: a New Paradigm for Beta
                                  Structural Motif Recognition with
                                  Application to Recognizing Beta Trefoils 777--795
               Luay Nakhleh and   
               Tandy Warnow and   
           C. Randal Linder and   
              Katherine St.John   Reconstructing Reticulate Evolution in
                                  Species --- Theory and Practice  . . . . 796--811
              David Sankoff and   
                     Phil Trinh   Chromosomal Breakpoint Reuse in Genome
                                  Sequence Rearrangement . . . . . . . . . 812--821
                 Eran Segal and   
                   Roded Sharan   A Discriminative Model for Identifying
                                  Spatial cis-Regulatory Modules . . . . . 822--834
               Roded Sharan and   
                Trey Ideker and   
               Brian Kelley and   
                 Ron Shamir and   
                Richard M. Karp   Identification of Protein Complexes by
                                  Comparative Analysis of Yeast and
                                  Bacterial Protein Interaction Data . . . 835--846
                  Yanni Sun and   
                  Jeremy Buhler   Designing Multiple Simultaneous Seeds
                                  for DNA Similarity Search  . . . . . . . 847--861
                 Xinyu Tang and   
         Bonnie Kirkpatrick and   
              Shawna Thomas and   
                 Guang Song and   
                 Nancy M. Amato   Using Motion Planning to Study RNA
                                  Folding Kinetics . . . . . . . . . . . . 862--881
                  Zhijin Wu and   
             Rafael A. Irizarry   Stochastic Models Inspired by
                                  Hybridization Theory for Short
                                  Oligonucleotide Arrays . . . . . . . . . 882--893
               Xiaoyue Zhao and   
               Haiyan Huang and   
               Terence P. Speed   Finding Short DNA Motifs Using Permuted
                                  Markov Models  . . . . . . . . . . . . . 894--906
                      Anonymous   Correction . . . . . . . . . . . . . . . 907--907

Journal of Computational Biology
Volume 12, Number 7, September, 2005

              Alexis Battle and   
                 Eran Segal and   
                  Daphne Koller   Probabilistic Discovery of Overlapping
                                  Cellular Processes and Their Regulation  909--927
                 Ydo Wexler and   
              Zohar Yakhini and   
            Yechezkel Kashi and   
                     Dan Geiger   Finding Approximate Tandem Repeats in
                                  Genomic Sequences  . . . . . . . . . . . 928--942
            Ross A. Lippert and   
           Clark M. Mobarry and   
                Brian P. Walenz   A Space-Efficient Construction of the
                                  Burrows--Wheeler Transform for Genomic
                                  Data . . . . . . . . . . . . . . . . . . 943--951
                    Jun Xie and   
                 Nak-Kyeong Kim   Bayesian Models and Markov Chain Monte
                                  Carlo Methods for Protein Motifs with
                                  the Secondary Characteristics  . . . . . 952--970
                   Jian Liu and   
                        Ming Li   Finding Cancer Biomarkers from Mass
                                  Spectrometry Data by Decision Lists  . . 971--979
                Itai Sharon and   
             Aaron Birkland and   
                 Kuan Chang and   
               Ran El-Yaniv and   
                     Golan Yona   Correcting BLAST $e$-Values for
                                  Low-Complexity Segments  . . . . . . . . 980--1003
            Robert F. Tichy and   
                 Stephan Wagner   Extremal Problems for Topological
                                  Indices in Combinatorial Chemistry . . . 1004--1013
           Menachem Kaufman and   
                David Bloch and   
               Naomi Zurgil and   
               Yana Shafran and   
              Mordechai Deutsch   A Cluster Pattern Algorithm for the
                                  Analysis of Multiparametric Cell Assays  1014--1028
               Dongxiao Zhu and   
             Alfred O. Hero and   
             Zhaohui S. Qin and   
                  Anand Swaroop   High Throughput Screening of
                                  Co-Expressed Gene Pairs with Controlled
                                  False Discovery Rate (FDR) and Minimum
                                  Acceptable Strength (MAS)  . . . . . . . 1029--1045

Journal of Computational Biology
Volume 12, Number 8, October, 2005

                 Sheng Zhao and   
             Russell D. Fernald   Comprehensive Algorithm for Quantitative
                                  Real-Time Polymerase Chain Reaction  . . 1047--1064
           Michele Morgante and   
          Alberto Policriti and   
         Nicola Vitacolonna and   
                 Andrea Zuccolo   Structured Motifs Search . . . . . . . . 1065--1082
              Rose Hoberman and   
              David Sankoff and   
                  Dannie Durand   The Statistical Analysis of Spatially
                                  Clustered Genes under the Maximum Gap
                                  Criterion  . . . . . . . . . . . . . . . 1083--1102
          Albert C.-C. Yang and   
          Ary L. Goldberger and   
                     C.-K. Peng   Genomic Classification Using an
                                  Information-Based Similarity Index:
                                  Application to the SARS Coronavirus  . . 1103--1116
             S. Rajasekaran and   
                   S. Balla and   
                    C.-H. Huang   Exact Algorithms for Planted Motif
                                  Problems . . . . . . . . . . . . . . . . 1117--1128
               A. D'Yachkov and   
                Frank Hwang and   
              Antony Macula and   
             Pavel Vilenkin and   
                  Chih-Wen Weng   A Construction of Pooling Designs with
                                  Some Happy Surprises . . . . . . . . . . 1129--1136

Journal of Computational Biology
Volume 12, Number 9, November, 2005

        Franco P. Preparata and   
               Louxin Zhang and   
                  Kwok Pui Choi   Quick, Practical Selection of Effective
                                  Seeds for Homology Search  . . . . . . . 1137--1152
             Changchuan Yin and   
              Stephen S.-T. Yau   A Fourier Characteristic of Coding
                                  Sequences: Origins and a Non-Fourier
                                  Approximation  . . . . . . . . . . . . . 1153--1165
         Ole F. Christensen and   
              Asger Hobolth and   
                 Jens L. Jensen   Pseudo-Likelihood Analysis of Codon
                                  Substitution Models with
                                  Neighbor-Dependent Rates . . . . . . . . 1166--1182
              Noah A. Rosenberg   Algorithms for Selecting Informative
                                  Marker Panels for Population Assignment  1183--1201
               Chu-Wen Yang and   
              Chin-Fu Hsiao and   
                 Chen-Kung Chou   Evaluation of Experimental Designs for
                                  Two-Color cDNA Microarrays . . . . . . . 1202--1220
                 Zeyar Aung and   
                   Kian-Lee Tan   Automatic $3$D Protein Structure
                                  Classification without Structural
                                  Alignment  . . . . . . . . . . . . . . . 1221--1241

Journal of Computational Biology
Volume 12, Number 10, December, 2005

                 Gad Kimmel and   
                     Ron Shamir   A Block-Free Hidden Markov Model for
                                  Genotypes and Its Application to Disease
                                  Association  . . . . . . . . . . . . . . 1243--1260
             Yao-Ting Huang and   
               Kun-Mao Chao and   
                      Ting Chen   An Approximation Algorithm for Haplotype
                                  Inference by Maximum Parsimony . . . . . 1261--1274
          Daniel M. Dunlavy and   
          Dianne P. O'leary and   
              Dmitri Klimov and   
                  D. Thirumalai   HOPE: a Homotopy Optimization Method for
                                  Protein Structure Prediction . . . . . . 1275--1288
              Gad M. Landau and   
               Laxmi Parida and   
                   Oren Weimann   Gene Proximity Analysis across Whole
                                  Genomes via PQ Trees$^1$ . . . . . . . . 1289--1306
          Wolfram Liebermeister   Predicting Physiological Concentrations
                                  of Metabolites from Their Molecular
                                  Structure  . . . . . . . . . . . . . . . 1307--1315
           Silvio C. E. Tosatto   The Victor/FRST Function for Model
                                  Quality Estimation . . . . . . . . . . . 1316--1327
               Arvind Gupta and   
        Ján Ma\vnuch and   
                Ladislav Stacho   Structure-Approximating Inverse Protein
                                  Folding Problem in the $2$D HP Model . . 1328--1345


Journal of Computational Biology
Volume 13, Number 1, January, 2006

                Joseph West and   
                 John Healy and   
             Michael Wigler and   
              William Casey and   
                     Bud Mishra   Validation of \bionameS. Pombe Sequence
                                  Assembly by Microarray Hybridization . . 1--20
               David Chiang and   
           Aravind K. Joshi and   
                    Ken A. Dill   A Grammatical Theory for the
                                  Conformational Changes of Simple Helix
                                  Bundles  . . . . . . . . . . . . . . . . 21--42
   Jakob Vesterstròm and   
              William R. Taylor   Flexible Secondary Structure Based
                                  Protein Structure Comparison Applied to
                                  the Detection of Circular Permutation    43--63
                  Moshe Havilio   Signal Deconvolution Based
                                  Expression-Detection and Background
                                  Adjustment for Microarray Data . . . . . 63--80
                Anna Gambin and   
               Jerzy Tiuryn and   
              Jerzy Tyszkiewicz   Alignment with Context Dependent Scoring
                                  Function . . . . . . . . . . . . . . . . 81--101
               Manoj Bhasin and   
          Ellis L. Reinherz and   
                 Pedro A. Reche   Recognition and Classification of
                                  Histones Using Support Vector Machine    102--112
                   Tim Hohm and   
           Philipp Limbourg and   
                Daniel Hoffmann   A Multiobjective Evolutionary Method for
                                  the Design of Peptidic Mimotopes . . . . 113--125
              Joanne I. Yeh and   
                     Lisong Mao   Prediction of Membrane Proteins in
                                  \bionameMycobacterium tuberculosis Using
                                  a Support Vector Machine Algorithm . . . 126--129

Journal of Computational Biology
Volume 13, Number 2, March, 2006

                  Satoru Miyano   Preface: Special RECOMB 2005 Issue . . . 131--132
                Jacob Scott and   
                Trey Ideker and   
            Richard M. Karp and   
                   Roded Sharan   Efficient Algorithms for Detecting
                                  Signaling Pathways in Protein
                                  Interaction Networks . . . . . . . . . . 133--144
            Ariel Jaimovich and   
                 Gal Elidan and   
             Hanah Margalit and   
                   Nir Friedman   Towards an Integrated Protein--Protein
                                  Interaction Network: a Relational Markov
                                  Network Approach . . . . . . . . . . . . 145--164
              Irit Gat-Viks and   
                 Amos Tanay and   
            Daniela Raijman and   
                     Ron Shamir   A Probabilistic Methodology for
                                  Integrating Knowledge and Experiments on
                                  Biological Networks  . . . . . . . . . . 165--181
       Mehmet Koyutürk and   
                  Yohan Kim and   
               Umut Topkara and   
        Shankar Subramaniam and   
       Wojciech Szpankowski and   
                   Ananth Grama   Pairwise Alignment of Protein
                                  Interaction Networks . . . . . . . . . . 182--199
            Brendan J. Frey and   
            Quaid D. Morris and   
              Timothy R. Hughes   GenRate: a Generative Model that Reveals
                                  Novel Transcripts in Genome-Tiling
                                  Microarray Data  . . . . . . . . . . . . 200--214
               Doron Lipson and   
             Yonatan Aumann and   
               Amir Ben-Dor and   
              Nathan Linial and   
                  Zohar Yakhini   Efficient Calculation of Interval Scores
                                  for DNA Copy Number Data Analysis  . . . 215--228
                 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   RIBRA --- An Error-Tolerant Algorithm
                                  for the NMR Backbone Assignment Problem  229--244
Chaya Ben-Zaken Zilberstein and   
         Michal Ziv-Ukelson and   
              Ron Y. Pinter and   
                  Zohar Yakhini   A High-Throughput Approach for
                                  Associating MicroRNAs with Their
                                  Activity Conditions  . . . . . . . . . . 245--266
                  Can Alkan and   
        Emre Karakoç and   
           Joseph H. Nadeau and   
           S. Cenk Sahinalp and   
                 Kaizhong Zhang   RNA--RNA Interaction Prediction and
                                  Antisense RNA Target Search  . . . . . . 267--282
               Vineet Bafna and   
                 Haixu Tang and   
                  Shaojie Zhang   Consensus Folding of Unaligned RNA
                                  Sequences Revisited  . . . . . . . . . . 283--295
           Kim R. Rasmussen and   
                 Jens Stoye and   
                Eugene W. Myers   Efficient $q$-Gram Filters for Finding
                                  All $ \epsilon $-Matches over a Given
                                  Length . . . . . . . . . . . . . . . . . 296--308
               Sing-Hoi Sze and   
                     Yue Lu and   
                    Qingwu Yang   A Polynomial Time Solvable Formulation
                                  of Multiple Sequence Alignment . . . . . 309--319
              Dannie Durand and   
Bjarni V. Halldórsson and   
                Benjamin Vernot   A Hybrid Micro--Macroevolutionary
                                  Approach to Gene Tree Reconstruction . . 320--335
               Igor Ulitsky and   
             David Burstein and   
               Tamir Tuller and   
                     Benny Chor   The Average Common Substring Approach to
                                  Phylogenomic Reconstruction  . . . . . . 336--350
           Teresa Przytycka and   
               George Davis and   
                   Nan Song and   
                  Dannie Durand   Graph Theoretical Insights into
                                  Evolution of Multidomain Proteins  . . . 351--363
              Marshall Bern and   
                 David Goldberg   \em De Novo Analysis of Peptide Tandem
                                  Mass Spectra by Spectral Graph
                                  Partitioning . . . . . . . . . . . . . . 364--378
            Samuel S. Gross and   
               Michael R. Brent   Using Multiple Alignments to Improve
                                  Gene Prediction  . . . . . . . . . . . . 379--393
                    Yan Liu and   
            Jaime Carbonell and   
              Peter Weigele and   
         Vanathi Gopalakrishnan   Protein Fold Recognition Using
                                  Segmentation Conditional Random Fields
                                  (SCRFs)  . . . . . . . . . . . . . . . . 394--406
              Maxim Shatsky and   
    Alexandra Shulman-Peleg and   
              Ruth Nussinov and   
                Haim J. Wolfson   The Multiple Common Point Set Problem
                                  and Its Application to Molecule Binding
                                  Pattern Detection  . . . . . . . . . . . 407--428
              Nicholas Chia and   
                 Ralf Bundschuh   A Practical Approach to Significance
                                  Assessment in Alignment with Gaps  . . . 429--441
              Anton Valouev and   
                     Lei Li and   
                 Yu-Chi Liu and   
          David C. Schwartz and   
                    Yi Yang and   
                   Yu Zhang and   
            Michael S. Waterman   Alignment of Optical Maps  . . . . . . . 442--462
          Chen-Hsiang Yeang and   
                 Tommi Jaakkola   Modeling the Combinatorial Functions of
                                  Multiple Transcription Factors . . . . . 463--480
              Eran Halperin and   
                     Elad Hazan   HAPLOFREQ --- Estimating Haplotype
                                  Frequencies Efficiently  . . . . . . . . 481--500
               Vineet Bafna and   
                   Vikas Bansal   Inference about Recombination from
                                  Haplotype Data: Lower Bounds and
                                  Recombination Hotspots . . . . . . . . . 501--521
               Zhihong Ding and   
            Vladimir Filkov and   
                   Dan Gusfield   A Linear-Time Algorithm for the Perfect
                                  Phylogeny Haplotyping (PPH) Problem  . . 522--553
           Matthew Mazowita and   
                 Lani Haque and   
                  David Sankoff   Stability of Rearrangement Measures in
                                  the Comparison of Genome Sequences . . . 554--566
              Anne Bergeron and   
             Julia Mixtacki and   
                     Jens Stoye   On Sorting by Translocations . . . . . . 567--578

Journal of Computational Biology
Volume 13, Number 3, April, 2006

   Sündüz Kele\cs and   
       Mark J. Van Der Laan and   
            Sandrine Dudoit and   
                Simon E. Cawley   Multiple Testing Methods For ChIP--Chip
                                  High Density Oligonucleotide Array Data  579--613
           Florian A. Potra and   
                   Xing Liu and   
Françoise Seillier-Moiseiwitsch and   
                Anindya Roy and   
                Yaming Hang and   
             Mark R. Marten and   
                 Babu Raman and   
                 Carol Whisnant   Protein Image Alignment via Piecewise
                                  Affine Transformations . . . . . . . . . 614--630
         Gianluca Pollastri and   
           Alessandro Vullo and   
             Paolo Frasconi and   
                   Pierre Baldi   Modular DAG--RNN Architectures for
                                  Assembling Coarse Protein Structures . . 631--650
             Pierre Nicolas and   
        Anne-Sophie Tocquet and   
              Vincent Miele and   
                  Florence Muri   A Reversible Jump Markov Chain Monte
                                  Carlo Algorithm for Bacterial Promoter
                                  Motifs Discovery . . . . . . . . . . . . 651--667
         Arun S. Konagurthu and   
               Peter J. Stuckey   Optimal Sum-of-Pairs Multiple Sequence
                                  Alignment Using Incremental Carrillo and
                                  Lipman Bounds  . . . . . . . . . . . . . 668--685
        Jonathan M. Carlson and   
         Arijit Chakravarty and   
                Robert H. Gross   BEAM: a Beam Search Algorithm for the
                                  Identification of \em Cis-Regulatory
                                  Elements in Groups of Genes  . . . . . . 686--701
             Jesper Jansson and   
             Ngo Trung Hieu and   
                  Wing-Kin Sung   Local Gapped Subforest Alignment and Its
                                  Application in Finding RNA Structural
                                  Motifs . . . . . . . . . . . . . . . . . 702--718
Sébastien Ferré and   
                   Ross D. King   Finding Motifs in Protein Secondary
                                  Structure for Use in Function Prediction 719--731
           Ion I. M\uandoiu and   
              Drago\cs Trinc\ua   Exact and Approximation Algorithms for
                                  DNA Tag Set Design . . . . . . . . . . . 732--744
           Chandan K. Reddy and   
              Hsiao-Dong Chiang   A Stability Boundary Based Method for
                                  Finding Saddle Points on Potential
                                  Energy Surfaces  . . . . . . . . . . . . 745--766
           Kristin L. Ayers and   
             Chiara Sabatti and   
                  Kenneth Lange   Reconstructing Ancestral Haplotypes with
                                  a Dictionary Model . . . . . . . . . . . 767--785
             Shuguang Huang and   
                    Yongming Qu   The Loss in Power When the Test of
                                  Differential Expression Is Performed
                                  under a Wrong Scale  . . . . . . . . . . 786--797
                N. Raghavan and   
              D. Amaratunga and   
                 J. Cabrera and   
                     A. Nie and   
                     J. Qin and   
                   M. McMillian   On Methods for Gene Function Scoring as
                                  a Means of Facilitating the
                                  Interpretation of Microarray Results . . 798--809
                Raya Khanin and   
                      Ernst Wit   How Scale-Free Are Biological Networks   810--818
                 Benny Chor and   
                Amit Khetan and   
                      Sagi Snir   Maximum Likelihood Molecular Clock Comb:
                                  Analytic Solutions . . . . . . . . . . . 819--837
           Andrew Golightly and   
            Darren J. Wilkinson   Bayesian Sequential Inference for
                                  Stochastic Kinetic Biochemical Network
                                  Models . . . . . . . . . . . . . . . . . 838--851

Journal of Computational Biology
Volume 13, Number 4, May, 2006

               Marcus Hjelm and   
       Mattias Höglund and   
                 Jens Lagergren   New Probabilistic Network Models and
                                  Algorithms for Oncogenesis . . . . . . . 853--865
       Arkadii G. D'Yachkov and   
          Anthony J. Macula and   
        Wendy K. Pogozelski and   
             Thomas E. Renz and   
        Vyacheslav V. Rykov and   
                David C. Torney   New $t$-Gap Insertion-Deletion-Like
                                  Metrics for DNA Hybridization
                                  Thermodynamic Modeling . . . . . . . . . 866--881
                   Dirk Metzler   Robust $E$-Values for Gapped Local
                                  Alignments . . . . . . . . . . . . . . . 882--896
           Ravi Vijayasatya and   
                 Amar Mukherjee   An Optimal Algorithm for Perfect
                                  Phylogeny Haplotyping  . . . . . . . . . 897--928
        Sumedha Gunewardena and   
              Peter Jeavons and   
                  Zhaolei Zhang   Enhancing the Prediction of
                                  Transcription Factor Binding Sites by
                                  Incorporating Structural Properties and
                                  Nucleotide Covariations  . . . . . . . . 929--945
           Vera P. Turutina and   
           Andrew A. Laskin and   
      Nikolay A. Kudryashov and   
     Konstantin G. Skryabin and   
             Eugene V. Korotkov   Identification of Amino Acid Latent
                                  Periodicity within 94 Protein Families   946--964
            Michael Cameron and   
           Hugh E. Williams and   
                   Adam Cannane   A Deterministic Finite Automaton for
                                  Faster Protein Hit Detection in BLAST    965--978
           Justin Colannino and   
              Mirela Damian and   
             Ferran Hurtado and   
                John Iacono and   
                Henk Meijer and   
          Suneeta Ramaswami and   
             Godfried Toussaint   An $ O(n \log n) $-Time Algorithm for
                                  the Restriction Scaffold Assignment
                                  Problem  . . . . . . . . . . . . . . . . 979--989
                Ding-Zhu Du and   
                F. K. Hwang and   
                   Weili Wu and   
                    Taieb Znati   New Construction for Transversal Design  990--995
                  E. Chudin and   
                S. Kruglyak and   
                S. C. Baker and   
                   S. Oeser and   
                  D. Barker and   
                 T. K. McDaniel   A Model of Technical Variation of
                                  Microarray Signals . . . . . . . . . . . 996--1003

Journal of Computational Biology
Volume 13, Number 5, June, 2006

              David Sankoff and   
                     Lani Haque   The Distribution of Genomic Distance
                                  between Random Genomes . . . . . . . . . 1005--1012
                Carmel Kent and   
              Gad M. Landau and   
             Michal Ziv-Ukelson   On the Complexity of Sparse Exon
                                  Assembly . . . . . . . . . . . . . . . . 1013--1027
         Aleksandr Morgulis and   
           E. Michael Gertz and   
 Alejandro A. Schäffer and   
                 Richa Agarwala   A Fast and Symmetric DUST Implementation
                                  to Mask Low-Complexity DNA Sequences . . 1028--1040
           Tatiana Maximova and   
                    Chen Keasar   A Novel Algorithm for Non-Bonded-List
                                  Updating in Molecular Simulations  . . . 1041--1048
              John Goutsias and   
                  Seungchan Kim   Stochastic Transcriptional Regulatory
                                  Systems with Time Delays: a Mean-Field
                                  Approximation  . . . . . . . . . . . . . 1049--1076
               David Chiang and   
           Aravind K. Joshi and   
                David B. Searls   Grammatical Representations of
                                  Macromolecular Structure . . . . . . . . 1077--1100
        Elizabeth S. Allman and   
                 John A. Rhodes   The Identifiability of Tree Topology for
                                  Phylogenetic Models, Including Covarion
                                  and Mixture Models . . . . . . . . . . . 1101--1113
         Bradley J. Beattie and   
              Peter N. Robinson   Binary State Pattern Clustering: a
                                  Digital Paradigm for Class and Biomarker
                                  Discovery in Gene Microarray Studies of
                                  Cancer . . . . . . . . . . . . . . . . . 1114--1130

Journal of Computational Biology
Volume 13, Number 6, July, 2006

          Angela P. Presson and   
                 Eric Sobel and   
              Kenneth Lange and   
               Jeanette C. Papp   Merging Microsatellite Data  . . . . . . 1131--1147
                    Jing Wu and   
                 David Haussler   Coding Exon Detection Using Comparative
                                  Sequences  . . . . . . . . . . . . . . . 1148--1164
                Yair Horesh and   
                 Ramit Mehr and   
                      Ron Unger   Designing an $ A* $ Algorithm for
                                  Calculating Edit Distance between
                                  Rooted-Unordered Trees . . . . . . . . . 1165--1176
               Michael C. Wendl   A General Coverage Theory for Shotgun
                                  DNA Sequencing . . . . . . . . . . . . . 1177--1196
   Einar Andreas Ròdland   Pseudoknots in RNA Secondary Structures:
                                  Representation, Enumeration, and
                                  Prevalence . . . . . . . . . . . . . . . 1197--1213
         M. Christodoulakis and   
              C. Iliopoulos and   
                L. Mouchard and   
               K. Perdikuri and   
              A. Tsakalidis and   
                    K. Tsichlas   Computation of Repetitions and
                                  Regularities of Biologically Weighted
                                  Sequences  . . . . . . . . . . . . . . . 1214--1231
             Meera Sitharam and   
         Mavis Agbandje-Mckenna   Modeling Virus Self-Assembly Pathways:
                                  Avoiding Dynamics Using Geometric
                                  Constraint Decomposition . . . . . . . . 1232--1265

Journal of Computational Biology
Volume 13, Number 7, September, 2006

               Lincong Wang and   
          Ramgopal R. Mettu and   
           Bruce Randall Donald   A Polynomial-Time Algorithm for \em De
                                  Novo Protein Backbone Structure
                                  Determination from Nuclear Magnetic
                                  Resonance Data . . . . . . . . . . . . . 1267--1288
        Adrian D. Haimovich and   
                Bruce Byrne and   
      Ramakrishna Ramaswamy and   
               William J. Welsh   Wavelet Analysis of DNA Walks  . . . . . 1289--1298
       Mehmet Koyutürk and   
                  Yohan Kim and   
        Shankar Subramaniam and   
       Wojciech Szpankowski and   
                   Ananth Grama   Detecting Conserved Interaction Patterns
                                  in Biological Networks . . . . . . . . . 1299--1322
                    Isaac Elias   Settling the Intractability of Multiple
                                  Alignment  . . . . . . . . . . . . . . . 1323--1339
              Anne Bergeron and   
                     Jens Stoye   On the Similarity of Sets of
                                  Permutations and Its Applications to
                                  Genome Comparison  . . . . . . . . . . . 1340--1354
                   Jinbo Xu and   
               Daniel Brown and   
                    Ming Li and   
                         Bin Ma   Optimizing Multiple Spaced Seeds for
                                  Homology Search  . . . . . . . . . . . . 1355--1368
              Jonathan M. Keith   Segmenting Eukaryotic Genomes with the
                                  Generalized Gibbs Sampler  . . . . . . . 1369--1383
           Florian A. Potra and   
                       Xing Liu   Aligning Families of Two-Dimensional
                                  Gels by a Combined Multiresolution
                                  Forward-Inverse Transformation Approach  1384--1395

Journal of Computational Biology
Volume 13, Number 8, October, 2006

               Firas Swidan and   
         Michal Ziv-Ukelson and   
                  Ron Y. Pinter   On the Repeat-Annotated Phylogenetic
                                  Tree Reconstruction Problem  . . . . . . 1397--1418
          Maria Luisa Bonet and   
          Katherine St.John and   
             Ruchi Mahindru and   
                    Nina Amenta   Approximating Subtree Distances Between
                                  Phylogenies  . . . . . . . . . . . . . . 1419--1434
                  Winfried Just   Reverse Engineering Discrete Dynamical
                                  Systems from Data Sets with Random Input
                                  Vectors  . . . . . . . . . . . . . . . . 1435--1456
             Joel E. Richardson   fjoin: Simple and Efficient Computation
                                  of Feature Overlaps  . . . . . . . . . . 1457--1464
              Gilles Didier and   
            Ivan Laprevotte and   
                Maude Pupin and   
            Alain Hénaut   Local Decoding of Sequences and
                                  Alignment-Free Comparison  . . . . . . . 1465--1476
             Giulia Menconi and   
              Roberto Marangoni   A Compression-Based Approach for Coding
                                  Sequences Identification. I. Application
                                  to Prokaryotic Genomes . . . . . . . . . 1477--1488
           Catherine Mooney and   
           Alessandro Vullo and   
             Gianluca Pollastri   Protein Structural Motif Prediction in
                                  Multidimensional $ \phi $--$ \psi $
                                  Space Leads to Improved Secondary
                                  Structure Prediction . . . . . . . . . . 1489--1502
            Frank Emmert-Streib   Algorithmic Computation of Knot
                                  Polynomials of Secondary Structure
                                  Elements of Proteins . . . . . . . . . . 1503--1512

Journal of Computational Biology
Volume 13, Number 9, November, 2006

               B. Moerkerke and   
                 E. Goetghebeur   Selecting ``Significant'' Differentially
                                  Expressed Genes from the Combined
                                  Perspective of the Null and the
                                  Alternative  . . . . . . . . . . . . . . 1513--1531
               Peter C. Y. Chen   A Discrete-Event Approach to
                                  Transcription Control with Dynamic
                                  Event-Controllability  . . . . . . . . . 1532--1545
             Derek A. Ruths and   
               Luay Nakhleh and   
          M. Sriram Iyengar and   
      Shrikanth A. G. Reddy and   
                 Prahlad T. Ram   Hypothesis Generation in Signaling
                                  Networks . . . . . . . . . . . . . . . . 1546--1557
          Ga\vsper Jakli\vc and   
           Toma\vz Pisanski and   
                 Milan Randi\'c   Characterization of Complex Biological
                                  Systems by Matrix Invariants . . . . . . 1558--1564
                    Yu Chen and   
              Gordon M. Crippen   Fold Recognition via a Tree  . . . . . . 1565--1573
           William J. Bruno and   
                John E. Pearson   Transformations that Preserve Detailed
                                  Balance in Markov Models . . . . . . . . 1574--1578
                Pengfei Han and   
              Xiuzhen Zhang and   
          Raymond S. Norton and   
                  Zhi-Ping Feng   Predicting Disordered Regions in
                                  Proteins Based on Decision Trees of
                                  Reduced Amino Acid Composition . . . . . 1579--1590
         Bart J. A. Mertens and   
               M. E. De Noo and   
      R. A. E. M. Tollenaar and   
                  A. M. Deelder   Mass Spectrometry Proteomic Diagnosis:
                                  Enacting the Double Cross-Validatory
                                  Paradigm . . . . . . . . . . . . . . . . 1591--1605
                Zhenqiu Liu and   
                  Shili Lin and   
                       Ming Tan   Genome-Wide Tagging SNPs with
                                  Entropy-Based Monte Carlo Method . . . . 1606--1614
             Nak-Kyeong Kim and   
                        Jun Xie   Protein Multiple Alignment Incorporating
                                  Primary and Secondary Structure
                                  Information  . . . . . . . . . . . . . . 1615--1629
              Andre Ribeiro and   
                    Rui Zhu and   
             Stuart A. Kauffman   A General Modeling Strategy for Gene
                                  Regulatory Networks with Stochastic
                                  Dynamics . . . . . . . . . . . . . . . . 1630--1639
                       P. Clote   Combinatorics of Saturated Secondary
                                  Structures of RNA  . . . . . . . . . . . 1640--1657

Journal of Computational Biology
Volume 13, Number 10, December, 2006

                  Noga Alon and   
                 Vera Asodi and   
             Charles Cantor and   
                Simon Kasif and   
                   John Rachlin   Multi-Node Graphs: a Framework for
                                  Multiplexed Biological Assays  . . . . . 1659--1672
               Lu-yong Wang and   
            Dorin Comaniciu and   
                  Daniel Fasulo   Exploiting Interactions among
                                  Polymorphisms Contributing to Complex
                                  Disease Traits with Boosted Generative
                                  Modeling . . . . . . . . . . . . . . . . 1673--1684
                   Laxmi Parida   Using PQ Structures for Genomic
                                  Rearrangement Phylogeny  . . . . . . . . 1685--1700
              Nicolas Lartillot   Conjugate Gibbs Sampling for Bayesian
                                  Phylogenetic Models  . . . . . . . . . . 1701--1722
                Pengfei Han and   
              Xiuzhen Zhang and   
          Raymond S. Norton and   
                  Zhi-Ping Feng   Predicting Disordered Regions in
                                  Proteins Based on Decision Trees of
                                  Reduced Amino Acid Composition . . . . . 1723--1734
             Nak-Kyeong Kim and   
                        Jun Xie   Protein Multiple Alignment Incorporating
                                  Primary and Secondary Structure
                                  Information  . . . . . . . . . . . . . . 1735--1748
               Sushmita Roy and   
                Terran Lane and   
                Chris Allen and   
          Anthony D. Aragon and   
      Margaret Werner-Washburne   A Hidden-State Markov Model for Cell
                                  Population Deconvolution . . . . . . . . 1749--1774
              Chun-Min Hung and   
             Yueh-Min Huang and   
                 Ming-Shi Chang   CSAM: Using Clustering-Hashing-Signal
                                  Anchoring Method to Explore Human Novel
                                  Genes  . . . . . . . . . . . . . . . . . 1775--1789


Journal of Computational Biology
Volume 14, Number 1, January, 2007

                Ilan Gronau and   
                   Shlomo Moran   Neighbor Joining Algorithms for
                                  Inferring Phylogenies via LCA Distances  1--15
          Baharak Rastegari and   
                    Anne Condon   Parsing Nucleic Acid Pseudoknotted
                                  Secondary Structure: Algorithm and
                                  Applications . . . . . . . . . . . . . . 16--32
               Sven Siebert and   
                  Rolf Backofen   A Dynamic Programming Approach for
                                  Finding Common Patterns in RNAs  . . . . 33--44
                   Laxmi Parida   Gapped Permutation Pattern Discovery for
                                  Gene Order Comparisons . . . . . . . . . 45--55
                Qingwu Yang and   
                   Sing-Hoi Sze   Path Matching and Graph Matching in
                                  Biological Networks  . . . . . . . . . . 56--67
                 Karen Lees and   
            Stephen Roberts and   
             Pari Skamnioti and   
                     Sarah Gurr   Gene Microarray Analysis Using Angular
                                  Distribution Decomposition . . . . . . . 68--83
              Morgan Bishop and   
          Anthony J. Macula and   
                Kayla Nimmo and   
                Lauren Wood and   
        Wendy K. Pogozelski and   
                 Thomas E. Renz   Group Testing to Annihilate Pairs
                                  Applied to DNA Cross-Hybridization
                                  Elimination Using SYBR Green I . . . . . 84--96
              Nilanjan Saha and   
            Layne T. Watson and   
              Karen Kafadar and   
         Naren Ramakrishnan and   
            Alexey Onufriev and   
          Shrinivasrao Mane and   
        Cecilia Vasquez-Robinet   Validation and Estimation of Parameters
                                  for a General Probabilistic Model of the
                                  PCR Process  . . . . . . . . . . . . . . 97--112

Journal of Computational Biology
Volume 14, Number 2, March, 2007

                Leming Zhou and   
                 Liliana Florea   Designing Sensitive and Specific Spaced
                                  Seeds for Cross-Species mRNA-to-Genome
                                  Alignment  . . . . . . . . . . . . . . . 113--130
          Pankaj K. Agarwal and   
           Nabil H. Mustafa and   
                      Yusu Wang   Fast Molecular Shape Matching Using
                                  Contact Maps . . . . . . . . . . . . . . 131--143
                   Dan Levy and   
         Christopher Reeder and   
            Bradford Loucas and   
                Lynn Hlatky and   
                 Allen Chen and   
          Michael Cornforth and   
                   Rainer Sachs   Interpreting Chromosome Aberration
                                  Spectra  . . . . . . . . . . . . . . . . 144--155
     Daniel \vStefankovi\vc and   
                    Eric Vigoda   Phylogeny of Mixture Models: Robustness
                                  of Maximum Likelihood and
                                  Non-Identifiable Distributions . . . . . 156--189
         J. Waldispühl and   
                       P. Clote   Computing the Partition Function and
                                  Sampling for Saturated Secondary
                                  Structures of RNA, with Respect to the
                                  Turner Energy Model  . . . . . . . . . . 190--215
                Isaac Elias and   
                   Tamir Tuller   Reconstruction of Ancestral Genomic
                                  Sequences Using Likelihood . . . . . . . 216--237
                      Yong Kong   Generalized Correlation Functions and
                                  Their Applications in Selection of
                                  Optimal Multiple Spaced Seeds for
                                  Homology Search  . . . . . . . . . . . . 238--254

Journal of Computational Biology
Volume 14, Number 3, April, 2007

                 Haifeng Li and   
              Anton Valouev and   
          David C. Schwartz and   
        Michael S. Waterman and   
                      Lei M. Li   A Quantile Method for Sizing Optical
                                  Maps . . . . . . . . . . . . . . . . . . 255--266
               Eric P. Xing and   
          Michael I. Jordan and   
                   Roded Sharan   Bayesian Haplotype Inference via the
                                  Dirichlet Process  . . . . . . . . . . . 267--284
            Mary Ellen Bock and   
            Claudio Garutti and   
              Concettina Guerra   Discovery of Similar Regions on Protein
                                  Surfaces . . . . . . . . . . . . . . . . 285--299
                   Laxmi Parida   Discovering Topological Motifs Using a
                                  Compact Notation . . . . . . . . . . . . 300--323
           Naftali Kaminski and   
                 Ziv Bar-Joseph   A Patient-Gene Model for Temporal
                                  Expression Profiles in Clinical Studies  324--338
        Grzegorz A. Rempala and   
           Kenneth S. Ramos and   
            Ted Kalbfleisch and   
                     Ivo Teneng   Validation of a Mathematical Model of
                                  Gene Transcription in Aggregated
                                  Cellular Systems: Application to L1
                                  Retrotransposition . . . . . . . . . . . 339--349
         Mariusz Lubomirski and   
        Michael R. D'Andrea and   
       Stanley M. Belkowski and   
             Javier Cabrera and   
             James M. Dixon and   
            Dhammika Amaratunga   A Consolidated Approach to Analyzing
                                  Data from High-Throughput Protein
                                  Microarrays with an Application to
                                  Immune Response Profiling in Humans  . . 350--359
              Noah A. Rosenberg   Counting Coalescent Histories  . . . . . 360--377

Journal of Computational Biology
Volume 14, Number 4, May, 2007

  Sébastien Angibaud and   
           Guillaume Fertin and   
                 Irena Rusu and   
       Stéphane Vialette   A Pseudo-Boolean Framework for Computing
                                  Rearrangement Distances between Genomes
                                  with Duplicates  . . . . . . . . . . . . 379--393
             Guillaume Blin and   
                 Eric Blais and   
             Danny Hermelin and   
             Pierre Guillon and   
         Mathieu Blanchette and   
               Nadia El-Mabrouk   Gene Maps Linearization Using Genomic
                                  Rearrangement Distances  . . . . . . . . 394--407
         Michal Ozery-Flato and   
                     Ron Shamir   Sorting by Reciprocal Translocations via
                                  Reversals Theory . . . . . . . . . . . . 408--422
                     Wei Xu and   
             Chunfang Zheng and   
                  David Sankoff   Paths and Cycles in Breakpoint Graph of
                                  Random Multichromosomal Genomes  . . . . 423--435
                  Zaky Adam and   
             Monique Turmel and   
             Claude Lemieux and   
                  David Sankoff   Common Intervals and Symmetric
                                  Difference in a Model-Free
                                  Phylogenomics, with an Application to
                                  Streptophyte Evolution . . . . . . . . . 436--445
    Abdoulaye Banire Diallo and   
        Vladimir Makarenkov and   
             Mathieu Blanchette   Exact and Heuristic Algorithms for the
                                  Indel Maximum Likelihood Problem . . . . 446--461
             Mathieu Lajoie and   
             Denis Bertrand and   
           Nadia El-Mabrouk and   
                Olivier Gascuel   Duplication and Inversion History of a
                                  Tandemly Repeated Genes Family . . . . . 462--478
    Damian Wójtowicz and   
                   Jerzy Tiuryn   Evolution of Gene Families Based on Gene
                                  Duplication, Loss, Accumulated Change,
                                  and Innovation . . . . . . . . . . . . . 479--495
                    N. Song and   
            R. D. Sedgewick and   
                      D. Durand   Domain Architecture Comparison for
                                  Multidomain Homology Identification  . . 496--516
                 Cuong Than and   
                Derek Ruths and   
               Hideki Innan and   
                   Luay Nakhleh   Confounding Factors in HGT Detection:
                                  Statistical Error, Coalescent Effects,
                                  and Multiple Solutions . . . . . . . . . 517--535

Journal of Computational Biology
Volume 14, Number 5, June, 2007

             Alberto Apostolico   Preface  . . . . . . . . . . . . . . . . 537--538
               Teresa Przytycka   Stability of Characters and Construction
                                  of Phylogenetic Trees  . . . . . . . . . 539--549
               Jim C. Huang and   
            Quaid D. Morris and   
                Brendan J. Frey   Bayesian Inference of MicroRNA Targets
                                  from Sequence and Expression Data  . . . 550--563
                   Jinbo Xu and   
                  Feng Jiao and   
                  Bonnie Berger   A Parameterized Algorithm for Protein
                                  Structure Alignment  . . . . . . . . . . 564--577
           Tsung-Han Chiang and   
      Mehmet Serkan Apaydin and   
         Douglas L. Brutlag and   
                  David Hsu and   
            Jean-Claude Latombe   Using Stochastic Roadmap Simulation to
                                  Predict Experimental Quantities in
                                  Protein Folding Kinetics: Folding Rates
                                  and Phi-Values . . . . . . . . . . . . . 578--593
            Michael Cameron and   
            Yaniv Bernstein and   
               Hugh E. Williams   Clustered Sequence Representation for
                                  Fast Homology Search . . . . . . . . . . 594--614
               Martin Bader and   
                 Enno Ohlebusch   Sorting by Weighted Reversals,
                                  Transpositions, and Inverted
                                  Transpositions . . . . . . . . . . . . . 615--636
                    Wei Xie and   
          Nikolaos V. Sahinidis   A Reduction-Based Exact Algorithm for
                                  the Contact Map Overlap Problem  . . . . 637--654
          Philipp W. Messer and   
             Ralf Bundschuh and   
             Martin Vingron and   
                 Peter F. Arndt   Effects of Long-Range Correlations in
                                  DNA on Sequence Alignment Score
                                  Statistics . . . . . . . . . . . . . . . 655--668
            Stefanie Scheid and   
                   Rainer Spang   Compensating for Unknown Confounders in
                                  Microarray Data Analysis Using Filtered
                                  Permutations . . . . . . . . . . . . . . 669--681
        Samuel A. Andersson and   
                 Jens Lagergren   Motif Yggdrasil: Sampling Sequence
                                  Motifs from a Tree Mixture Model . . . . 682--697

Journal of Computational Biology
Volume 14, Number 6, July, 2007

             Alberto Apostolico   Preface  . . . . . . . . . . . . . . . . 699--700
          Stanislav Angelov and   
                Boulos Harb and   
             Sampath Kannan and   
             Sanjeev Khanna and   
                   Junhyong Kim   Efficient Enumeration of
                                  Phylogenetically Informative Substrings  701--723
     Nicholas D. Pattengale and   
           Eric J. Gottlieb and   
            Bernard M. E. Moret   Efficiently Computing the
                                  Robinson--Foulds Metric  . . . . . . . . 724--735
            David Heckerman and   
                 Carl Kadie and   
            Jennifer Listgarten   Leveraging Information Across HLA
                                  Alleles/Supertypes Improves Epitope
                                  Prediction . . . . . . . . . . . . . . . 736--746
       Mehmet Koyutürk and   
       Wojciech Szpankowski and   
                   Ananth Grama   Assessing Significance of Connectivity
                                  and Conservation in Protein Interaction
                                  Networks . . . . . . . . . . . . . . . . 747--764
        Chakra Chennubhotla and   
                     Ivet Bahar   Markov Methods for Hierarchical
                                  Coarse-Graining of Large Protein
                                  Dynamics . . . . . . . . . . . . . . . . 765--776
                Xiaoduan Ye and   
           Alan M. Friedman and   
           Chris Bailey-Kellogg   Hypergraph Model of Multi-Residue
                                  Interactions in Proteins:
                                  Sequentially-Constrained Partitioning
                                  Algorithms for Optimization of
                                  Site-Directed Protein Recombination  . . 777--790
              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   The MASH Pipeline for Protein Function
                                  Prediction and an Algorithm for the
                                  Geometric Refinement of $3$D Motifs  . . 791--816
                 Benny Chor and   
                   Tamir Tuller   Biological Networks: Comparison,
                                  Conservation, and Evolution via Relative
                                  Description Length . . . . . . . . . . . 817--838
              Shawna Thomas and   
                 Xinyu Tang and   
                Lydia Tapia and   
                 Nancy M. Amato   Simulating Protein Motions with Rigidity
                                  Analysis . . . . . . . . . . . . . . . . 839--855
                 Ydo Wexler and   
          Chaya Zilberstein and   
             Michal Ziv-Ukelson   A Study of Accessible Motifs and RNA
                                  Folding Complexity . . . . . . . . . . . 856--872

Journal of Computational Biology
Volume 14, Number 7, September, 2007

 Nevzat Onur Domaniç and   
            Franco P. Preparata   A Novel Approach to the Detection of
                                  Genomic Approximate Tandem Repeats in
                                  the Levenshtein Metric . . . . . . . . . 873--891
       Manikandan Narayanan and   
                Richard M. Karp   Comparing Protein Interaction Networks
                                  via a Graph Match-and-Split Algorithm    892--907
    Isana Veksler-Lublinsky and   
         Michal Ziv-Ukelson and   
               Danny Barash and   
                    Klara Kedem   A Structure-Based Flexible Search Method
                                  for Motifs in RNA  . . . . . . . . . . . 908--926
         Réka Albert and   
           Bhaskar DasGupta and   
             Riccardo Dondi and   
               Sema Kachalo and   
             Eduardo Sontag and   
       Alexander Zelikovsky and   
               Kelly Westbrooks   A Novel Method for Signal Transduction
                                  Network Inference from Indirect
                                  Experimental Evidence  . . . . . . . . . 927--949
               Liqing Zhang and   
                Layne T. Watson   Note on the Computation of Critical
                                  Effective Population Sizes . . . . . . . 950--960
            Frank Emmert-Streib   The Chronic Fatigue Syndrome: a
                                  Comparative Pathway Analysis . . . . . . 961--972
                M. Andrecut and   
                 S. A. Kauffman   A Physical Analogy of the Genetic Toggle
                                  Switch . . . . . . . . . . . . . . . . . 973--983
              Stefan Zeiser and   
       Johannes Müller and   
              Volkmar Liebscher   Modeling the Hes1 Oscillator . . . . . . 984--1000
    Manolis Christodoulakis and   
           G. Brian Golding and   
       Costas S. Iliopoulos and   
Yoan José Pinzón Ardila and   
               William F. Smyth   Efficient Algorithms for Counting and
                                  Reporting Segregating Sites in Genomic
                                  Sequences  . . . . . . . . . . . . . . . 1001--1010
                  Yi Y. Shi and   
           Gerald A. Miller and   
             Oleg Denisenko and   
                  Hong Qian and   
                 Karol Bomsztyk   Quantitative Model for Binary
                                  Measurements of Protein-Protein
                                  Interactions . . . . . . . . . . . . . . 1011--1023

Journal of Computational Biology
Volume 14, Number 8, October, 2007

                     Xue Wu and   
             Chau-Wen Tseng and   
                 Nathan Edwards   HMMatch: Peptide Identification by
                                  Spectral Matching of Tandem Mass Spectra
                                  Using Hidden Markov Models . . . . . . . 1025--1043
        Zakharia M. Frenkel and   
             Edward N. Trifonov   Evolutionary Networks in the Formatted
                                  Protein Sequence Space . . . . . . . . . 1044--1057
            Beckett Sterner and   
                Rohit Singh and   
                  Bonnie Berger   Predicting and Annotating Catalytic
                                  Residues: An Information Theoretic
                                  Approach . . . . . . . . . . . . . . . . 1058--1073
              Rolf Backofen and   
               Shihyen Chen and   
             Danny Hermelin and   
              Gad M. Landau and   
        Mikhail A. Roytberg and   
               Oren Weimann and   
                 Kaizhong Zhang   Locality and Gaps in RNA Comparison  . . 1074--1087
           Morgan A. Bishop and   
       Arkadii G. D'Yachkov and   
          Anthony J. Macula and   
             Thomas E. Renz and   
            Vyacheslav V. Rykov   Free Energy Gap and Statistical
                                  Thermodynamic Fidelity of DNA Codes  . . 1088--1104
              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   Estimating the Relative Contribution of
                                  dNTP Pool Imbalance and APOBEC3G/3F
                                  Editing to HIV Evolution \em In Vivo . . 1105--1114
   Aleksandar Stojmirovi\'c and   
                      Yi-Kuo Yu   Information Flow in Interaction Networks 1115--1143

Journal of Computational Biology
Volume 14, Number 9, November, 2007

                   Laxmi Parida   Statistical Significance of Large Gene
                                  Clusters . . . . . . . . . . . . . . . . 1145--1159
                   Zheng Fu and   
                   Xin Chen and   
             Vladimir Vacic and   
                   Peng Nan and   
                 Yang Zhong and   
                      Tao Jiang   MSOAR: a High-Throughput Ortholog
                                  Assignment System Based on Genome
                                  Rearrangement  . . . . . . . . . . . . . 1160--1175
          Francis L. Martin and   
          Matthew J. German and   
                  Ernst Wit and   
               Thomas Fearn and   
         Narasimhan Ragavan and   
              Hubert M. Pollock   Identifying Variables Responsible for
                                  Clustering in Discriminant Analysis of
                                  Data from Infrared Microspectroscopy of
                                  a Biological Sample  . . . . . . . . . . 1176--1184
          Hendrik Fuß and   
            Werner Dubitzky and   
          C. Stephen Downes and   
                  Mary Jo Kurth   Deactivation of Src Family Kinases:
                                  Hypothesis Testing Using a Monte Carlo
                                  Sensitivity Analysis of Systems-Level
                                  Properties . . . . . . . . . . . . . . . 1185--1200
                 Tetsuo Shibuya   Efficient Substructure RMSD Query
                                  Algorithms . . . . . . . . . . . . . . . 1201--1207
               Yongxi Cheng and   
                    Ding-Zhu Du   Efficient Constructions of Disjunct
                                  Matrices with Applications to DNA
                                  Library Screening  . . . . . . . . . . . 1208--1216
               Achim Tresch and   
              T. Beissbarth and   
           H. Sültmann and   
                   R. Kuner and   
                 A. Poustka and   
                      A. Buness   Discrimination of Direct and Indirect
                                  Interactions in a Network of Regulatory
                                  Effects  . . . . . . . . . . . . . . . . 1217--1228
            Ilkka Havukkala and   
               Stijn Vanderlooy   On the Reliable Identification of Plant
                                  Sequences Containing a Polyadenylation
                                  Site . . . . . . . . . . . . . . . . . . 1229--1245

Journal of Computational Biology
Volume 14, Number 10, December, 2007

               Dan Gusfield and   
               Vikas Bansal and   
               Vineet Bafna and   
                    Yun S. Song   A Decomposition Theory for Phylogenetic
                                  Networks and Incompatible Characters . . 1247--1272
                Yun S. Song and   
               Zhihong Ding and   
               Dan Gusfield and   
         Charles H. Langley and   
                      Yufeng Wu   Algorithms to Distinguish the Role of
                                  Gene-Conversion from Single-Crossover
                                  Recombination in the Derivation of SNP
                                  Sequences in Populations . . . . . . . . 1273--1286
         Scott C. Schmidler and   
            Joseph E. Lucas and   
                Terrence G. Oas   Statistical Estimation of Statistical
                                  Mechanical Models: Helix-Coil Theory and
                                  Peptide Helicity Prediction  . . . . . . 1287--1310
               Dongxiao Zhu and   
             Alfred O. Hero III   Bayesian Hierarchical Model for
                                  Large-Scale Covariance Matrix Estimation 1311--1326
             Michael Hirsch and   
              Stephen Swift and   
                     Xiohui Liu   Optimal Search Space for Clustering Gene
                                  Expression Data via Consensus  . . . . . 1327--1341
                     Binhai Zhu   Protein Local Structure Alignment Under
                                  the Discrete Fréchet Distance . . . . . . 1343--1351
       Magnus Åstrand and   
              Petter Mostad and   
                    Mats Rudemo   Improved Covariance Matrix Estimators
                                  for Weighted Analysis of Microarray Data 1353--1367


Journal of Computational Biology
Volume 15, Number 1, January, 2008

                  F. Picard and   
               J.-J. Daudin and   
                  M. Koskas and   
                 S. Schbath and   
                       S. Robin   Assessing the Exceptionality of Network
                                  Motifs . . . . . . . . . . . . . . . . . 1--20
                M. Andrecut and   
                 S. A. Kauffman   On the Sparse Reconstruction of Gene
                                  Networks . . . . . . . . . . . . . . . . 21--30
               W. A. Lorenz and   
                   Y. Ponty and   
                       P. Clote   Asymptotics of RNA Shapes  . . . . . . . 31--63
          Rosemarie Swanson and   
        Ioannis Kagiampakis and   
                  Jerry W. Tsai   An Information Measure of the Quality of
                                  Protein Secondary Structure Prediction   65--79
             Dumitru Brinza and   
           Alexander Zelikovsky   Design and Validation of Methods
                                  Searching for Risk Factors in Genotype
                                  Case-Control Studies . . . . . . . . . . 81--90
                  Sagi Snir and   
               Tandy Warnow and   
                     Satish Rao   Short Quartet Puzzling: a New
                                  Quartet-Based Phylogeny Reconstruction
                                  Algorithm  . . . . . . . . . . . . . . . 91--103
                   C. Bidot and   
                    F. Gruy and   
               C.-S. Haudin and   
              F. El Hentati and   
                     B. Guy and   
                     C. Lambert   Mathematical Modeling of T-Cell
                                  Activation Kinetic . . . . . . . . . . . 105--128

Journal of Computational Biology
Volume 15, Number 2, March, 2008

                  Xiaoqiu Huang   Sequence Alignment with an Appropriate
                                  Substitution Matrix  . . . . . . . . . . 129--138
              Hosna Jabbari and   
                Anne Condon and   
                    Shelly Zhao   Novel and Efficient RNA Secondary
                                  Structure Prediction Using Hierarchical
                                  Folding  . . . . . . . . . . . . . . . . 139--163
        Ramu Anandakrishnan and   
                Alexey Onufriev   Analysis of Basic Clustering Algorithms
                                  for Numerical Estimation of Statistical
                                  Averages in Biomolecules . . . . . . . . 165--184
               Jutta Gebert and   
           Susanne Motameny and   
              Ulrich Faigle and   
         Christian V. Forst and   
                Rainer Schrader   Identifying Genes of Gene Regulatory
                                  Networks Using Formal Concept Analysis   185--194
               Yongxi Cheng and   
                    Ding-Zhu Du   New Constructions of One- and Two-Stage
                                  Pooling Designs  . . . . . . . . . . . . 195--205
Guzmán Santafé and   
             Jose A. Lozano and   
         Pedro Larrañaga   Inference of Population Structure Using
                                  Genetic Markers and a Bayesian Model
                                  Averaging Approach for Clustering  . . . 207--220
              Thomas Stolte and   
          Volker Hösel and   
       Johannes Müller and   
               Michael Speicher   Modeling Clonal Expansion from M-FISH
                                  Experiments  . . . . . . . . . . . . . . 221--230

Journal of Computational Biology
Volume 15, Number 3, April, 2008

              George Nicola and   
             Colin A. Smith and   
                  Ruben Abagyan   New Method for the Assessment of All
                                  Drug-Like Pockets Across a Structural
                                  Genome . . . . . . . . . . . . . . . . . 231--240
                        Jing Li   Prioritize and Select SNPs for
                                  Association Studies with Multi-Stage
                                  Designs  . . . . . . . . . . . . . . . . 241--257
               Utz-Uwe Haus and   
              Steffen Klamt and   
                  Tamon Stephen   Computing Knock-Out Strategies in
                                  Metabolic Networks . . . . . . . . . . . 259--268
              A. J. Adewale and   
                    I. Dinu and   
               J. D. Potter and   
                     Q. Liu and   
                       Y. Yasui   Pathway Analysis of Microarray Data via
                                  Regression . . . . . . . . . . . . . . . 269--277
                    Jing Wu and   
                        Jun Xie   Computation-Based Discovery of \em
                                  Cis-Regulatory Modules by Hidden Markov
                                  Model  . . . . . . . . . . . . . . . . . 279--290
        Mikael Bodén and   
              Rohan D. Teasdale   Determining Nucleolar Association from
                                  Sequence by Leveraging Protein-Protein
                                  Interactions . . . . . . . . . . . . . . 291--304
                Raya Khanin and   
             Veronica Vinciotti   Computational Modeling of
                                  Post-Transcriptional Gene Regulation by
                                  MicroRNAs  . . . . . . . . . . . . . . . 305--316
             James O. Wrabl and   
                Nick V. Grishin   Statistics of Random Protein
                                  Superpositions: $p$-Values for Pairwise
                                  Structure Alignment  . . . . . . . . . . 317--355

Journal of Computational Biology
Volume 15, Number 4, May, 2008

             Enno Ohlebusch and   
                   Stefan Kurtz   Space Efficient Computation of Rare
                                  Maximal Exact Matches between Multiple
                                  Sequences  . . . . . . . . . . . . . . . 357--377
         Valery Polyanovsky and   
        Mikhail A. Roytberg and   
           Vladimir G. Tumanyan   Reconstruction of Genuine Pair-Wise
                                  Sequence Alignment . . . . . . . . . . . 379--391
            Vladimir Filkov and   
                   Nameeta Shah   A Simple Model of the Modular Structure
                                  of Transcriptional Regulation in Yeast   393--405
          Jonathan M. Keith and   
                Peter Adams and   
             Stuart Stephen and   
                John S. Mattick   Delineating Slowly and Rapidly Evolving
                                  Fractions of the \bionameDrosophila
                                  Genome . . . . . . . . . . . . . . . . . 407--430
           Patrick C. H. Ma and   
               Keith C. C. Chan   UPSEC: an Algorithm for Classifying
                                  Unaligned Protein Sequences into
                                  Functional Families  . . . . . . . . . . 431--443
        Olga Tcheremenskaia and   
        Alessandro Giuliani and   
                Maurizio Tomasi   PROFALIGN Algorithm Identifies the
                                  Regions Containing Folding Determinants
                                  by Scoring Pairs of Hydrophobic Profiles
                                  of Remotely Related Proteins . . . . . . 445--455
                  Jian Feng and   
           Daniel Q. Naiman and   
                    Bret Cooper   Combined Dynamic Arrays for Storing and
                                  Searching Semi-Ordered Tandem Mass
                                  Spectrometry Data  . . . . . . . . . . . 457--468

Journal of Computational Biology
Volume 15, Number 5, June, 2008

               Huy Hoang Do and   
              Kwok Pui Choi and   
        Franco P. Preparata and   
              Wing Kin Sung and   
                   Louxin Zhang   Spectrum-Based \em De Novo Repeat
                                  Detection in Genomic Sequences . . . . . 469--488
                   Buhm Han and   
                  Banu Dost and   
               Vineet Bafna and   
                  Shaojie Zhang   Structural Alignment of Pseudoknotted
                                  RNA  . . . . . . . . . . . . . . . . . . 489--504
                 Zhiyu Zhao and   
                     Bin Fu and   
        Francisco J. Alanis and   
           Christopher M. Summa   Feedback Algorithm and Web-Server for
                                  Protein Structure Alignment  . . . . . . 505--524
          Anthony J. Macula and   
          Alexander Schliep and   
           Morgan A. Bishop and   
                 Thomas E. Renz   New, Improved, and Practical $k$-Stem
                                  Sequence Similarity Measures for Probe
                                  Design . . . . . . . . . . . . . . . . . 525--534
              Zhixiang Chen and   
                     Bin Fu and   
           Robert Schweller and   
                Boting Yang and   
                 Zhiyu Zhao and   
                     Binhai Zhu   Linear Time Probabilistic Algorithms for
                                  the Singular Haplotype Reconstruction
                                  Problem from SNP Fragments . . . . . . . 535--546

Journal of Computational Biology
Volume 15, Number 6, July, 2008

                Utz J. Pape and   
               Sven Rahmann and   
                Fengzhu Sun and   
                 Martin Vingron   Compound Poisson Approximation of the
                                  Number of Occurrences of a Position
                                  Frequency Matrix (PFM) on Both Strands   547--564
               Torsten Blum and   
              Oliver Kohlbacher   Using Atom Mapping Rules for an Improved
                                  Detection of Relevant Routes in Weighted
                                  Metabolic Networks . . . . . . . . . . . 565--576
               Anne Kupczok and   
         Arndt Von Haeseler and   
                 Steffen Klaere   An Exact Algorithm for the Geodesic
                                  Distance between Phylogenetic Trees  . . 577--591
                    Xu Ling and   
                     Xin He and   
                   Dong Xin and   
                     Jiawei Han   Efficiently Identifying Max-Gap Clusters
                                  in Pairwise Genome Comparison  . . . . . 593--609
                 David Gold and   
               Bani Mallick and   
                  Kevin Coombes   Real-Time Gene Expression: Statistical
                                  Challenges in Design and Inference . . . 611--623
          Andrew K. C. Wong and   
                  Wai-Ho Au and   
               Keith C. C. Chan   Discovering High-Order Patterns of Gene
                                  Expression Levels  . . . . . . . . . . . 625--637
         Katharina T. Huber and   
                Martin Lott and   
            Vincent Moulton and   
               Andreas Spillner   The Complexity of Deriving Multi-Labeled
                                  Trees from Bipartitions  . . . . . . . . 639--651

Journal of Computational Biology
Volume 15, Number 7, September, 2008

                    Terry Speed   Preface  . . . . . . . . . . . . . . . . 653--653
     Anthony A. Philippakis and   
           Aaron M. Qureshi and   
          Michael F. Berger and   
                Martha L. Bulyk   Design of Compact, Universal DNA
                                  Microarrays for Protein Binding
                                  Microarray Experiments . . . . . . . . . 655--665
                      Yufeng Wu   Association Mapping of Complex Diseases
                                  with Ancestral Recombination Graphs:
                                  Models and Efficient Algorithms  . . . . 667--684
       Ole Schulz-Trieglaff and   
               Rene Hussong and   
         Clemens Gröpl and   
         Andreas Leinenbach and   
        Andreas Hildebrandt and   
            Christian Huber and   
                   Knut Reinert   Computational Quantification of Peptides
                                  from LC-MS Data  . . . . . . . . . . . . 685--704
              Marshall Bern and   
                 David Goldberg   Improved Ranking Functions for Protein
                                  and Modification-Site Identifications    705--719
                 Ydo Wexler and   
                     Dan Geiger   Variational Upper and Lower Bounds for
                                  Probabilistic Graphical Models . . . . . 721--735
    Dina Schneidman-Duhovny and   
                Oranit Dror and   
                Yuval Inbar and   
              Ruth Nussinov and   
                Haim J. Wolfson   Deterministic Pharmacophore Detection
                                  via Multiple Flexible Alignment of
                                  Drug-Like Molecules  . . . . . . . . . . 737--754
       Hetunandan Kamisetty and   
               Eric P. Xing and   
        Christopher J. Langmead   Free Energy Estimates of All-Atom
                                  Protein Structures Using Generalized
                                  Belief Propagation . . . . . . . . . . . 755--766
                     Yue Lu and   
                   Sing-Hoi Sze   Multiple Sequence Alignment Based on
                                  Profile Alignment of Intermediate
                                  Sequences  . . . . . . . . . . . . . . . 767--777
          Hiroyuki Kuwahara and   
                 Chris J. Myers   Production-Passage-Time Approximation: a
                                  New Approximation Method to Accelerate
                                  the Simulation Process of Enzymatic
                                  Reactions  . . . . . . . . . . . . . . . 779--792
         Michal Ozery-Flato and   
                     Ron Shamir   Sorting Genomes with Centromeres by
                                  Translocations . . . . . . . . . . . . . 793--812
              Anshul Nigham and   
                      David Hsu   Protein Conformational Flexibility
                                  Analysis with Noisy Data . . . . . . . . 813--828
               T. M. Murali and   
               Corban G. Rivera   Network Legos: Building Blocks of
                                  Cellular Wiring Diagrams . . . . . . . . 829--844
             Antonio Piccolboni   Multivariate Segmentation in the
                                  Analysis of Transcription Tiling Array
                                  Data . . . . . . . . . . . . . . . . . . 845--856
                 Wenyi Wang and   
          Benilton Carvalho and   
        Nathaniel D. Miller and   
           Jonathan Pevsner and   
       Aravinda Chakravarti and   
             Rafael A. Irizarry   Estimating Genome-Wide Copy Number Using
                                  Allele-Specific Mixture Models . . . . . 857--866
           Chun-Nam John Yu and   
          Thorsten Joachims and   
                  Ron Elber and   
              Jaroslaw Pillardy   Support Vector Training of Protein
                                  Alignment Models . . . . . . . . . . . . 867--880
               Wah-Heng Lee and   
                  Wing-Kin Sung   RB-Finder: an Improved Distance-Based
                                  Sliding Window Method to Detect
                                  Recombination Breakpoints  . . . . . . . 881--898
               Chen Yanover and   
        Ora Schueler-Furman and   
                     Yair Weiss   Minimizing and Learning Energy Functions
                                  for Side-Chain Prediction  . . . . . . . 899--911
                  Banu Dost and   
               Tomer Shlomi and   
                Nitin Gupta and   
               Eytan Ruppin and   
               Vineet Bafna and   
                   Roded Sharan   QNet: a Tool for Querying Protein
                                  Interaction Networks . . . . . . . . . . 913--925
               Noah Zaitlen and   
         Manuel Reyes-Gomez and   
            David Heckerman and   
                  Nebojsa Jojic   Shift-Invariant Adaptive Double
                                  Threading: Learning MHC II--Peptide
                                  Binding  . . . . . . . . . . . . . . . . 927--942

Journal of Computational Biology
Volume 15, Number 8, October, 2008

               Glenn Tesler and   
                  Dannie Durand   Preface  . . . . . . . . . . . . . . . . 943--946
             Chunfang Zheng and   
                   Qian Zhu and   
                  David Sankoff   Descendants of Whole Genome Duplication
                                  within Gene Order Phylogeny  . . . . . . 947--964
                     Ai Xia and   
        Maria V. Sharakhova and   
              Igor V. Sharakhov   Reconstructing Ancestral Autosomal
                                  Arrangements in the \bionameAnopheles
                                  gambiae Complex  . . . . . . . . . . . . 965--980
            Benjamin Vernot and   
            Maureen Stolzer and   
              Aiton Goldman and   
                  Dannie Durand   Reconciliation with Non-Binary Species
                                  Trees  . . . . . . . . . . . . . . . . . 981--1006
                    Jian Ma and   
              Aakrosh Ratan and   
             Brian J. Raney and   
             Bernard B. Suh and   
               Louxin Zhang and   
                Webb Miller and   
                 David Haussler   DUPCAR: Reconstructing Contiguous
                                  Ancestral Regions with Duplications  . . 1007--1027
                  Simon Gog and   
                   Martin Bader   Fast Algorithms for Transforming Back
                                  and Forth between a Signed Permutation
                                  and Its Equivalent Simple Permutation    1029--1041
              Cedric Chauve and   
        Jean-Philippe Doyon and   
               Nadia El-Mabrouk   Gene Family Evolution by Duplication,
                                  Speciation, and Loss . . . . . . . . . . 1043--1062
             Denis Bertrand and   
             Mathieu Lajoie and   
               Nadia El-Mabrouk   Inferring Ancestral Gene Orders for a
                                  Family of Tandemly Arrayed Genes . . . . 1063--1077
              William Arndt and   
                     Jijun Tang   Improving Reversal Median Computation
                                  Using Commuting Reversals and Cycle
                                  Information  . . . . . . . . . . . . . . 1079--1092
  Sébastien Angibaud and   
           Guillaume Fertin and   
                 Irena Rusu and   
   Annelyse Thévenin and   
       Stéphane Vialette   Efficient Tools for Computing the Number
                                  of Breakpoints and the Number of
                                  Adjacencies between Two Genomes with
                                  Duplicate Genes  . . . . . . . . . . . . 1093--1115
               Max A. Alekseyev   Multi-Break Rearrangements and
                                  Breakpoint Re-Uses: From Circular to
                                  Linear Genomes . . . . . . . . . . . . . 1117--1131
                      Anonymous   Correction . . . . . . . . . . . . . . . 1132--1132

Journal of Computational Biology
Volume 15, Number 9, November, 2008

               Laxmi Parida and   
          Marta Melé and   
          Francesc Calafell and   
             Jaume Bertranpetit   Estimating the Ancestral Recombinations
                                  Graph (ARG) as Compatible Networks of
                                  SNP Patterns . . . . . . . . . . . . . . 1133--1153
             Justin Kennedy and   
              Ion M\uandoiu and   
              Bogdan Pa\csaniuc   Genotype Error Detection Using Hidden
                                  Markov Models of Haplotype Diversity . . 1155--1171
                M. Andrecut and   
                   S. Huang and   
                 S. A. Kauffman   Heuristic Approach to Sparse
                                  Approximation of Gene Regulatory
                                  Networks . . . . . . . . . . . . . . . . 1173--1186
                 Lee A. Newberg   Significance of Gapped Sequence
                                  Alignments . . . . . . . . . . . . . . . 1187--1194
          Hillary S. W. Han and   
            Christian M. Reidys   Pseudoknot RNA Structures with
                                  Arc-Length $ \geq 4 $  . . . . . . . . . 1195--1208
            Kanti V. Mardia and   
             Vysaul B. Nyirongo   Simulating Virtual Protein $ C_\alpha $
                                  Traces with Applications . . . . . . . . 1209--1220
María Elena Díaz and   
            Guillermo Ayala and   
         Teresa León and   
              Roberto Zoncu and   
                   Derek Toomre   Analyzing Protein-Protein
                                  Spatial-Temporal Dependencies from Image
                                  Sequences Using Fuzzy Temporal Random
                                  Sets . . . . . . . . . . . . . . . . . . 1221--1236

Journal of Computational Biology
Volume 15, Number 10, December, 2008

             Xianyang Jiang and   
         Dominique Lavenier and   
              Stephen S.-T. Yau   Coding Region Prediction Based on a
                                  Universal DNA Sequence Representation
                                  Method . . . . . . . . . . . . . . . . . 1237--1256
                    Gang Ma and   
            Christian M. Reidys   Canonical RNA Pseudoknot Structures  . . 1257--1273
                  Jing Xiao and   
               Lusheng Wang and   
                Xiaowen Liu and   
                      Tao Jiang   An Efficient Voting Algorithm for
                                  Finding Additive Biclusters with Random
                                  Background . . . . . . . . . . . . . . . 1275--1293
              Jialiang Yang and   
                   Louxin Zhang   Run Probabilities of Seed-Like Patterns
                                  and Identifying Good Transition Seeds    1295--1313
              Antonio Lijoi and   
      Ramsés H. Mena and   
             Igor Prünster   A Bayesian Nonparametric Approach for
                                  Comparing Clustering Structures in EST
                                  Libraries  . . . . . . . . . . . . . . . 1315--1327
         Miranda van Uitert and   
            Wouter Meuleman and   
                Lodewyk Wessels   Biclustering Sparse Binary Genomic Data  1329--1345
         Man-Hung Eric Tang and   
               Anders Krogh and   
                    Ole Winther   BayesMD: Flexible Biological Modeling
                                  for Motif Discovery  . . . . . . . . . . 1347--1363
           Riccardo Porreca and   
              Samuel Drulhe and   
              Hidde de Jong and   
      Giancarlo Ferrari-Trecate   Structural Identification of
                                  Piecewise-Linear Models of Genetic
                                  Regulatory Networks  . . . . . . . . . . 1365--1380


Journal of Computational Biology
Volume 16, Number 1, January, 2009

             Lee A. Newberg and   
            Charles E. Lawrence   Exact Calculation of Distributions on
                                  Integers, with Application to Sequence
                                  Alignment  . . . . . . . . . . . . . . . 1--18
  Alireza Hadj Khodabakhshi and   
        Ján Ma\vnuch and   
               Arash Rafiey and   
                   Arvind Gupta   Stable Structure-Approximating Inverse
                                  Protein Folding in $2$D
                                  Hydrophobic-Polar-Cysteine (HPC) Model   19--30
                      Yong Kong   Statistical Distributions of
                                  Pyrosequencing . . . . . . . . . . . . . 31--42
            Paola Bonizzoni and   
            Giancarlo Mauri and   
            Graziano Pesole and   
            Ernesto Picardi and   
                Yuri Pirola and   
                Raffaella Rizzi   Detecting Alternative Gene Structures
                                  from Spliced ESTs: a Computational
                                  Approach . . . . . . . . . . . . . . . . 43--66
 Valéria Lima Passos and   
            Frans E. S. Tan and   
              Bjorn Winkens and   
           Martijn P. F. Berger   Optimal Designs for One- and Two-Color
                                  Microarrays Using Mixed Models: a
                                  Comparative Evaluation of Their
                                  Efficiencies . . . . . . . . . . . . . . 67--83
             Tamjidul Hoque and   
               Madhu Chetty and   
                   Abdul Sattar   Extended HP Model for Protein Structure
                                  Prediction . . . . . . . . . . . . . . . 85--103
        Ran Libeskind-Hadas and   
          Michael A. Charleston   On the Computational Complexity of the
                                  Reticulate Cophylogeny Reconstruction
                                  Problem  . . . . . . . . . . . . . . . . 105--117
                     Hao Ge and   
                       Min Qian   Boolean Network Approach to Negative
                                  Feedback Loops of the p53 Pathways:
                                  Synchronized Dynamics and Stochastic
                                  Limit Cycles . . . . . . . . . . . . . . 119--132

Journal of Computational Biology
Volume 16, Number 2, February, 2009

          Henry C. M. Leung and   
                 Qian Xiang and   
                  S. M. Yiu and   
             Francis Y. L. Chin   Predicting Protein Complexes from PPI
                                  Data: a Core-Attachment Approach . . . . 133--144
              Xiaoning Qian and   
               Sing-Hoi Sze and   
                 Byung-Jun Yoon   Querying Pathways in Protein Interaction
                                  Networks Based on Hidden Markov Models   145--157
      Fereydoun Hormozdiari and   
             Raheleh Salari and   
              Michael Hsing and   
   Alexander Schönhuth and   
              Simon K. Chan and   
           S. Cenk Sahinalp and   
                Artem Cherkasov   The Effect of Insertions and Deletions
                                  on Wirings in Protein-Protein
                                  Interaction Networks: a Large-Scale
                                  Study  . . . . . . . . . . . . . . . . . 159--167
         Jason E. McDermott and   
           Ronald C. Taylor and   
               Hyunjin Yoon and   
                   Fred Heffron   Bottlenecks and Hubs in Inferred
                                  Networks Are Important for Virulence in
                                  \bionameSalmonella typhimurium . . . . . 169--180
                Shaul Karni and   
              Hermona Soreq and   
                   Roded Sharan   A Network-Based Method for Predicting
                                  Disease-Causing Genes  . . . . . . . . . 181--189
         Elhanan Borenstein and   
              Marcus W. Feldman   Topological Signatures of Species
                                  Interactions in Metabolic Networks . . . 191--200
                Karen Sachs and   
              Solomon Itani and   
          Jennifer Carlisle and   
             Garry P. Nolan and   
                 Dana Pe'er and   
       Douglas A. Lauffenburger   Learning Signaling Network Structures
                                  with Sparsely Distributed Data . . . . . 201--212
             Robert Castelo and   
               Alberto Roverato   Reverse Engineering Molecular Regulatory
                                  Networks from Microarray Data with
                                  qp-Graphs  . . . . . . . . . . . . . . . 213--227
             Daniel Marbach and   
           Thomas Schaffter and   
          Claudio Mattiussi and   
                 Dario Floreano   Generating Realistic \em In Silico Gene
                                  Networks for Performance Assessment of
                                  Reverse Engineering Methods  . . . . . . 229--239
            Francesco Iorio and   
        Roberto Tagliaferri and   
              Diego di Bernardo   Identifying Network of Drug Mode of
                                  Action by Gene Expression Profiling  . . 241--251
             Saket Navlakha and   
          Michael C. Schatz and   
                 Carl Kingsford   Revealing Biological Modules via Graph
                                  Summarization  . . . . . . . . . . . . . 253--264
                    Xi Chen and   
                      Lily Wang   Integrating Biological Knowledge with
                                  Gene Expression Profiles for Survival
                                  Prediction of Cancer . . . . . . . . . . 265--278
                Gal Chechik and   
                  Daphne Koller   Timing of Gene Expression Responses to
                                  Environmental Changes  . . . . . . . . . 279--290
           Balaji Veeramani and   
                  Joel S. Bader   Metabolic Flux Correlations, Genetic
                                  Interactions, and Disease  . . . . . . . 291--302
               Tamir Tuller and   
             Udi Rubinstein and   
                   Dani Bar and   
          Michael Gurevitch and   
               Eytan Ruppin and   
                  Martin Kupiec   Higher-Order Genomic Organization of
                                  Cellular Functions in Yeast  . . . . . . 303--316
                      Leping Li   GADEM: a Genetic Algorithm Guided
                                  Formation of Spaced Dyads Coupled with
                                  an EM Algorithm for Motif Discovery  . . 317--329
             J. William Lee and   
            Tomasz Zemojtel and   
             Eugene Shakhnovich   Systems-Level Evidence of
                                  Transcriptional Co-Regulation of Yeast
                                  Protein Complexes  . . . . . . . . . . . 331--339
                 Guo-Cheng Yuan   Targeted Recruitment of Histone
                                  Modifications in Humans Predicted by
                                  Genomic Sequences  . . . . . . . . . . . 341--355
              Zhen Xuan Yeo and   
             Hock Chuan Yeo and   
         Joan Keng Suan Yeo and   
                  Ai Li Yeo and   
                      Ye Li and   
                 Neil D. Clarke   Inferring Transcription Factor Targets
                                  from Gene Expression Changes and
                                  Predicted Promoter Occupancy . . . . . . 357--368
                  Albert Erives   Non-Homologous Structured CRMs from the
                                  \bionameCiona Genome . . . . . . . . . . 369--377
                   G. Russo and   
                 M. Di Bernardo   How to Synchronize Biological Clocks . . 379--393
              Bogusaw Kluge and   
                Anna Gambin and   
               Wojciech Niemiro   Modeling Exopeptidase Activity from
                                  LC-MS Data . . . . . . . . . . . . . . . 395--406

Journal of Computational Biology
Volume 16, Number 3, March, 2009

                Ali Shojaie and   
             George Michailidis   Analysis of Gene Sets Based on the
                                  Underlying Regulatory Network  . . . . . 407--426
                 Junfeng Gu and   
                 Honglin Li and   
             Hualiang Jiang and   
                   Xicheng Wang   Optimizing Energy Potential for Protein
                                  Fold Recognition with Parametric
                                  Evaluation Function  . . . . . . . . . . 427--442
          Michelle R. Lacey and   
                   Jason Calmes   A Sharp Error Probability Estimate for
                                  the Reconstruction of Phylogenetic
                                  Quartets by the Four-Point Method  . . . 443--456
               Renqiang Min and   
             Anthony Bonner and   
                Jingjing Li and   
                  Zhaolei Zhang   Learned Random-Walk Kernels and
                                  Empirical-Map Kernels for Protein
                                  Sequence Classification  . . . . . . . . 457--474
          Juliette Blanchet and   
                Matthieu Vignes   A Model-Based Approach to Gene
                                  Clustering with Missing Observation
                                  Reconstruction in a Markov Random Field
                                  Framework  . . . . . . . . . . . . . . . 475--486
            Scott Grandison and   
               Carl Roberts and   
              Richard J. Morris   The Application of $3$D Zernike Moments
                                  for the Description of ``Model-Free''
                                  Molecular Structure, Functional Motion,
                                  and Structural Reliability . . . . . . . 487--500
              David Soloveichik   Robust Stochastic Chemical Reaction
                                  Networks and Bounded Tau-Leaping . . . . 501--522

Journal of Computational Biology
Volume 16, Number 4, April, 2009

             David Dynerman and   
             Erick Butzlaff and   
              Julie C. Mitchell   CUSA and CUDE: GPU-Accelerated Methods
                                  for Estimating Solvent Accessible
                                  Surface Area and Desolvation . . . . . . 523--537
           Andre S. Ribeiro and   
       Olli-Pekka Smolander and   
               Tiina Rajala and   
        Antti Häkkinen and   
                 Olli Yli-Harja   Delayed Stochastic Model of
                                  Transcription at the Single Nucleotide
                                  Level  . . . . . . . . . . . . . . . . . 539--553
          Andrey Ilatovskiy and   
               Michael Petukhov   Genome-Wide Search for Local DNA
                                  Segments with Anomalous GC-Content . . . 555--564
           Waibhav D. Tembe and   
            John V. Pearson and   
                 Nils Homer and   
                James Lowey and   
                 Edward Suh and   
                 David W. Craig   Statistical Comparison Framework and
                                  Visualization Scheme for Ranking-Based
                                  Algorithms in High-Throughput
                                  Genome-Wide Studies  . . . . . . . . . . 565--577
   Aleksandar Stojmirovi\'c and   
                      Yi-Kuo Yu   Geometric Aspects of Biological Sequence
                                  Comparison . . . . . . . . . . . . . . . 579--610
        József Dombi and   
   Attila Kertész-Farkas   Applying Fuzzy Technologies to
                                  Equivalence Learning in Protein
                                  Classification . . . . . . . . . . . . . 611--623
      Lucinda K. Southworth and   
              Stuart K. Kim and   
                    Art B. Owen   Properties of Balanced Permutations  . . 625--638

Journal of Computational Biology
Volume 16, Number 5, May, 2009

                    Yan Liu and   
            Jaime Carbonell and   
     Vanathi Gopalakrishnan and   
                  Peter Weigele   Conditional Graphical Models for Protein
                                  Structural Motif Recognition . . . . . . 639--657
            Sang-Cheol Seok and   
              Michael Evans and   
            Veronica J. Vieland   Fast and Accurate Calculation of a
                                  Computationally Intensive Statistic for
                                  Mapping Disease Genes  . . . . . . . . . 659--676
           Christine De Mol and   
                Sofia Mosci and   
            Magali Traskine and   
               Alessandro Verri   A Regularized Method for Selecting
                                  Nested Groups of Relevant Genes from
                                  Microarray Data  . . . . . . . . . . . . 677--690
                Zheng Rong Yang   Predict Collagen Hydroxyproline Sites
                                  Using Support Vector Machines  . . . . . 691--702
          Alexander G. Georgiev   Interpretable Numerical Descriptors of
                                  Amino Acid Space . . . . . . . . . . . . 703--723
               Utz-Uwe Haus and   
           Kathrin Niermann and   
             Klaus Truemper and   
              Robert Weismantel   Logic Integer Programming Models for
                                  Signaling Networks . . . . . . . . . . . 725--743
                Ye-In Chang and   
             Jiun-Rung Chen and   
                  Yueh-Chi Tsai   Mining Subspace Clusters from DNA
                                  Microarray Data Using Large Itemset
                                  Techniques . . . . . . . . . . . . . . . 745--768

Journal of Computational Biology
Volume 16, Number 6, June, 2009

  Alireza Hadj Khodabakhshi and   
        Ján Ma\vnuch and   
               Arash Rafiey and   
                   Arvind Gupta   Inverse Protein Folding in $3$D
                                  Hexagonal Prism Lattice under HPC Model  769--802
                Ho-Lin Chen and   
                Anne Condon and   
                  Hosna Jabbari   An $O$ ( $ n^5$ ) Algorithm for MFE
                                  Prediction of Kissing Hairpins and
                                  $4$-Chains in Nucleic Acids  . . . . . . 803--815
                      Yong Kong   Statistical Distributions of Sequencing
                                  by Synthesis with Probabilistic
                                  Nucleotide Incorporation . . . . . . . . 817--827
            Jörn Behre and   
                Stefan Schuster   Modeling Signal Transduction in Enzyme
                                  Cascades with the Concept of Elementary
                                  Flux Modes . . . . . . . . . . . . . . . 829--844
           Niels Richard Hansen   Statistical Models for Local Occurrences
                                  of RNA Structures  . . . . . . . . . . . 845--858
             Filippo Geraci and   
             Mauro Leoncini and   
         Manuela Montangero and   
           Marco Pellegrini and   
                 M. Elena Renda   K-Boost: a Scalable Algorithm for
                                  High-Quality Clustering of Microarray
                                  Gene Expression Data . . . . . . . . . . 859--873
               Elias August and   
      Antonis Papachristodoulou   A New Computational Tool for
                                  Establishing Model Parameter
                                  Identifiability  . . . . . . . . . . . . 875--885
                      Anonymous   Correction . . . . . . . . . . . . . . . 886--886

Journal of Computational Biology
Volume 16, Number 7, July, 2009

              Xiaoqiu Huang and   
                 Martin Vingron   Maximum Similarity: a New Formulation of
                                  Phylogenetic Reconstruction  . . . . . . 887--896
         Niranjan Nagarajan and   
                      Mihai Pop   Parametric Complexity of Sequence
                                  Assembly: Theory and Applications to
                                  Next Generation Sequencing . . . . . . . 897--908
                M. Andrecut and   
                  D. Foster and   
                H. Carteret and   
                 S. A. Kauffman   Maximal Information Transfer and
                                  Behavior Diversity in Random Threshold
                                  Networks . . . . . . . . . . . . . . . . 909--916
               Xiaodong Cai and   
                   Zhi-Min Yuan   Stochastic Modeling and Simulation of
                                  the p53-MDM2/MDMX Loop . . . . . . . . . 917--933
                   Peng Qiu and   
            Sylvia K. Plevritis   Simultaneous Class Discovery and
                                  Classification of Microarray Data Using
                                  Spectral Analysis  . . . . . . . . . . . 935--944
                  Yuki Kato and   
             Tatsuya Akutsu and   
                  Hiroyuki Seki   Dynamic Programming Algorithms and
                                  Grammatical Modeling for Protein
                                  Beta-Sheet Prediction  . . . . . . . . . 945--957
   Kilian Bartholomé and   
             Clemens Kreutz and   
                    Jens Timmer   Estimation of Gene Induction Enables a
                                  Relevance-Based Ranking of Gene Sets . . 959--967

Journal of Computational Biology
Volume 16, Number 8, August, 2009

                      Anonymous   Special RECOMB 2008 Issue  . . . . . . . 969--969
        Caroline C. Friedel and   
               Jan Krumsiek and   
                    Ralf Zimmer   Bootstrapping the Interactome:
                                  Unsupervised Identification of Protein
                                  Complexes in Yeast . . . . . . . . . . . 971--987
               Maxim Kalaev and   
               Vineet Bafna and   
                   Roded Sharan   Fast and Accurate Alignment of Multiple
                                  Protein Networks . . . . . . . . . . . . 989--999
             Jason Flannick and   
                Antal Novak and   
               Chuong B. Do and   
       Balaji S. Srinivasan and   
              Serafim Batzoglou   Automatic Parameter Learning for
                                  Multiple Local Network Alignment . . . . 1001--1022
           Michael R. Mehan and   
        Juan Nunez-Iglesias and   
        Mrinal Kalakrishnan and   
        Michael S. Waterman and   
         Xianghong Jasmine Zhou   An Integrative Network Approach to Map
                                  the Transcriptome to the Phenome . . . . 1023--1034
                 Yanxin Shi and   
          Michael Klutstein and   
               Itamar Simon and   
               Tom Mitchell and   
                 Ziv Bar-Joseph   A Combined Expression-Interaction Model
                                  for Inferring the Temporal Activity of
                                  Transcription Factors  . . . . . . . . . 1035--1049
                   Yu Zhang and   
                Giltae Song and   
     Tomá\vs Vina\vr and   
              Eric D. Green and   
                Adam Siepel and   
                    Webb Miller   Evolutionary History Reconstruction for
                                  Mammalian Complex Gene Clusters  . . . . 1051--1070
             J. G. Burleigh and   
               M. S. Bansal and   
                    A. Wehe and   
                  O. Eulenstein   Locating Large-Scale Gene Duplication
                                  Events through Reconciled Trees:
                                  Implications for Identifying Ancient
                                  Polyploidy Events in Plants  . . . . . . 1071--1083
      Sebastian Böcker and   
             Katharina Jahn and   
             Julia Mixtacki and   
                     Jens Stoye   Computation of Median Gene Clusters  . . 1085--1099
              Paul Medvedev and   
                 Michael Brudno   Maximum Likelihood Genome Assembly . . . 1101--1116
                Michael Sammeth   Complete Alternative Splicing Events Are
                                  Bubbles in Splicing Graphs . . . . . . . 1117--1140
            Sivan Bercovici and   
                     Dan Geiger   Inferring Ancestries Efficiently in
                                  Admixed Populations with Linkage
                                  Disequilibrium . . . . . . . . . . . . . 1141--1150
                  Wei Zheng and   
           Alan M. Friedman and   
           Chris Bailey-Kellogg   Algorithms for Joint Optimization of
                                  Stability and Diversity in Planning
                                  Combinatorial Libraries of Chimeric
                                  Proteins . . . . . . . . . . . . . . . . 1151--1168
             Ritendra Datta and   
                  Marshall Bern   Spectrum Fusion: Using Multiple Mass
                                  Spectra for De Novo Peptide Sequencing   1169--1182
               Yong Fuga Li and   
            Randy J. Arnold and   
                   Yixue Li and   
          Predrag Radivojac and   
               Quanhu Sheng and   
                     Haixu Tang   A Bayesian Approach to Protein Inference
                                  Problem in Shotgun Proteomics  . . . . . 1183--1193

Journal of Computational Biology
Volume 16, Number 9, September, 2009

                  Mary Sehl and   
   Alexander V. Alekseyenko and   
               Kenneth L. Lange   Accurate Stochastic Simulation via the
                                  Step Anticipation $ \tau $-Leaping (SAL)
                                  Algorithm  . . . . . . . . . . . . . . . 1195--1208
              Jens Ledet Jensen   A Note on the Linear Memory Baum--Welch
                                  Algorithm  . . . . . . . . . . . . . . . 1209--1210
              Catherine Eng and   
              Charu Asthana and   
             Bertrand Aigle and   
 Sébastien Hergalant and   
  Jean-François Mari and   
                 Pierre Leblond   A New Data Mining Approach for the
                                  Detection of Bacterial Promoters
                                  Combining Stochastic and Combinatorial
                                  Methods  . . . . . . . . . . . . . . . . 1211--1225
           Hanen Ben Hassen and   
              Afif Masmoudi and   
                    Ahmed Rebai   Inference in Signal Transduction
                                  Pathways Using EM Algorithm and an
                                  Implicit Algorithm: Incomplete Data Case 1227--1240
                Qiang Cheng and   
                      Jie Cheng   Sparsity Optimization Method for
                                  Multivariate Feature Screening for Gene
                                  Expression Analysis  . . . . . . . . . . 1241--1252
                    Jin Jun and   
                Paul Ryvkin and   
            Edward Hemphill and   
                   Craig Nelson   Duplication Mechanism and Disruptions in
                                  Flanking Regions Determine the Fate of
                                  Mammalian Gene Duplicates  . . . . . . . 1253--1266
      Géraldine Jean and   
        David James Sherman and   
                 Macha Nikolski   Mining the Semantics of Genome
                                  Super-Blocks to Infer Ancestral
                                  Architectures  . . . . . . . . . . . . . 1267--1284

Journal of Computational Biology
Volume 16, Number 10, October, 2009

               Craig Nelson and   
       Stéphane Vialette   RECOMB--Comparative Genomics Special
                                  Issue  . . . . . . . . . . . . . . . . . 1285--1286
   S\`everine Bérard and   
              Annie Chateau and   
              Cedric Chauve and   
            Christophe Paul and   
                   Eric Tannier   Computation of Perfect DCJ Rearrangement
                                  Scenarios with Linear and Circular
                                  Chromosomes  . . . . . . . . . . . . . . 1287--1309
         Sophia Yancopoulos and   
              Richard Friedberg   DCJ Path Formulation for Genome
                                  Transformations which Include
                                  Insertions, Deletions, and Duplications  1311--1338
         Krister M. Swenson and   
                     Yu Lin and   
              Vaibhav Rajan and   
            Bernard M. E. Moret   Hurdles and Sorting by Inversions:
                                  Combinatorial, Statistical, and
                                  Experimental Results . . . . . . . . . . 1339--1351
              David Sankoff and   
             Chunfang Zheng and   
               P. Kerr Wall and   
         Claude dePamphilis and   
           Jim Leebens-Mack and   
               Victor A. Albert   Towards Improved Reconstruction of
                                  Ancestral Gene Order in Angiosperm
                                  Phylogeny  . . . . . . . . . . . . . . . 1353--1367
                  Andrew Wei Xu   A Fast and Exact Algorithm for the
                                  Median of Three Problem: a Graph
                                  Decomposition Approach . . . . . . . . . 1369--1381
               Melvin Zhang and   
                  Hon Wai Leong   Gene Team Tree: a Hierarchical
                                  Representation of Gene Teams for All Gap
                                  Lengths  . . . . . . . . . . . . . . . . 1383--1398
        Jean-Philippe Doyon and   
              Cedric Chauve and   
                   Sylvie Hamel   Space of Gene/Species Trees
                                  Reconciliations and Parsimonious Models  1399--1418
         Daniel R. Schrider and   
          James C. Costello and   
                Matthew W. Hahn   All Human-Specific Gene Losses Are
                                  Present in the Genome as Pseudogenes . . 1419--1427
                    Jin Jun and   
                Paul Ryvkin and   
            Edward Hemphill and   
                Ion Mandoiu and   
                   Craig Nelson   The Birth of New Genes by RNA- and
                                  DNA-Mediated Duplication during
                                  Mammalian Evolution  . . . . . . . . . . 1429--1444
         Michal Ozery-Flato and   
                     Ron Shamir   Sorting Cancer Karyotypes by Elementary
                                  Operations . . . . . . . . . . . . . . . 1445--1460
Abdoulaye Baniré Diallo and   
            Dunarel Badescu and   
         Mathieu Blanchette and   
            Vladimir Makarenkov   A Whole Genome Study and Identification
                                  of Specific Carcinogenic Regions of the
                                  Human Papilloma Viruses  . . . . . . . . 1461--1473
             Denis Bertrand and   
         Mathieu Blanchette and   
               Nadia El-Mabrouk   Genetic Map Refinement Using a
                                  Comparative Genomic Approach . . . . . . 1475--1486
           Bernhard Haubold and   
         Peter Pfaffelhuber and   
     Mirjana Domazet-Los\=o and   
                   Thomas Wiehe   Estimating Mutation Distances from
                                  Unaligned Genomes  . . . . . . . . . . . 1487--1500

Journal of Computational Biology
Volume 16, Number 11, November, 2009

                 Yunxia Sui and   
               Xiaoyue Zhao and   
           Terence P. Speed and   
                      Zhijin Wu   Background Adjustment for DNA
                                  Microarrays Using a Database of
                                  Microarray Experiments . . . . . . . . . 1501--1515
                 John P. McCrow   Alignment of Phylogenetically
                                  Unambiguous Indels in \bionameShewanella 1517--1528
               Yongxi Cheng and   
                Ding-Zhu Du and   
                   Ker-I Ko and   
                     Guohui Lin   On the Parameterized Complexity of
                                  Pooling Design . . . . . . . . . . . . . 1529--1537
                Ming-Wei Su and   
               Hsiu-Man Lin and   
              Hanna S. Yuan and   
                  Woei-Chyn Chu   Categorizing Host-Dependent RNA Viruses
                                  by Principal Component Analysis of Their
                                  Codon Usage Preferences  . . . . . . . . 1539--1547
          Fenix W. D. Huang and   
            Wade W. J. Peng and   
            Christian M. Reidys   Folding $3$-Noncrossing RNA Pseudoknot
                                  Structures . . . . . . . . . . . . . . . 1549--1575
               Matteo Comin and   
          Concettina Guerra and   
                 Frank Dellaert   Binding Balls: Fast Detection of Binding
                                  Sites Using a Property of Spherical
                                  Fourier Transform  . . . . . . . . . . . 1577--1591
                    M. Andrecut   Parallel GPU Implementation of Iterative
                                  PCA Algorithms . . . . . . . . . . . . . 1593--1599
             Kouichi Kimura and   
              Yutaka Suzuki and   
               Sumio Sugano and   
                    Asako Koike   Computation of Rank and Select Functions
                                  on Hierarchical Binary String and Its
                                  Application to Genome Mapping Problems
                                  for Short-Read DNA Sequences . . . . . . 1601--1613

Journal of Computational Biology
Volume 16, Number 12, December, 2009

             Gesine Reinert and   
                 David Chew and   
                Fengzhu Sun and   
            Michael S. Waterman   Alignment-Free Sequence Comparison (I):
                                  Statistics and Power . . . . . . . . . . 1615--1634
              Nadia Pisanti and   
              Henry Soldano and   
        Mathilde Carpentier and   
                   Joel Pothier   A Relational Extension of the Notion of
                                  Motifs: Application to the Common $3$D
                                  Protein Substructures Searching Problem  1635--1660
                Zhenqiu Liu and   
       Ronald B. Gartenhaus and   
               Xue-Wen Chen and   
          Charles D. Howell and   
                       Ming Tan   Survival Prediction and Gene
                                  Identification with Penalized Global AUC
                                  Maximization . . . . . . . . . . . . . . 1661--1670
               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   The Accurate Prediction of Protein
                                  Family from Amino Acid Sequence by
                                  Measuring Features of Sequence Fragments 1671--1688
              Li-Yeh Chuang and   
            Cheng-Huei Yang and   
                Cheng-Hong Yang   Tabu Search and Binary Particle Swarm
                                  Optimization for Feature Selection Using
                                  Microarray Data  . . . . . . . . . . . . 1689--1703
            Andrei S. Rodin and   
        Anatoliy Litvinenko and   
                 Kathy Klos and   
         Alanna C. Morrison and   
             Trevor Woodage and   
               Josef Coresh and   
                Eric Boerwinkle   Use of Wrapper Algorithms Coupled with a
                                  Random Forests Classifier for Variable
                                  Selection in Large-Scale Genomic
                                  Association Studies  . . . . . . . . . . 1705--1718
                      Yi He and   
              Changjun Chen and   
                        Yi Xiao   United-Residue (UNRES) Langevin Dynamics
                                  Simulations of trpzip2 Folding . . . . . 1719--1730
                Li-Ching Wu and   
          Jorng-Tzong Horng and   
                   Yong-An Chen   A Computation to Integrate the Analysis
                                  of Genetic Variations Occurring within
                                  Regulatory Elements and Their Possible
                                  Effects  . . . . . . . . . . . . . . . . 1731--1747


Journal of Computational Biology
Volume 17, Number 1, January, 2010

   Alexander Schönhuth and   
             Raheleh Salari and   
      Fereydoun Hormozdiari and   
            Artem Cherkasov and   
               S. Cenk Sahinalp   Towards Improved Assessment of
                                  Functional Similarity in Large-Scale
                                  Screens: a Study on Indel Length . . . . 1--20
                    Lan Liu and   
                 Yonghui Wu and   
            Stefano Lonardi and   
                      Tao Jiang   Efficient Genome-Wide TagSNP Selection
                                  Across Populations via the Linkage
                                  Disequilibrium Criterion . . . . . . . . 21--37
              Regina Samaga and   
              Axel Von Kamp and   
                  Steffen Klamt   Computing Combinatorial Intervention
                                  Strategies and Failure Modes in
                                  Signaling Networks . . . . . . . . . . . 39--53
             Vladimir Vacic and   
        Lilia M. Iakoucheva and   
            Stefano Lonardi and   
              Predrag Radivojac   Graphlet Kernels for Prediction of
                                  Functional Residues in Protein
                                  Structures . . . . . . . . . . . . . . . 55--72
     Nirmalya Bandyopadhyay and   
                  Tamer Kahveci   GBA Manager: an Online Tool for Querying
                                  Low-Complexity Regions in Proteins . . . 73--77
                 Scott Mann and   
                  Jinyan Li and   
            Yi-Ping Phoebe Chen   Insights into Bacterial Genome
                                  Composition through Variable Target GC
                                  Content Profiling  . . . . . . . . . . . 79--96
                Juhyun Jung and   
                 Taewoo Ryu and   
             Yongdeuk Hwang and   
                Eunjung Lee and   
                     Doheon Lee   Prediction of Extracellular Matrix
                                  Proteins Based on Distinctive Sequence
                                  and Domain Characteristics . . . . . . . 97--105

Journal of Computational Biology
Volume 17, Number 2, February, 2010

       Dimitrije Jevremovic and   
              Cong T. Trinh and   
           Friedrich Srienc and   
                   Daniel Boley   On Algebraic Properties of Extreme
                                  Pathways in Metabolic Networks . . . . . 107--119
              Hyungwon Choi and   
             Zhaohui S. Qin and   
                 Debashis Ghosh   A Double-Layered Mixture Model for the
                                  Joint Analysis of DNA Copy Number and
                                  Gene Expression Data . . . . . . . . . . 121--137
                 Nha Nguyen and   
                 Heng Huang and   
         Soontorn Oraintara and   
                          An Vo   Stationary Wavelet Packet Transform and
                                  Dependent Laplacian Bivariate Shrinkage
                                  Estimator for Array-CGH Data Smoothing   139--152
             Mert Karaka\cs and   
               Nils Woetzel and   
                    Jens Meiler   BCL::Contact --- Low Confidence Fold
                                  Recognition Hits Boost Protein Contact
                                  Prediction and \em De Novo Structure
                                  Determination  . . . . . . . . . . . . . 153--168
                   Peng Qiu and   
          Andrew J. Gentles and   
            Sylvia K. Plevritis   Reducing the Computational Complexity of
                                  Information Theoretic Approaches for
                                  Reconstructing Gene Regulatory Networks  169--176
                  Shuo Jiao and   
                   Shunpu Zhang   Estimating the Proportion of
                                  Equivalently Expressed Genes in
                                  Microarray Data Based on Transformed
                                  Test Statistics  . . . . . . . . . . . . 177--187
            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   Computing the Stochastic Dynamics of
                                  Phosphorylation Networks . . . . . . . . 189--199

Journal of Computational Biology
Volume 17, Number 3, March, 2010

                      Anonymous   RECOMB Main Conference 2009  . . . . . . 201--201
                 Tetsuo Shibuya   Searching Protein $3$-D Structures in
                                  Linear Time  . . . . . . . . . . . . . . 203--219
                 Zengyou He and   
                  Chao Yang and   
                   Can Yang and   
               Robert Z. Qi and   
          Jason Po-Ming Tam and   
                    Weichuan Yu   Optimization-Based Peptide Mass
                                  Fingerprinting for Protein Mixture
                                  Identification . . . . . . . . . . . . . 221--235
            Sharon Bruckner and   
          Falk Hüffner and   
            Richard M. Karp and   
                 Ron Shamir and   
                   Roded Sharan   Topology-Free Querying of Protein
                                  Interaction Networks . . . . . . . . . . 237--252
                    Yong Lu and   
             Roni Rosenfeld and   
              Gerard J. Nau and   
                 Ziv Bar-Joseph   Cross Species Expression Analysis of
                                  Innate Immune Response . . . . . . . . . 253--268
         Bonnie Kirkpatrick and   
              Eran Halperin and   
                Richard M. Karp   Haplotype Inference in Complex Pedigrees 269--280
          Veli Mäkinen and   
            Gonzalo Navarro and   
         Jouni Sirén and   
        Niko Välimäki   Storage and Retrieval of Highly
                                  Repetitive Sequence Collections  . . . . 281--308
          Arvind Ramanathan and   
          Pratul K. Agarwal and   
            Maria Kurnikova and   
        Christopher J. Langmead   An Online Approach for Mining Collective
                                  Behaviors from Molecular Dynamics
                                  Simulations  . . . . . . . . . . . . . . 309--324
     Alexandre Donzé and   
            Gilles Clermont and   
        Christopher J. Langmead   Parameter Synthesis in Nonlinear
                                  Dynamical Systems: Application to
                                  Systems Biology  . . . . . . . . . . . . 325--336
     Nicholas D. Pattengale and   
             Masoud Alipour and   
  Olaf R. P. Bininda-Emonds and   
        Bernard M. E. Moret and   
          Alexandros Stamatakis   How Many Bootstrap Replicates Are
                                  Necessary? . . . . . . . . . . . . . . . 337--354
              Oliver Stegle and   
         Katherine J. Denby and   
              Emma J. Cooke and   
              David L. Wild and   
          Zoubin Ghahramani and   
           Karsten M. Borgwardt   A Robust Bayesian Two-Sample Test for
                                  Detecting Intervals of Differential Gene
                                  Expression in Microarray Time Series . . 355--367
                 Ali Bashir and   
                    Qing Lu and   
              Dennis Carson and   
        Benjamin J. Raphael and   
              Yu-Tsueng Liu and   
                   Vineet Bafna   Optimizing PCR Assays for DNA-Based
                                  Cancer Diagnostics . . . . . . . . . . . 369--381
                   Dan Gusfield   The Multi-State Perfect Phylogeny
                                  Problem with Missing and Removable Data:
                                  Solutions via Integer-Programming and
                                  Chordal Graph Theory . . . . . . . . . . 383--399
                Xiang Zhang and   
                   Feng Pan and   
                 Yuying Xie and   
                    Fei Zou and   
                       Wei Wang   COE: a General Approach for Efficient
                                  Genome-Wide Two-Locus Epistasis Test in
                                  Disease Association Study  . . . . . . . 401--415
            Osvaldo Zagordi and   
            Lukas Geyrhofer and   
                Volker Roth and   
              Niko Beerenwinkel   Deep Sequencing of a Genetically
                                  Heterogeneous Sample: Local Haplotype
                                  Reconstruction and Read Error Correction 417--428
          Mathias Möhl and   
             Sebastian Will and   
                  Rolf Backofen   Lifting Prediction to Alignment of RNA
                                  Pseudoknots  . . . . . . . . . . . . . . 429--442
Mathieu Lavallée-Adam and   
            Benoit Coulombe and   
             Mathieu Blanchette   Detection of Locally Over-Represented GO
                                  Terms in Protein-Protein Interaction
                                  Networks . . . . . . . . . . . . . . . . 443--457
                  Wei Zheng and   
           Karl E. Griswold and   
           Chris Bailey-Kellogg   Protein Fragment Swapping: a Method for
                                  Asymmetric, Selective Site-Directed
                                  Recombination  . . . . . . . . . . . . . 459--475
              B. J. Hescott and   
         M. D. M. Leiserson and   
                L. J. Cowen and   
                   D. K. Slonim   Evaluating Between-Pathway Models with
                                  Expression Data  . . . . . . . . . . . . 477--487
         Krister M. Swenson and   
              Vaibhav Rajan and   
                     Yu Lin and   
            Bernard M. E. Moret   Sorting Signed Permutations by
                                  Inversions in $ O(n \log n) $ Time . . . 489--501
             Saket Navlakha and   
                James White and   
         Niranjan Nagarajan and   
                  Mihai Pop and   
                 Carl Kingsford   Finding Biologically Accurate
                                  Clusterings in Hierarchical Tree
                                  Decompositions Using the Variation of
                                  Information  . . . . . . . . . . . . . . 503--516
           Suzanne S. Sindi and   
            Benjamin J. Raphael   Identification and Frequency Estimation
                                  of Inversion Polymorphisms from
                                  Haplotype Data . . . . . . . . . . . . . 517--531
              Eun Yong Kang and   
                    Chun Ye and   
              Ilya Shpitser and   
                  Eleazar Eskin   Detecting the Presence and Absence of
                                  Causal Relationships between Expression
                                  of Yeast Genes with Very Few Samples . . 533--546
              Hyun Min Kang and   
            Noah A. Zaitlen and   
                  Eleazar Eskin   EMINIM: an Adaptive and Memory-Efficient
                                  Algorithm for Genotype Imputation  . . . 547--560
            John Kececioglu and   
                   Eagu Kim and   
                 Travis Wheeler   Aligning Protein Sequences with
                                  Predicted Secondary Structure  . . . . . 561--580

Journal of Computational Biology
Volume 17, Number 4, April, 2010

               Zhiyuan Zhai and   
                Shih-Yen Ku and   
                 Yihui Luan and   
             Gesine Reinert and   
        Michael S. Waterman and   
                    Fengzhu Sun   The Power of Detecting Enriched
                                  Patterns: an HMM Approach  . . . . . . . 581--592
                 Tetsuo Shibuya   Searching Protein Three-Dimensional
                                  Structures in Faster Than Linear Time    593--602
               Haixiang Shi and   
             Bertil Schmidt and   
                 Weiguo Liu and   
    Wolfgang Müller-Wittig   A Parallel Algorithm for Error
                                  Correction in High-Throughput Short-Read
                                  Data on CUDA-Enabled Graphics Hardware   603--615
        Mikael Bodén and   
            Graham Dellaire and   
              Kevin Burrage and   
              Timothy L. Bailey   A Bayesian Network Model of Proteins'
                                  Association with Promyelocytic Leukemia
                                  (PML) Nuclear Bodies . . . . . . . . . . 617--630
                    Gang Wu and   
                 Ying Zhang and   
                      Yimin Wei   Krylov Subspace Algorithms for Computing
                                  GeneRank for the Analysis of Microarray
                                  Data Mining  . . . . . . . . . . . . . . 631--646
                  Namsu Ahn and   
                   Sungsoo Park   Finding an Upper Bound for the Number of
                                  Contacts in Hydrophobic-Hydrophilic
                                  Protein Structure Prediction Model . . . 647--656

Journal of Computational Biology
Volume 17, Number 5, May, 2010

                Qingwu Yang and   
                 Gangman Yi and   
              Fenghui Zhang and   
            Michael R. Thon and   
                   Sing-Hoi Sze   Identifying Gene Clusters within
                                  Localized Regions in Multiple Genomes    657--668
      Fereydoun Hormozdiari and   
             Raheleh Salari and   
               Vineet Bafna and   
               S. Cenk Sahinalp   Protein-Protein Interaction Network
                                  Evaluation for Identifying Potential
                                  Drug Targets . . . . . . . . . . . . . . 669--684
              Yen-Lin Huang and   
                   Chin Lung Lu   Sorting by Reversals, Generalized
                                  Transpositions, and Translocations Using
                                  Permutation Groups . . . . . . . . . . . 685--705
            Antonio Cardone and   
            R. Wayne Albers and   
              Ram D. Sriram and   
                 Harish C. Pant   Evaluation of the Interaction of
                                  Cyclin-Dependent Kinase 5 with Activator
                                  p25 and with p25-Derived Inhibitor CIP   707--721
               Claude Berge and   
            Nicolas Froloff and   
  Ravi Kiran Reddy Kalathur and   
               Myriam Maumy and   
               Olivier Poch and   
     Wolfgang Raffelsberger and   
                 Nicolas Wicker   Multidimensional Fitting for
                                  Multivariate Data Analysis . . . . . . . 723--732
           Patrick C. H. Ma and   
               Keith C. C. Chan   Discovering Interesting Motif-Sets for
                                  Multi-Class Protein Sequence
                                  Classification . . . . . . . . . . . . . 733--743
           Myung-Hoon Chung and   
                   Chul Koo Kim   Non-Random Mating Involving Inheritance
                                  of Social Status . . . . . . . . . . . . 745--754
             Ivan Molineris and   
             Gabriele Sales and   
           Federico Bianchi and   
        Ferdinando Di Cunto and   
                Michele Caselle   A New Approach for the Identification of
                                  Processed Pseudogenes  . . . . . . . . . 755--765

Journal of Computational Biology
Volume 17, Number 6, June, 2010

                  Fumei Lam and   
               Ryan Tarpine and   
                  Sorin Istrail   The Imperfect Ancestral Recombination
                                  Graph Reconstruction Problem: Upper
                                  Bounds for Recombination and Homoplasy   767--781
                  Feng Zhao and   
                  Jian Peng and   
              Joe Debartolo and   
              Karl F. Freed and   
           Tobin R. Sosnick and   
                       Jinbo Xu   A Probabilistic and Continuous Model of
                                  Protein Conformational Space for
                                  Template-Free Modeling . . . . . . . . . 783--798
            Frederick A. Matsen   constNJ: an Algorithm to Reconstruct
                                  Sets of Phylogenetic Trees Satisfying
                                  Pairwise Topological Constraints . . . . 799--818
           Mats Aspnäs and   
              Kimmo Mattila and   
         Kristoffer Osowski and   
                 Jan Westerholm   Code Optimization of the Subroutine to
                                  Remove Near Identical Matches in the
                                  Sequence Database Homology Search Tool
                                  PSI-BLAST  . . . . . . . . . . . . . . . 819--823
                 Howsun Jow and   
 Madhuchhanda Bhattacharjee and   
               Richard Boys and   
               Darren Wilkinson   The Integration of Genetic Maps Using
                                  Bayesian Inference . . . . . . . . . . . 825--840
        Ján Ma\vnuch and   
            Ladislav Stacho and   
                Christine Stoll   Two Lower Bounds for Self-Assemblies at
                                  Temperature 1  . . . . . . . . . . . . . 841--852
         Elena S. Dimitrova and   
       M. Paola Vera Licona and   
                 John McGee and   
          Reinhard Laubenbacher   Discretization of Time Series Data . . . 853--868

Journal of Computational Biology
Volume 17, Number 7, July, 2010

Adrián López García De Lomana and   
               Qasim K. Beg and   
            G. De Fabritiis and   
           Jordi Vill\`a-Freixa   Statistical Analysis of Global
                                  Connectivity and Activity Distributions
                                  in Cellular Networks . . . . . . . . . . 869--878
                 Shuguang Huang   Statistical Issues in Subpopulation
                                  Analysis of High Content Imaging Data    879--894
             Scott C. James and   
                   Varun Boriah   Modeling Algae Growth in an Open-Channel
                                  Raceway  . . . . . . . . . . . . . . . . 895--906
               Lusheng Wang and   
                     Binhai Zhu   On the Tractability of Maximal Strip
                                  Recovery . . . . . . . . . . . . . . . . 907--914
              Minghui Jiang and   
            Pedro J. Tejada and   
           Ramoni O. Lasisi and   
             Shanhong Cheng and   
               D. Scott Fechser   $K$-Partite RNA Secondary Structures . . 915--925
               Huilan Chang and   
              Hong-Bin Chen and   
                    Hung-Lin Fu   Identification and Classification
                                  Problems on Pooling Designs for
                                  Inhibitor Models . . . . . . . . . . . . 927--941
           Marcos R. Betancourt   Comparison between Molecular Dynamic
                                  Based and Knowledge Based Potentials for
                                  Protein Side Chains  . . . . . . . . . . 943--952

Journal of Computational Biology
Volume 17, Number 8, August, 2010

               Ewa Szczurek and   
         Przemys\law Biecek and   
               Jerzy Tiuryn and   
                 Martin Vingron   Introducing Knowledge into Differential
                                  Expression Analysis  . . . . . . . . . . 953--967
           Ana Graça and   
           Inês Lynce and   
  João Marques-Silva and   
            Arlindo L. Oliveira   Haplotype Inference by Pure Parsimony: a
                                  Survey . . . . . . . . . . . . . . . . . 969--992
               Peter Minary and   
                 Michael Levitt   Conformational Optimization with Natural
                                  Degrees of Freedom: a Novel Stochastic
                                  Chain Closure Algorithm  . . . . . . . . 993--1010
         Alberto Apostolico and   
                   Fabio Cunial   The Subsequence Composition of
                                  Polypeptides . . . . . . . . . . . . . . 1011--1049
         Michal Ziv-Ukelson and   
              Irit Gat-Viks and   
                 Ydo Wexler and   
                     Ron Shamir   A Faster Algorithm for Simultaneous
                                  Alignment and Folding of RNA . . . . . . 1051--1065
               Bong-Rae Kim and   
            Timothy McMurry and   
                   Wei Zhao and   
                Rongling Wu and   
                    Arthur Berg   Wavelet-Based Functional Clustering for
                                  Patterns of High-Dimensional Dynamic
                                  Gene Expression  . . . . . . . . . . . . 1067--1080
              Xiaodong Pang and   
              Linxiang Zhou and   
              Mingjun Zhang and   
                   Fang Xie and   
                    Long Yu and   
                 Lili Zhang and   
                    Lina Xu and   
                    Xinyi Zhang   A Mathematical Model for Peptide
                                  Inhibitor Design . . . . . . . . . . . . 1081--1093

Journal of Computational Biology
Volume 17, Number 9, September, 2010

                      Anonymous   Preface  . . . . . . . . . . . . . . . . 1095--1096
              Cedric Chauve and   
           Haris Gavranovic and   
            Aida Ouangraoua and   
                   Eric Tannier   Yeast Ancestral Genome Reconstructions:
                                  The Possibilities of Computational
                                  Methods II . . . . . . . . . . . . . . . 1097--1112
                Zhenyu Yang and   
                  David Sankoff   Natural Parameter Values for Generalized
                                  Gene Adjacency . . . . . . . . . . . . . 1113--1128
         A\"\ida Ouangraoua and   
                  Anne Bergeron   Combinatorial Structure of Genome
                                  Rearrangements Scenarios . . . . . . . . 1129--1144
 Marília D. V. Braga and   
                     Jens Stoye   The Solution Space of Sorting by DCJ . . 1145--1165
              Cedric Chauve and   
               Utz-Uwe Haus and   
              Tamon Stephen and   
                  Vivija P. You   Minimal Conflicting Sets for the
                                  Consecutive Ones Property in Ancestral
                                  Genome Reconstruction  . . . . . . . . . 1167--1181
             Guillaume Blin and   
                 David Faye and   
                     Jens Stoye   Finding Nested Common Intervals
                                  Efficiently  . . . . . . . . . . . . . . 1183--1194
                  Andrew Wei Xu   The Median Problems on Linear
                                  Multichromosomal Genomes: Graph
                                  Representation and Fast Exact Solutions  1195--1211
              Anne Bergeron and   
              Paul Medvedev and   
                     Jens Stoye   Rearrangement Models and Single-Cut
                                  Operations . . . . . . . . . . . . . . . 1213--1225
                Giltae Song and   
               Louxin Zhang and   
                Tomas Vinar and   
                    Webb Miller   CAGE: Combinatorial Analysis of
                                  Gene-Cluster Evolution . . . . . . . . . 1227--1242
        João Delgado and   
           Inês Lynce and   
                Vasco Manquinho   Computing the Summed Adjacency
                                  Disruption Number between Two Genomes
                                  with Duplicate Genes . . . . . . . . . . 1243--1265
     Tomá\vs Vina\vr and   
     Bro\vna Brejová and   
                Giltae Song and   
                    Adam Siepel   Reconstructing Histories of Complex Gene
                                  Clusters on a Phylogeny  . . . . . . . . 1267--1279
               Chih-Hao Hsu and   
                   Yu Zhang and   
           Ross C. Hardison and   
              Eric D. Green and   
                    Webb Miller   An Effective Method for Detecting Gene
                                  Conversion Events in Whole Genomes . . . 1281--1297
                  Zaky Adam and   
                  David Sankoff   A Statistically Fair Comparison of
                                  Ancestral Genome Reconstructions, Based
                                  on Breakpoint and Rearrangement
                                  Distances  . . . . . . . . . . . . . . . 1299--1314
              Mahdi Belcaid and   
              Anne Bergeron and   
               Guylaine Poisson   Mosaic Graphs and Comparative Genomics
                                  in Phage Communities . . . . . . . . . . 1315--1326
               Tamir Tuller and   
                Hadas Birin and   
              Martin Kupiec and   
                   Eytan Ruppin   Reconstructing Ancestral Genomic
                                  Sequences by Co-Evolution: Formal
                                  Definitions, Computational Issues, and
                                  Biological Examples  . . . . . . . . . . 1327--1344

Journal of Computational Biology
Volume 17, Number 10, October, 2010

                   Laxmi Parida   Ancestral Recombinations Graph: a
                                  Reconstructability Perspective Using
                                  Random-Graphs Framework  . . . . . . . . 1345--1370
               Ben Grainger and   
        Michael I. Sadowski and   
              William R. Taylor   Re-Evaluating the ``Rules'' of Protein
                                  Topology . . . . . . . . . . . . . . . . 1371--1384
                  Zhijin Wu and   
                Martin J. Aryee   Subset Quantile Normalization Using
                                  Negative Control Features  . . . . . . . 1385--1395
               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   Error Tolerant Indexing and Alignment of
                                  Short Reads with Covering Template
                                  Families . . . . . . . . . . . . . . . . 1397--1411
                  Zengti Li and   
                Suogang Gao and   
                 Hongjie Du and   
                   Feng Zou and   
                       Weili Wu   Efficient Error-Correcting Pooling
                                  Designs Constructed from
                                  Pseudo-Symplectic Spaces Over a Finite
                                  Field  . . . . . . . . . . . . . . . . . 1413--1423
              Haiying Zhang and   
                      Bing Zhou   On the Maximal Interval Subgraph of a
                                  Tree . . . . . . . . . . . . . . . . . . 1425--1433
               Arvind Gupta and   
         Mohammad M. Karimi and   
        Ján Ma\vnuch and   
            Ladislav Stacho and   
                  Xiaohong Zhao   Haplotype Inferring via Galled-Tree
                                  Networks Is NP-Complete  . . . . . . . . 1435--1449
              Duong D. Doan and   
          Patricia A. Evans and   
               Joseph D. Horton   A Near-Linear Time Algorithm for
                                  Haplotype Determination on General
                                  Pedigrees  . . . . . . . . . . . . . . . 1451--1465

Journal of Computational Biology
Volume 17, Number 11, November, 2010

                    Lin Wan and   
             Gesine Reinert and   
                Fengzhu Sun and   
            Michael S. Waterman   Alignment-Free Sequence Comparison (II):
                                  Theoretical Power of Comparison
                                  Statistics . . . . . . . . . . . . . . . 1467--1490
       Nikita A. Sakhanenko and   
                 David J. Galas   Markov Logic Networks in the Analysis of
                                  Genetic Data . . . . . . . . . . . . . . 1491--1508
                Ilan Gronau and   
               Shlomo Moran and   
                    Irad Yavneh   Adaptive Distance Measures for Resolving
                                  K2P Quartets: Metric Separation versus
                                  Stochastic Noise . . . . . . . . . . . . 1509--1518
  Sébastien Boisvert and   
 François Laviolette and   
                Jacques Corbeil   Ray: Simultaneous Assembly of Reads from
                                  a Mix of High-Throughput Sequencing
                                  Technologies . . . . . . . . . . . . . . 1519--1533
                  Sagi Snir and   
                Edward Trifonov   A Novel Technique for Detecting Putative
                                  Horizontal Gene Transfer in the Sequence
                                  Space  . . . . . . . . . . . . . . . . . 1535--1548
              Xiaohong Zhao and   
            Lance E. Palmer and   
            Randall Bolanos and   
           Cristian Mircean and   
                 Dan Fasulo and   
            Gayle M. Wittenberg   EDAR: an Efficient Error Detection and
                                  Removal Algorithm for Next Generation
                                  Sequencing Data  . . . . . . . . . . . . 1549--1560
                   Xin Chen and   
                   Jian-Yi Yang   Constructing Consensus Genetic Maps in
                                  Comparative Analysis . . . . . . . . . . 1561--1573
        Christian M. Reidys and   
                   Rita R. Wang   Shapes of RNA Pseudoknot Structures  . . 1575--1590

Journal of Computational Biology
Volume 17, Number 12, December, 2010

              Sarah Behrens and   
                 Martin Vingron   Studying the Evolution of Promoter
                                  Sequences: a Waiting Time Problem  . . . 1591--1606
                  Xugang Ye and   
                  Yi-Kuo Yu and   
            Stephen F. Altschul   Compositional Adjustment of Dirichlet
                                  Mixture Priors . . . . . . . . . . . . . 1607--1620
                      Qing Zhou   On Weight Matrix and Free Energy Models
                                  for Sequence Motif Detection . . . . . . 1621--1638
                Marc Herant and   
                    Micah Dembo   Cytopede: a Three-Dimensional Tool for
                                  Modeling Cell Motility on a Flat Surface 1639--1677
                    Xin Liu and   
                     Ya-Pu Zhao   Substitution Matrices of Residue
                                  Triplets Derived from Protein Blocks . . 1679--1687
                Xinan Zhang and   
              Yingdong Zhao and   
              Avidan U. Neumann   Partial Immunity and Vaccination for
                                  Influenza  . . . . . . . . . . . . . . . 1689--1696
             Hock Peng Chan and   
         Nancy Ruonan Zhang and   
               Louis H. Y. Chen   Importance Sampling of Word Patterns in
                                  DNA and Protein Sequences  . . . . . . . 1697--1709
               Oscar Luaces and   
     José R. Quevedo and   
 Miguel Pérez-Enciso and   
          Jorge Díez and   
   Juan José Del Coz and   
              Antonio Bahamonde   Explaining the Genetic Basis of Complex
                                  Quantitative Traits through Prediction
                                  Models . . . . . . . . . . . . . . . . . 1711--1723


Journal of Computational Biology
Volume 18, Number 1, January, 2011

              Cuong V. Than and   
              Noah A. Rosenberg   Consistency Properties of Species Tree
                                  Inference by Minimizing Deep
                                  Coalescences . . . . . . . . . . . . . . 1--15
                   Ryan Day and   
                 Xiaotao Qu and   
          Rosemarie Swanson and   
              Zach Bohannan and   
               Robert Bliss and   
                     Jerry Tsai   Relative Packing Groups in
                                  Template-Based Structure Prediction:
                                  Cooperative Effects of True Positive
                                  Constraints  . . . . . . . . . . . . . . 17--26
              Rumen Andonov and   
     Noël Malod-Dognin and   
                   Nicola Yanev   Maximum Contact Map Overlap Revisited    27--41
            Markus Heinonen and   
         Sampsa Lappalainen and   
    Taneli Mielikäinen and   
                     Juho Rousu   Computing Atom Mappings for Biochemical
                                  Reactions without Subgraph Isomorphism   43--58
                  Y. Ovadia and   
                 D. Fielder and   
                   C. Conow and   
             R. Libeskind-Hadas   The Cophylogeny Reconstruction Problem
                                  Is NP-Complete . . . . . . . . . . . . . 59--65
                 J. F. Weng and   
               D. A. Thomas and   
                     I. Mareels   Maximum Parsimony, Substitution Model,
                                  and Probability Phylogenetic Trees . . . 67--80
          Elisabetta Marras and   
      Antonella Travaglione and   
              Enrico Capobianco   Manifold Learning in Protein
                                  Interactomes . . . . . . . . . . . . . . 81--96
          Thomas K. F. Wong and   
                  T. W. Lam and   
              Wing-Kin Sung and   
        Brenda W. Y. Cheung and   
                      S. M. Yiu   Structural Alignment of RNA with Complex
                                  Pseudoknot Structure . . . . . . . . . . 97--108
            Paul A. Jenkins and   
            Robert C. Griffiths   Inference from Samples of DNA Sequences
                                  Using a Two-Locus Model  . . . . . . . . 109--127
                      Anonymous   Correction . . . . . . . . . . . . . . . 129--129

Journal of Computational Biology
Volume 18, Number 2, February, 2011

             Manolis Kellis and   
            Andrea Califano and   
                 Ziv Bar-Joseph   Preface  . . . . . . . . . . . . . . . . 131--131
               Liat Perlman and   
             Assaf Gottlieb and   
                  Nir Atias and   
               Eytan Ruppin and   
                   Roded Sharan   Combining Drug and Gene Similarity
                                  Measures for Drug-Target Elucidation . . 133--145
            Pradeep Bandaru and   
              Mukesh Bansal and   
                  Ilya Nemenman   Mass Conservation and Inference of
                                  Metabolic Networks from High-Throughput
                                  Mass Spectrometry Data . . . . . . . . . 147--154
                 Patrick Ng and   
                      Uri Keich   Alignment Constrained Sampling . . . . . 155--168
               Chang F. Quo and   
         Richard A. Moffitt and   
     Alfred H. Merrill, Jr. and   
                    May D. Wang   Adaptive Control Model Reveals
                                  Systematic Feedback and Key Molecules in
                                  Metabolic Pathway Regulation . . . . . . 169--182
           Alberto Corradin and   
         Barbara Di Camillo and   
          Vincenzo Ciminale and   
             Gianna Toffolo and   
                Claudio Cobelli   Sensitivity Analysis of Retrovirus
                                  HTLV-1 Transactivation . . . . . . . . . 183--193
       Athanasios Polynikis and   
             Giulia Cuccato and   
         Stefania Criscuolo and   
           Stephen J. Hogan and   
          Mario Di Bernardo and   
              Diego Di Bernardo   Design and Construction of a Versatile
                                  Synthetic Network for Bistable Gene
                                  Expression in Mammalian Systems  . . . . 195--203

Journal of Computational Biology
Volume 18, Number 3, March, 2011

                  Bonnie Berger   Preface: 14$^{th}$ International
                                  Conference on Research in Computational
                                  Molecular Biology (RECOMB 2010)  . . . . 205--205
                  Nir Atias and   
                   Roded Sharan   An Algorithmic Framework for Predicting
                                  Side Effects of Drugs  . . . . . . . . . 207--218
                  Ferhat Ay and   
             Manolis Kellis and   
                  Tamer Kahveci   SubMAP: Aligning Metabolic Pathways with
                                  Subnetwork Mappings  . . . . . . . . . . 219--235
            Sivan Bercovici and   
                     Dan Geiger   Admixture Aberration Analysis:
                                  Application to Mapping in Admixed
                                  Population Using Pooled DNA  . . . . . . 237--249
         José Caldas and   
                   Samuel Kaski   Hierarchical Generative Biclustering for
                                  MicroRNA Expression Analysis . . . . . . 251--261
         Salim A. Chowdhury and   
               Rod K. Nibbe and   
             Mark R. Chance and   
           Mehmet Koyutürk   Subnetwork State Functions Define
                                  Dysregulated Subnetworks in Cancer . . . 263--281
           Manfred Claassen and   
            Ruedi Aebersold and   
             Joachim M. Buhmann   Proteome Coverage Prediction for
                                  Integrated Proteomics Datasets . . . . . 283--293
            Timothy Danford and   
               Robin Dowell and   
            Sudeep Agarwala and   
              Paula Grisafi and   
                Gerald Fink and   
                  David Gifford   Discovering Regulatory Overlapping RNA
                                  Transcripts  . . . . . . . . . . . . . . 295--303
              Jianxing Feng and   
                     Wei Li and   
                      Tao Jiang   Inference of Isoforms from Short
                                  Sequence Reads . . . . . . . . . . . . . 305--321
Bjarni V. Halldórsson and   
               Derek Aguiar and   
               Ryan Tarpine and   
                  Sorin Istrail   The Clark Phaseable Sample Size Problem:
                                  Long-Range Phasing and Loss of
                                  Heterozygosity in GWAS . . . . . . . . . 323--333
             Michael Hirsch and   
    Bernhard Schölkopf and   
                 Michael Habeck   A Blind Deconvolution Approach for
                                  Improving the Resolution of Cryo-EM
                                  Density Maps . . . . . . . . . . . . . . 335--346
               Richard Jang and   
                    Xin Gao and   
                        Ming Li   Towards Fully Automated Structure-Based
                                  NMR Resonance Assignment of
                                  $^{15}$N-Labeled Proteins From
                                  Automatically Picked Peaks . . . . . . . 347--363
               Wei-Chun Kao and   
                    Yun S. Song   naiveBayesCall: an Efficient Model-Based
                                  Base-Calling Algorithm for
                                  High-Throughput Sequencing . . . . . . . 365--377
            David R. Kelley and   
                 Carl Kingsford   Extracting Between-Pathway Models from
                                  E-MAP Interactions Using Expected Graph
                                  Compression  . . . . . . . . . . . . . . 379--390
             Adam Kowalczyk and   
                Justin Bedo and   
              Thomas Conway and   
          Bryan Beresford-Smith   The Poisson Margin Test for
                                  Normalization-Free Significance Analysis
                                  of NGS Data  . . . . . . . . . . . . . . 391--400
         Christos Kozanitis and   
             Chris Saunders and   
            Semyon Kruglyak and   
               Vineet Bafna and   
                George Varghese   Compressing Genomic Sequence Fragments
                                  Using SlimGene . . . . . . . . . . . . . 401--413
                  Fumei Lam and   
         Charles H. Langley and   
                    Yun S. Song   On the Genealogy of Asexual Diploids . . 415--428
          Jonathan Laserson and   
             Vladimir Jojic and   
                  Daphne Koller   Genovo: \em De Novo Assembly for
                                  Metagenomes  . . . . . . . . . . . . . . 429--443
              Navodit Misra and   
               Guy Blelloch and   
                    R. Ravi and   
               Russell Schwartz   Generalized Buneman Pruning for
                                  Inferring the Most Parsimonious
                                  Multi-State Phylogeny  . . . . . . . . . 445--457
          Bogdan Pa\csaniuc and   
               Noah Zaitlen and   
                  Eran Halperin   Accurate Estimation of Expression Levels
                                  of Homologous Genes in RNA-seq
                                  Experiments  . . . . . . . . . . . . . . 459--468
             Benedict Paten and   
              Mark Diekhans and   
                  Dent Earl and   
               John St.John and   
                    Jian Ma and   
                Bernard Suh and   
                 David Haussler   Cactus Graphs for Genome Comparisons . . 469--481
              Manu N. Setty and   
            Alexander Gusev and   
                    Itsik Pe'er   HLA Type Inference via Haplotypes
                                  Identical by Descent . . . . . . . . . . 483--493
                Itai Sharon and   
            Sivan Bercovici and   
              Ron Y. Pinter and   
                   Tomer Shlomi   Pathway-Based Functional Analysis of
                                  Metagenomes  . . . . . . . . . . . . . . 495--505
               Fabio Vandin and   
                  Eli Upfal and   
            Benjamin J. Raphael   Algorithms for Detecting Significantly
                                  Mutated Pathways in Cancer . . . . . . . 507--522
                  Yu-Wei Wu and   
                      Yuzhen Ye   A Novel Abundance-Based Algorithm for
                                  Binning Metagenomic Sequences Using
                                  $l$-tuples . . . . . . . . . . . . . . . 523--534

Journal of Computational Biology
Volume 18, Number 4, April, 2011

             Roberto Grossi and   
       Andrea Pietracaprina and   
              Nadia Pisanti and   
              Geppino Pucci and   
                  Eli Upfal and   
                   Fabio Vandin   MADMX: a Strategy for Maximal Dense
                                  Motif Extraction . . . . . . . . . . . . 535--545
                  Karin Noy and   
                Fadi Towfic and   
        Gayle M. Wittenberg and   
                  Daniel Fasulo   Shape-Based Feature Matching Improves
                                  Protein Identification via LC-MS and
                                  Tandem MS  . . . . . . . . . . . . . . . 547--557
               A. Graudenzi and   
                   R. Serra and   
                 M. Villani and   
                 A. Colacci and   
                 S. A. Kauffman   Robustness Analysis of a Boolean Model
                                  of Gene Regulatory Network with Memory   559--577
                  S. Grusea and   
                 E. Pardoux and   
                 O. Chabrol and   
                  P. Pontarotti   Compound Poisson Approximation and
                                  Testing for Gene Clusters with Multigene
                                  Families . . . . . . . . . . . . . . . . 579--594
             Valeria Fionda and   
                 Luigi Palopoli   Biological Network Querying Techniques:
                                  Analysis and Comparison  . . . . . . . . 595--625
               Shu-Bo Zhang and   
               Song-Yu Zhou and   
                Jian-Guo He and   
                 Jian-Huang Lai   Phylogeny Inference Based on Spectral
                                  Graph Clustering . . . . . . . . . . . . 627--637
            Sajid A. Marhon and   
               Stefan C. Kremer   Gene Prediction Based on DNA Spectral
                                  Analysis: a Literature Review  . . . . . 639--676

Journal of Computational Biology
Volume 18, Number 5, May, 2011

                    Lu Meng and   
                Fengzhu Sun and   
              Xuegong Zhang and   
            Michael S. Waterman   Sequence Alignment as Hypothesis Testing 677--691
             Shuai Cheng Li and   
                  Dongbo Bu and   
                   Jinbo Xu and   
                        Ming Li   Finding Nearly Optimal GDT Scores  . . . 693--704
             Nahla A. Belal and   
               Lenwood S. Heath   A Theoretical Model for Whole Genome
                                  Alignment  . . . . . . . . . . . . . . . 705--728
    Wessel N. Van Wieringen and   
            Mark A. Van De Wiel   Exploratory Factor Analysis of Pathway
                                  Copy Number Data with an Application
                                  Towards the Integration with Gene
                                  Expression Data  . . . . . . . . . . . . 729--741
             Lavanya Kannan and   
                     Hua Li and   
               Arcady Mushegian   A Polynomial-Time Algorithm Computing
                                  Lower and Upper Bounds of the Rooted
                                  Subtree Prune and Regraft Distance . . . 743--757
               Xiaoyan Zhao and   
                   Sing-Hoi Sze   Motif Finding in DNA Sequences Based on
                                  Skipping Nonconserved Positions in
                                  Background Markov Chains . . . . . . . . 759--770
           Gregory Kucherov and   
               Tamar Pinhas and   
             Michal Ziv-Ukelson   Regular Language Constrained Sequence
                                  Alignment Revisited  . . . . . . . . . . 771--781

Journal of Computational Biology
Volume 18, Number 6, June, 2011

            Alan Veliz-Cuba and   
              Brandilyn Stigler   Boolean Models Can Explain Bistability
                                  in the \bionamelac Operon  . . . . . . . 783--794
              Tade Souaiaia and   
               Zach Frazier and   
                      Ting Chen   ComB: SNP Calling and Mapping Analysis
                                  for Color and Nucleotide Space Platforms 795--807
              Norbert Dojer and   
         Przemys\law Biecek and   
                   Jerzy Tiuryn   Bi-Billboard: Symmetrization and Careful
                                  Choice of Informant Species Results in
                                  Higher Accuracy of Regulatory Element
                                  Prediction . . . . . . . . . . . . . . . 809--819
            Jacek Blazewicz and   
          Marek Figlerowicz and   
             Marta Kasprzak and   
            Martyna Nowacka and   
            Agnieszka Rybarczyk   RNA Partial Degradation Problem:
                                  Motivation, Complexity, Algorithm  . . . 821--834
            Frans E. S. Tan and   
     Valéria Lima Passos   On the $A$-Optimality Criterion for
                                  Finding Two-Color Microarray Optimal
                                  Designs  . . . . . . . . . . . . . . . . 835--841
          Marcin Pacholczyk and   
                   Marek Kimmel   Exploring the Landscape of
                                  Protein-Ligand Interaction Energy Using
                                  Probabilistic Approach . . . . . . . . . 843--850
              Hong-Bin Chen and   
              Annalisa De Bonis   An Almost Optimal Algorithm for
                                  Generalized Threshold Group Testing with
                                  Inhibitors . . . . . . . . . . . . . . . 851--864

Journal of Computational Biology
Volume 18, Number 7, July, 2011

           Pavel A. Pevzner and   
                     Ron Shamir   Preface: 2$^{nd}$ Satellite Meeting on
                                  Bioinformatics Education, Research in
                                  Computational Molecular Biology
                                  (RECOMB--BE 2010)  . . . . . . . . . . . 865--865
                     Jeff Elhai   Humans, Computers, and the Route to
                                  Biological Insights: Regaining Our
                                  Capacity for Surprise  . . . . . . . . . 867--878
                        Jian Ma   Reconstructing the History of
                                  Large-Scale Genomic Changes: Biological
                                  Questions and Computational Challenges   879--893
              Seung-Jin Sul and   
            Tiffani L. Williams   Big Cat Phylogenies, Consensus Trees,
                                  and Computational Thinking . . . . . . . 895--906
                   Bahar Taneri   Is there Room for Ethics within
                                  Bioinformatics Education?  . . . . . . . 907--916
           Eugene V. Koonin and   
              Pere Puigb\`o and   
                   Yuri I. Wolf   Comparison of Phylogenetic Trees and
                                  Search for a Central Trend in the
                                  ``Forest of Life'' . . . . . . . . . . . 917--924

Journal of Computational Biology
Volume 18, Number 8, August, 2011

                  Yi-Kuo Yu and   
            Stephen F. Altschul   The Complexity of the Dirichlet Model
                                  for Multiple Alignment Data  . . . . . . 925--939
                  Xugang Ye and   
                  Yi-Kuo Yu and   
            Stephen F. Altschul   On the Inference of Dirichlet Mixture
                                  Priors for Protein Sequence Comparison   941--954
Bjarni V. Halldórsson and   
  Daníel F. Gudbjartsson   An Algorithm for Detecting High
                                  Frequency Copy Number Polymorphisms
                                  Using SNP Arrays . . . . . . . . . . . . 955--966
                  Sagi Snir and   
                   Lior Pachter   Tracing the Most Parsimonious Indel
                                  History  . . . . . . . . . . . . . . . . 967--986
                Valerio Freschi   Improved Biological Network
                                  Reconstruction Using Graph Laplacian
                                  Regularization . . . . . . . . . . . . . 987--996
                   B. Knapp and   
                 S. Frantal and   
                  M. Cibena and   
               W. Schreiner and   
                       P. Bauer   Is an Intuitive Convergence Definition
                                  of Molecular Dynamics Simulations Solely
                                  Based on the Root Mean Square Deviation
                                  Possible?  . . . . . . . . . . . . . . . 997--1005
       Jesun Sahariar Firoz and   
                Masud Hasan and   
          Ashik Zinnat Khan and   
                M. Sohel Rahman   The 1.375 Approximation Algorithm for
                                  Sorting by Transpositions Can Run in $
                                  O(n \log n) $ Time . . . . . . . . . . . 1007--1011
              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   DBCAT: Database of CpG Islands and
                                  Analytical Tools for Identifying
                                  Comprehensive Methylation Profiles in
                                  Cancer Cells . . . . . . . . . . . . . . 1013--1017

Journal of Computational Biology
Volume 18, Number 9, September, 2011

                      Anonymous   Preface: Satellite Workshop on
                                  Comparative Genomics, Research in
                                  Computational Molecular Biology
                                  (RECOMB-CG 2010) . . . . . . . . . . . . 1019--1021
             Roland Wittler and   
        Ján Ma\vnuch and   
           Murray Patterson and   
                     Jens Stoye   Consistency of Sequence-Based Gene
                                  Clusters . . . . . . . . . . . . . . . . 1023--1039
         A\"\ida Ouangraoua and   
         Krister M. Swenson and   
                  Cedric Chauve   A $2$-Approximation for the Minimum
                                  Duplication Speciation Problem . . . . . 1041--1053
                     Yu Lin and   
            Bernard M. E. Moret   A New Genomic Evolutionary Model for
                                  Rearrangements, Duplications, and Losses
                                  that Applies across Eukaryotes and
                                  Prokaryotes  . . . . . . . . . . . . . . 1055--1064
              Robert Warren and   
                  David Sankoff   Genome Aliquoting Revisited  . . . . . . 1065--1075
                  Minghui Jiang   The Zero Exemplar Distance Problem . . . 1077--1086
            Mukul S. Bansal and   
                  Guy Banay and   
          J. Peter Gogarten and   
                     Ron Shamir   Detecting Highways of Horizontal Gene
                                  Transfer . . . . . . . . . . . . . . . . 1087--1114
            Emmanuel Mongin and   
                  Ken Dewar and   
             Mathieu Blanchette   Mapping Association between Long-Range
                                  cis-Regulatory Regions and Their
                                  Target Genes Using Synteny . . . . . . . 1115--1130
                     Y. Lin and   
                   V. Rajan and   
                 B. M. E. Moret   Fast and Accurate Phylogenetic
                                  Reconstruction from High-Resolution
                                  Whole-Genome Data and a Novel Robustness
                                  Estimator  . . . . . . . . . . . . . . . 1131--1139
             Raluca Uricaru and   
            Alban Mancheron and   
                    Eric Rivals   Novel Definition and Algorithm for
                                  Chaining Fragments with Proportional
                                  Overlaps . . . . . . . . . . . . . . . . 1141--1154
             Hugo Devillers and   
  Hél\`ene Chiapello and   
             Sophie Schbath and   
               Meriem El Karoui   Robustness Assessment of Whole Bacterial
                                  Genome Segmentations . . . . . . . . . . 1155--1165
 Marília D. V. Braga and   
               Eyla Willing and   
                     Jens Stoye   Double Cut and Join with Insertions and
                                  Deletions  . . . . . . . . . . . . . . . 1167--1184
    Olivier Tremblay Savard and   
                Yves Gagnon and   
             Denis Bertrand and   
               Nadia El-Mabrouk   Genome Halving and Double Distance with
                                  Losses . . . . . . . . . . . . . . . . . 1185--1199
                 Ghada Badr and   
         Krister M. Swenson and   
                  David Sankoff   Listing All Parsimonious Reversal
                                  Sequences: New Algorithms and
                                  Perspectives . . . . . . . . . . . . . . 1201--1210
          Atheer A. Matroud and   
     Christopher P. Tuffley and   
               Michael D. Hendy   An Algorithm to Solve the Motif
                                  Alignment Problem for Approximate Nested
                                  Tandem Repeats in Biological Sequences   1211--1218
         A\"\ida Ouangraoua and   
              Anne Bergeron and   
             Krister M. Swenson   Theory and Practice of Ultra-Perfection  1219--1230
       Jakub Ková\vc and   
              Robert Warren and   
 Marília D. V. Braga and   
                     Jens Stoye   Restricted DCJ Model: Rearrangement
                                  Problems with Chromosome Reincorporation 1231--1241
        Ján Ma\vnuch and   
               Murray Patterson   The Complexity of the Gapped
                                  Consecutive-Ones Property Problem for
                                  Matrices of Bounded Maximum Degree . . . 1243--1253
                 Katharina Jahn   Efficient Computation of Approximate
                                  Gene Clusters Based on Reference
                                  Occurrences  . . . . . . . . . . . . . . 1255--1274

Journal of Computational Biology
Volume 18, Number 10, October, 2011

             Tatsuya Akutsu and   
         Avraham A. Melkman and   
            Takeyuki Tamura and   
                Masaki Yamamoto   Determining a Singleton Attractor of a
                                  Boolean Network with Nested Canalyzing
                                  Functions  . . . . . . . . . . . . . . . 1275--1290
             Alex Graudenzi and   
              Roberto Serra and   
              Marco Villani and   
             Chiara Damiani and   
          Annamaria Colacci and   
             Stuart A. Kauffman   Dynamical Properties of a Boolean Model
                                  of Gene Regulatory Network with Memory   1291--1303
             Joshua Collins and   
                Simone Linz and   
                 Charles Semple   Quantifying Hybridization in Realistic
                                  Time . . . . . . . . . . . . . . . . . . 1305--1318
  Emiliano Barreto-Hernadez and   
    Margarida Gama-Carvalho and   
                   Lisete Sousa   Pre-Processing Optimization of RNA
                                  Immunoprecipitation Microarray Data  . . 1319--1328
                   Hoon Kim and   
             John Watkinson and   
           Dimitris Anastassiou   Biomarker Discovery Using Statistically
                                  Significant Gene Sets  . . . . . . . . . 1329--1338
        Cédric Saule and   
    Mireille Régnier and   
         Jean-Marc Steyaert and   
                   Alain Denise   Counting RNA Pseudoknotted Structures    1339--1351
   Fabrício M. Lopes and   
      Roberto M. Cesar, Jr. and   
             Luciano Da F.Costa   Gene Expression Complex Networks:
                                  Synthesis, Identification, and Analysis  1353--1367

Journal of Computational Biology
Volume 18, Number 11, November, 2011

                   Vineet Bafna   Preface: Research in Computational
                                  Molecular Biology (RECOMB 2011)  . . . . 1369--1369
            Hosein Mohimani and   
               Wei-Ting Liu and   
              Yu-Liang Yang and   
  Susana P. Gaudêncio and   
            William Fenical and   
       Pieter C. Dorrestein and   
               Pavel A. Pevzner   Multiplex De Novo Sequencing of Peptide
                                  Antibiotics  . . . . . . . . . . . . . . 1371--1381
          Kerstin Scheubert and   
           Franziska Hufsky and   
             Florian Rasche and   
          Sebastian Böcker   Computing Fragmentation Trees from
                                  Metabolite Multiple Mass Spectrometry
                                  Data . . . . . . . . . . . . . . . . . . 1383--1397
       Mark D. M. Leiserson and   
                Diana Tatar and   
            Lenore J. Cowen and   
            Benjamin J. Hescott   Inferring Mechanisms of Compensation
                                  from E-MAP and SGA Data Using Local
                                  Search Algorithms for Max Cut  . . . . . 1399--1409
                     Xin Li and   
                        Jing Li   Haplotype Reconstruction in Large
                                  Pedigrees with Untyped Individuals
                                  through IBD Inference  . . . . . . . . . 1411--1421
               Tobias Petri and   
        Robert Küffner and   
                    Ralf Zimmer   Experiment Specific Expression Patterns  1423--1435
            Dana Silverbush and   
          Michael Elberfeld and   
                   Roded Sharan   Optimally Orienting Physical Networks    1437--1448
               Glenn Hickey and   
             Mathieu Blanchette   A Probabilistic Model for Sequence
                                  Alignment with Context-Sensitive Indels  1449--1464
Jérôme Waldispühl and   
                     Yann Ponty   An Unbiased Adaptive Sampling Algorithm
                                  for the Exploration of RNA Mutational
                                  Landscapes Under Evolutionary Pressure   1465--1479
         Bonnie Kirkpatrick and   
             Shuai Cheng Li and   
            Richard M. Karp and   
                  Eran Halperin   Pedigree Reconstruction Using Identity
                                  by Descent . . . . . . . . . . . . . . . 1481--1493
             Daniel Newkirk and   
            Jacob Biesinger and   
                 Alvin Chon and   
             Kyoko Yokomori and   
                    Xiaohui Xie   AREM: Aligning Short Reads from
                                  ChIP-Sequencing by Expectation
                                  Maximization . . . . . . . . . . . . . . 1495--1505
          Jeffrey W. Martin and   
             Anthony K. Yan and   
       Chris Bailey-Kellogg and   
                   Pei Zhou and   
                Bruce R. Donald   A Geometric Arrangement Algorithm for
                                  Structure Determination of Symmetric
                                  Protein Homo-Oligomers from NOEs and
                                  RDCs . . . . . . . . . . . . . . . . . . 1507--1523
                 Shay Zakov and   
              Yoav Goldberg and   
            Michael Elhadad and   
             Michal Ziv-ukelson   Rich Parameterization Improves RNA
                                  Structure Prediction . . . . . . . . . . 1525--1542
                     Yun Yu and   
               Tandy Warnow and   
                   Luay Nakhleh   Algorithms for MDC-Based Multi-Locus
                                  Phylogeny Inference: Beyond Rooted
                                  Binary Gene Trees on Single Alleles  . . 1543--1559
                Sinan Erten and   
               Gurkan Bebek and   
           Mehmet Koyutürk   Vavien: an Algorithm for Prioritizing
                                  Candidate Disease Genes Based on
                                  Topological Similarity of Proteins in
                                  Interaction Networks . . . . . . . . . . 1561--1574
           Allison P. Heath and   
          George N. Bennett and   
               Lydia E. Kavraki   An Algorithm for Efficient
                                  Identification of Branched Metabolic
                                  Pathways . . . . . . . . . . . . . . . . 1575--1597
              Navodit Misra and   
               Guy Blelloch and   
                    R. Ravi and   
               Russell Schwartz   An Optimization-Based Sampling Scheme
                                  for Phylogenetic Trees . . . . . . . . . 1599--1609
               Jae Hoon Sul and   
                   Buhm Han and   
                  Eleazar Eskin   Increasing Power of Groupwise
                                  Association Test with Likelihood Ratio
                                  Test . . . . . . . . . . . . . . . . . . 1611--1624
              Paul Medvedev and   
                   Son Pham and   
              Mark Chaisson and   
               Glenn Tesler and   
                  Pavel Pevzner   Paired de Bruijn Graphs: a Novel
                                  Approach for Incorporating Mate Pair
                                  Information into Genome Assemblers . . . 1625--1634
            Solomon Shenker and   
       Charles W. O'Donnell and   
           Srinivas Devadas and   
              Bonnie Berger and   
Jérôme Waldispühl   Efficient Traversal of Beta-Sheet
                                  Protein Folding Pathways Using Ensemble
                                  Models . . . . . . . . . . . . . . . . . 1635--1647
         Fabian L. Wauthier and   
          Michael I. Jordan and   
                  Nebojsa Jojic   Nonparametric Combinatorial Sequence
                                  Models . . . . . . . . . . . . . . . . . 1649--1660
              Jianyang Zeng and   
            Kyle E. Roberts and   
                   Pei Zhou and   
           Bruce Randall Donald   A Bayesian Approach for Determining
                                  Protein Side-Chain Rotamer Conformations
                                  Using Unassigned NOE Data  . . . . . . . 1661--1679
                   Song Gao and   
              Wing-Kin Sung and   
             Niranjan Nagarajan   Opera: Reconstructing Optimal Genomic
                                  Scaffolds with High-Throughput
                                  Paired-End Sequences . . . . . . . . . . 1681--1691
                     Wei Li and   
              Jianxing Feng and   
                      Tao Jiang   IsoLasso: a LASSO Regression Approach to
                                  RNA-Seq Based Transcriptome Assembly . . 1693--1707
                Tien-Ho Lin and   
             Ziv Bar-Joseph and   
               Robert F. Murphy   Learning Cellular Sorting Pathways Using
                                  Protein Interactions and Sequence Motifs 1709--1722
                 Amnon Amir and   
                         Or Zuk   Bacterial Community Reconstruction Using
                                  Compressed Sensing . . . . . . . . . . . 1723--1741
           Andrew S. Parker and   
           Karl E. Griswold and   
           Chris Bailey-Kellogg   Optimization of Combinatorial
                                  Mutagenesis  . . . . . . . . . . . . . . 1743--1756

Journal of Computational Biology
Volume 18, Number 12, December, 2011

          Himanshu Chandola and   
             Anthony K. Yan and   
             Shobha Potluri and   
            Bruce R. Donald and   
           Chris Bailey-Kellogg   NMR Structural Inference of Symmetric
                                  Homo-Oligomers . . . . . . . . . . . . . 1757--1775
             Jiun-Rung Chen and   
                    Ye-In Chang   An Up-Down Bit Pattern Approach to
                                  Coregulated and Negative-Coregulated
                                  Gene Clustering of Microarray Data . . . 1777--1791
            Markus E. Nebel and   
        Christian M. Reidys and   
                   Rita R. Wang   Loops in Canonical RNA Pseudoknot
                                  Structures . . . . . . . . . . . . . . . 1793--1806
            Rafa\l Adamczak and   
          Jaroslaw Pillardy and   
           Brinda K. Vallat and   
                Jaroslaw Meller   Fast Geometric Consensus Approach for
                                  Protein Model Quality Assessment . . . . 1807--1818
               Matteo Comin and   
                Davide Verzotto   The Irredundant Class Method for Remote
                                  Homology Detection of Protein Sequences  1819--1829
               Meng-Rong Li and   
                  Yu-Ju Lin and   
               Tzong-Hann Shieh   The Flux Model of the Movement of Tumor
                                  Cells and Healthy Cells Using a System
                                  of Nonlinear Heat Equations  . . . . . . 1831--1839


Journal of Computational Biology
Volume 19, Number 1, January, 2012

             Hugo Devillers and   
                 Sophie Schbath   Separating Significant Matches from
                                  Spurious Matches in DNA Sequences  . . . 1--12
     Afshin Fayyaz Movaghar and   
           Guillaume Launay and   
             Sophie Schbath and   
Jean-François Gibrat and   
       François Rodolphe   Statistical Significance of Threading
                                  Scores . . . . . . . . . . . . . . . . . 13--29
              Guy Karlebach and   
                     Ron Shamir   Constructing Logical Models of Gene
                                  Regulatory Networks by Integrating
                                  Transcription Factor--DNA Interactions
                                  with Expression Data: an Entropy-Based
                                  Approach . . . . . . . . . . . . . . . . 30--41
                 Xiguo Yuan and   
            David J. Miller and   
              Junying Zhang and   
           David Herrington and   
                       Yue Wang   An Overview of Population Genetic Data
                                  Simulation . . . . . . . . . . . . . . . 42--54
              Ritsuko Onuki and   
                 Ryo Yamada and   
              Rui Yamaguchi and   
            Minoru Kanehisa and   
                 Tetsuo Shibuya   Population Model--Based Inter-Diplotype
                                  Similarity Measure for Accurate
                                  Diplotype Clustering . . . . . . . . . . 55--67
              Li-Yeh Chuang and   
            Cheng-Huei Yang and   
              Jung-Chike Li and   
                Cheng-Hong Yang   A Hybrid BPSO-CGA Approach for Gene
                                  Selection and Classification of
                                  Microarray Data  . . . . . . . . . . . . 68--82
              Pawe\l Winter and   
                 Rasmus Fonseca   Adjustable Chain Trees for Proteins  . . 83--99

Journal of Computational Biology
Volume 19, Number 2, February, 2012

            Andrea Califano and   
             Manolis Kellis and   
            Gustavo Stolovitzky   Preface: RECOMB Systems Biology,
                                  Regulatory Genomics, and DREAM 2011
                                  Special Issue  . . . . . . . . . . . . . 101--101
   Emanuel Gonçalves and   
                Rui Pereira and   
               Isabel Rocha and   
                   Miguel Rocha   Optimization Approaches for the \em In
                                  Silico Discovery of Optimal Targets for
                                  Gene Over/Underexpression  . . . . . . . 102--114
                      Roee Amit   Anti-Cooperative and Cooperative
                                  Protein-Protein Interactions between
                                  TetR Isoforms on Synthetic Enhancers . . 115--125
          Thomas Sakoparnig and   
            Tobias Kockmann and   
                Renato Paro and   
           Christian Beisel and   
              Niko Beerenwinkel   Binding Profiles of Chromatin-Modifying
                                  Proteins Are Predictive for
                                  Transcriptional Activity and
                                  Promoter-Proximal Pausing  . . . . . . . 126--138
          Nnamdi E. Ihuegbu and   
             Gary D. Stormo and   
                  Jeremy Buhler   Fast, Sensitive Discovery of Conserved
                                  Genome-Wide Motifs . . . . . . . . . . . 139--147
            Carlo Cosentino and   
               Luca Salerno and   
           Antonio Passanti and   
             Alessio Merola and   
            Declan G. Bates and   
                Francesco Amato   Structural Bistability of the GAL
                                  Regulatory Network and Characterization
                                  of its Domains of Attraction . . . . . . 148--162
            Yael Silberberg and   
             Assaf Gottlieb and   
              Martin Kupiec and   
               Eytan Ruppin and   
                   Roded Sharan   Large-Scale Elucidation of Drug Response
                                  Pathways in Humans . . . . . . . . . . . 163--174
                 Xinyi Yang and   
           Jennifer E. Dent and   
              Christine Nardini   An $S$-System Parameter Estimation
                                  Method (SPEM) for Biological Networks    175--187
            Federica Eduati and   
         Barbara di Camillo and   
          Michael Karbiener and   
          Marcel Scheideler and   
              Davide Cor\`a and   
            Michele Caselle and   
                 Gianna Toffolo   Dynamic Modeling of miRNA-mediated
                                  Feed-Forward Loops . . . . . . . . . . . 188--199
             Alexandra Dana and   
                   Tamir Tuller   Efficient Manipulations of Synonymous
                                  Mutations for Controlling Translation
                                  Rate: an Analytical Approach . . . . . . 200--231
                Liram Vardi and   
               Eytan Ruppin and   
                   Roded Sharan   A Linearized Constraint-Based Approach
                                  for Modeling Signaling Networks  . . . . 232--240
                    Yi Wang and   
          Henry C. M. Leung and   
                  S. M. Yiu and   
             Francis Y. L. Chin   MetaCluster 4.0: a Novel Binning
                                  Algorithm for NGS Reads and Huge Number
                                  of Species . . . . . . . . . . . . . . . 241--249

Journal of Computational Biology
Volume 19, Number 3, March, 2012

                   Kai Song and   
                   Ze Zhang and   
              Tuo-Peng Tong and   
                        Fang Wu   Classifier Assessment and Feature
                                  Selection for Recognizing Short Coding
                                  Sequences of Human Genes . . . . . . . . 251--260
            Alberto Ceselli and   
     Sandro Luciano Fornili and   
               Giovanni Righini   Algorithms for the Design of Maximum
                                  Hydropathic Complementarity Molecules    261--270
              Olivier David and   
    Catherine Larédo and   
       Raphaël Leblois and   
         Brigitte Schaeffer and   
                 Nicolas Vergne   Coalescent-Based DNA Barcoding:
                                  Multilocus Analysis and Robustness . . . 271--278
            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   Computational Techniques for Human
                                  Genome Resequencing Using Mated Gapped
                                  Reads  . . . . . . . . . . . . . . . . . 279--292
            Ethan M. Jewett and   
              Noah A. Rosenberg   iGLASS: an Improvement to the GLASS
                                  Method for Estimating Species Trees from
                                  Gene Trees . . . . . . . . . . . . . . . 293--315
       Nikita A. Sakhanenko and   
                 David J. Galas   Probabilistic Logic Methods and Some
                                  Applications to Biology and Medicine . . 316--336

Journal of Computational Biology
Volume 19, Number 4, April, 2012

                  Banu Dost and   
              Nuno Bandeira and   
               Xiangqian Li and   
               Zhouxin Shen and   
           Steven P. Briggs and   
                   Vineet Bafna   Accurate Mass Spectrometry Based Protein
                                  Quantification via Shared Peptides . . . 337--348
Sébastien Li-Thiao-Té and   
              Benno Schwikowski   Feature Detection with Controlled Error
                                  Rates in LC/MS Images  . . . . . . . . . 349--364
          Thomas K. F. Wong and   
                      S. M. Yiu   Structural Alignment of RNA with Triple
                                  Helix Structure  . . . . . . . . . . . . 365--378
   Aleksandar Stojmirovi\'c and   
                      Yi-kuo Yu   Information Flow in Interaction Networks
                                  II: Channels, Path Lengths, and
                                  Potentials . . . . . . . . . . . . . . . 379--403
                  Yen Hung Chen   The $k$ Partition-Distance Problem . . . 404--417
               Serena Arima and   
                  Luca Tardella   Improved Harmonic Mean Estimator for
                                  Phylogenetic Model Evidence  . . . . . . 418--438
               Arvind Gupta and   
        Ján Ma\vnuch and   
            Ladislav Stacho and   
                  Xiaohong Zhao   Algorithm for Haplotype Inference via
                                  Galled-Tree Networks with Simple Galls   439--454

Journal of Computational Biology
Volume 19, Number 5, May, 2012

            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   SPAdes: a New Genome Assembly Algorithm
                                  and Its Applications to Single-Cell
                                  Sequencing . . . . . . . . . . . . . . . 455--477
            Deepayan Sarkar and   
            Steve Goldstein and   
          David C. Schwartz and   
              Michael A. Newton   Statistical Significance of Optical Map
                                  Alignments . . . . . . . . . . . . . . . 478--492
              Genki Terashi and   
             Tetsuo Shibuya and   
          Mayuko Takeda-Shitaka   LB3D: a Protein Three-Dimensional
                                  Substructure Search Program Based on the
                                  Lower Bound of a Root Mean Square
                                  Deviation Value  . . . . . . . . . . . . 493--503
          Nimrod Bar-Yaakov and   
            Zehava Grossman and   
                Nathan Intrator   Using Iterative Ridge Regression to
                                  Explore Associations Between Conditioned
                                  Variables  . . . . . . . . . . . . . . . 504--518
           Mikael Falconnet and   
                  Sarah Behrens   Accurate Estimations of Evolutionary
                                  Times in the Context of Strong CpG
                                  Hypermutability  . . . . . . . . . . . . 519--531
            Michiaki Hamada and   
                   Kiyoshi Asai   A Classification of Bioinformatics
                                  Algorithms from the Viewpoint of
                                  Maximizing Expected Accuracy (MEA) . . . 532--549
              Sarah Behrens and   
               Cyril Nicaud and   
              Pierre Nicod\`eme   An Automaton Approach for Waiting Times
                                  in DNA Evolution . . . . . . . . . . . . 550--562
     Maysson Al-Haj Ibrahim and   
               Sabah Jassim and   
  Michael Anthony Cawthorne and   
              Kenneth Langlands   A Topology-Based Score for Pathway
                                  Enrichment . . . . . . . . . . . . . . . 563--573

Journal of Computational Biology
Volume 19, Number 6, June, 2012

                  Ting Chen and   
              Paul Marjoram and   
                Fengzhu Sun and   
         Jasmine Xianghong Zhou   Preface: Special Issue . . . . . . . . . 575--576
               Derek Aguiar and   
                  Sorin Istrail   HapCompass: a Fast Cycle Basis Algorithm
                                  for Accurate Haplotype Assembly of
                                  Sequence Data  . . . . . . . . . . . . . 577--590
     Md. Shamsuzzoha Bayzid and   
                   Tandy Warnow   Estimating Optimal Species Trees from
                                  Incomplete Gene Trees Under Deep
                                  Coalescence  . . . . . . . . . . . . . . 591--605
            Zachary Frazier and   
                    Frank Alber   A Computational Approach to Increase
                                  Time Scales in Brownian Dynamics--Based
                                  Reaction-Diffusion Modeling  . . . . . . 606--618
                Qinghui Gao and   
               Christine Ho and   
                Yingmin Jia and   
          Jingyi Jessica Li and   
                   Haiyan Huang   Biclustering of Linear Patterns In Gene
                                  Expression Data  . . . . . . . . . . . . 619--631
          Laura J. Helmkamp and   
            Ethan M. Jewett and   
              Noah A. Rosenberg   Improvements to a Class of Distance
                                  Matrix Methods for Inferring Species
                                  Trees from Gene Trees  . . . . . . . . . 632--649
                 Paul Joyce and   
                  Alan Genz and   
              Erkan Ozge Buzbas   Efficient Simulation and Likelihood
                                  Methods for Non-Neutral Multi-Allele
                                  Models . . . . . . . . . . . . . . . . . 650--661
            Marcus Kinsella and   
                   Vineet Bafna   Combinatorics of the
                                  Breakage--Fusion--Bridge Mechanism . . . 662--678
                    Yinglei Lai   Change-Point Analysis of Paired
                                  Allele-Specific Copy Number Variation
                                  Data . . . . . . . . . . . . . . . . . . 679--693
                  Ofer Lavi and   
                Gideon Dror and   
                     Ron Shamir   Network-Induced Classification Kernels
                                  for Gene Expression Profile Analysis . . 694--709
                 Wenyuan Li and   
                   Chao Dai and   
               Chun-Chi Liu and   
         Xianghong Jasmine Zhou   Algorithm to Identify Frequent Coupled
                                  Modules from Two-Layered Network Series:
                                  Application to Study Transcription and
                                  Splicing Coupling  . . . . . . . . . . . 710--730
                     Li Luo and   
                    Yun Zhu and   
                   Momiao Xiong   A Novel Genome-Information Content-Based
                                  Statistic for Genome-Wide Association
                                  Analysis Designed for Next-Generation
                                  Sequencing Data  . . . . . . . . . . . . 731--744
        Ioanna Manolopoulou and   
               Brent C. Emerson   Phylogeographic Ancestral Inference
                                  Using the Coalescent Model on Haplotype
                                  Trees  . . . . . . . . . . . . . . . . . 745--755
               Mary Sara McPeek   BLUP Genotype Imputation for
                                  Case-Control Association Testing with
                                  Related Individuals and Missing Data . . 756--765
                 Shengyu Ni and   
                 Martin Vingron   R2KS: a Novel Measure for Comparing Gene
                                  Expression Based on Ranked Gene Lists    766--775
               Dhruv Grover and   
            Juan Nunez-Iglesias   Betamax: Towards Optimal Sampling
                                  Strategies for High-Throughput Screens   776--784
                 Tiago Rito and   
         Charlotte M. Deane and   
                 Gesine Reinert   The Importance of Age and High Degree,
                                  in Protein-Protein Interaction Networks  785--795
             Sophie Schbath and   
    Véronique Martin and   
          Matthias Zytnicki and   
             Julien Fayolle and   
              Valentin Loux and   
    Jean-François Gibrat   Mapping Reads on a Genomic Sequence: an
                                  Algorithmic Overview and a Practical
                                  Comparative Analysis . . . . . . . . . . 796--813
               Mingjie Wang and   
                  Yuzhen Ye and   
                     Haixu Tang   A \em de Bruijn Graph Approach to the
                                  Quantification of Closely-Related
                                  Genomes in a Microbial Community . . . . 814--825
                  Jialin Xu and   
                       Yu Zhang   A Generalized Linear Model for Peak
                                  Calling in ChIP-Seq Data . . . . . . . . 826--838
               Zhiyuan Zhai and   
             Gesine Reinert and   
                   Kai Song and   
        Michael S. Waterman and   
                 Yihui Luan and   
                    Fengzhu Sun   Normal and Compound Poisson
                                  Approximations for Pattern Occurrences
                                  in NGS Reads . . . . . . . . . . . . . . 839--854
                 Jing Zhang and   
              C.-C. Jay Kuo and   
                     Liang Chen   VERSE: a Varying Effect Regression for
                                  Splicing Elements Discovery  . . . . . . 855--865

Journal of Computational Biology
Volume 19, Number 7, July, 2012

          Hillary S. W. Han and   
            Christian M. Reidys   The 5'-3' Distance of RNA Secondary
                                  Structures . . . . . . . . . . . . . . . 867--878
             Pawe\l Gniewek and   
           Andrzej Kolinski and   
                  Dominik Gront   Optimization of Profile-to-Profile
                                  Alignment Parameters for One-Dimensional
                                  Threading  . . . . . . . . . . . . . . . 879--886
          Torben Tvedebrink and   
        Poul Svante Eriksen and   
       Helle Smidt Mogensen and   
                  Niels Morling   Identifying Contributors of DNA Mixtures
                                  by Means of Quantitative Information of
                                  STR Typing . . . . . . . . . . . . . . . 887--902
                  Yichao He and   
                Haiyan Tian and   
                Xinlu Zhang and   
                Zhiwei Wang and   
                    Suogang Gao   Nonadaptive Algorithms for Threshold
                                  Group Testing with Inhibitors and
                                  Error-Tolerance  . . . . . . . . . . . . 903--910
               Fabio Cunial and   
             Alberto Apostolico   Phylogeny Construction with Rigid Gapped
                                  Motifs . . . . . . . . . . . . . . . . . 911--927
  Jòrgen E. Andersen and   
          Fenix W. D. Huang and   
           Robert C. Penner and   
            Christian M. Reidys   Topology of RNA-RNA Interaction
                                  Structures . . . . . . . . . . . . . . . 928--943

Journal of Computational Biology
Volume 19, Number 8, August, 2012

                 Eyal Cohen and   
                     Benny Chor   Detecting Phylogenetic Signals in
                                  Eukaryotic Whole Genome Sequences  . . . 945--956
                 Gangman Yi and   
            Michael R. Thon and   
                   Sing-Hoi Sze   Supervised Protein Family Classification
                                  and New Family Construction  . . . . . . 957--967
                   Elias August   Using Noise for Model-Testing  . . . . . 968--977
            Matthew Sperrin and   
                    Thomas Jaki   Recovering Independent Associations in
                                  Genetics: a Comparison . . . . . . . . . 978--987

Journal of Computational Biology
Volume 19, Number 9, September, 2012

              Hamid Bolouri and   
                Walter L. Ruzzo   Integration of 198 ChIP-seq Datasets
                                  Reveals Human \em cis-Regulatory Regions 989--997
         Bonnie Kirkpatrick and   
               Yakir Reshef and   
            Hilary Finucane and   
               Haitao Jiang and   
                 Binhai Zhu and   
                Richard M. Karp   Comparing Pedigree Graphs  . . . . . . . 998--1014
         M. González and   
        C. Gutiérrez and   
             R. Martínez   Expectation-Maximization Algorithm for
                                  Determining Natural Selection of
                                  Y-Linked Genes Through Two-Sex Branching
                                  Processes  . . . . . . . . . . . . . . . 1015--1026
                     Min Wu and   
                 Xiao-li Li and   
            Chee-Keong Kwoh and   
               See-Kiong Ng and   
                   Limsoon Wong   Discovery of Protein Complexes with
                                  Core-Attachment Structures from Tandem
                                  Affinity Purification (TAP) Data . . . . 1027--1042
        M. Shahriar Hossain and   
               Monika Akbar and   
              Nicholas F. Polys   Narratives in the Network: Interactive
                                  Methods for Mining Cell Signaling
                                  Networks . . . . . . . . . . . . . . . . 1043--1059
        Christina Schindler and   
            Wolfgang B. Fischer   Sequence Alignment of Viral Channel
                                  Proteins with Cellular Ion Channels  . . 1060--1072
                    Yun Cui and   
             Jesper Jansson and   
                  Wing-Kin Sung   Polynomial-Time Algorithms for Building
                                  a Consensus MUL-Tree . . . . . . . . . . 1073--1088

Journal of Computational Biology
Volume 19, Number 10, October, 2012

                Tomoya Mori and   
            Takeyuki Tamura and   
             Daiji Fukagawa and   
            Atsuhiro Takasu and   
              Etsuji Tomita and   
                 Tatsuya Akutsu   A Clique-Based Method Using Dynamic
                                  Programming for Computing Edit Distance
                                  Between Unordered Trees  . . . . . . . . 1089--1104
          Hillary S. W. Han and   
            Christian M. Reidys   A Phase Transition in Energy-Filtered
                                  RNA Secondary Structures . . . . . . . . 1105--1119
           Azadeh Saffarian and   
             Mathieu Giraud and   
           Antoine de Monte and   
         Hél\`ene Touzet   RNA Locally Optimal Secondary Structures 1120--1133
            Markus E. Nebel and   
                 Frank Weinberg   Algebraic and Combinatorial Properties
                                  of Common RNA Pseudoknot Classes with
                                  Applications . . . . . . . . . . . . . . 1134--1150
           Huwaida S. Rabie and   
                Ian W. Saunders   A Simulation Study to Assess a Variable
                                  Selection Method for Selecting Single
                                  Nucleotide Polymorphisms Associated with
                                  Disease  . . . . . . . . . . . . . . . . 1151--1161
               Rajat S. Roy and   
              Kevin C. Chen and   
        Anirvan M. Sengupta and   
              Alexander Schliep   SLIQ: Simple Linear Inequalities for
                                  Efficient Contig Scaffolding . . . . . . 1162--1175
          Narendra M. Dixit and   
          Piyush Srivastava and   
            Nisheeth K. Vishnoi   A Finite Population Model of Molecular
                                  Evolution: Theory and Computation  . . . 1176--1202
             Rasmus Fonseca and   
                  Pawe\l Winter   Bounding Volumes for Proteins: a
                                  Comparative Study  . . . . . . . . . . . 1203--1213

Journal of Computational Biology
Volume 19, Number 11, November, 2012

                   I-Lin Lu and   
                  Hsiuying Wang   Protein-specific Scoring Method for
                                  Ligand Discovery . . . . . . . . . . . . 1215--1226
         Celine Scornavacca and   
                Simone Linz and   
              Benjamin Albrecht   A First Step Toward Computing All
                                  Hybridization Networks For Two Rooted
                                  Binary Phylogenetic Trees  . . . . . . . 1227--1242
                    M. Veselsky   Order of Precedence and Age of Y-DNA
                                  Haplotypes . . . . . . . . . . . . . . . 1243--1250
                   M. Ehler and   
                  F. Filbir and   
                  H. N. Mhaskar   Locally Learning Biomedical Data Using
                                  Diffusion Frames . . . . . . . . . . . . 1251--1264

Journal of Computational Biology
Volume 19, Number 12, December, 2012

                Michiaki Hamada   Direct Updating of an RNA Base-Pairing
                                  Probability Matrix with Marginal
                                  Probability Constraints  . . . . . . . . 1265--1276
          Hiroshi Toyoizumi and   
                Hideo Tsubouchi   Estimating the Number of Double-Strand
                                  Breaks Formed During Meiosis from
                                  Partial Observation  . . . . . . . . . . 1277--1283
                Jia-Hao Fan and   
                Jianer Chen and   
                   Sing-Hoi Sze   Identifying Complexes from Protein
                                  Interaction Networks According to
                                  Different Types of Neighborhood Density  1284--1294
                   R. Reyes and   
               D. Gamermann and   
                A. Montagud and   
                  D. Fuente and   
                  J. Triana and   
    J. F. Urchueguía and   
P. Fernández de Córdoba   Automation on the Generation of
                                  Genome-Scale Metabolic Models  . . . . . 1295--1306
           Young Hwan Chang and   
                   Joe Gray and   
                  Claire Tomlin   Optimization-based Inference for
                                  Temporally Evolving Networks with
                                  Applications in Biology  . . . . . . . . 1307--1323
                Baikang Pei and   
                  Dong-Guk Shin   Reconstruction of Biological Networks by
                                  Incorporating Prior Knowledge into
                                  Bayesian Network Models  . . . . . . . . 1324--1334


Journal of Computational Biology
Volume 20, Number 1, January, 2013

             Viet-An Nguyen and   
         Jordan Boyd-Graber and   
            Stephen F. Altschul   Dirichlet Mixtures, the Dirichlet
                                  Process, and the Structure of Protein
                                  Space  . . . . . . . . . . . . . . . . . 1--18
              Lianping Yang and   
              Xiangde Zhang and   
              Tianming Wang and   
                      Hegui Zhu   Large Local Analysis of the Unaligned
                                  Genome and Its Application . . . . . . . 19--29
        Guilherme P. Telles and   
           Nalvo F. Almeida and   
             Rosane Minghim and   
      Maria Emilia M. T. Walter   Live Phylogeny . . . . . . . . . . . . . 30--37
             Zhi-Zhong Chen and   
                   Lusheng Wang   An Ultrafast Tool for Minimum Reticulate
                                  Networks . . . . . . . . . . . . . . . . 38--41
                 Hong Huang and   
                      Yongji Li   MASTtreedist: Visualization of Tree
                                  Space Based on Maximum Agreement Subtree 42--49
        Elizabeth S. Allman and   
            James H. Degnan and   
                 John A. Rhodes   Species Tree Inference by the STAR
                                  Method and Its Generalizations . . . . . 50--61

Journal of Computational Biology
Volume 20, Number 2, February, 2013

                     Benny Chor   Preface: RECOMB 2012 . . . . . . . . . . 63--63
                   Kai Song and   
                    Jie Ren and   
               Zhiyuan Zhai and   
                 Xuemei Liu and   
               Minghua Deng and   
                    Fengzhu Sun   Alignment-Free Sequence Comparison Based
                                  on Next-Generation Sequencing Reads  . . 64--79
                     Dan He and   
                   Buhm Han and   
                  Eleazar Eskin   Hap-seq: an Optimal Algorithm for
                                  Haplotype Phasing with Imputation Using
                                  Sequencing Data  . . . . . . . . . . . . 80--92
             Sebastien Roch and   
                      Sagi Snir   Recovering the Treelike Trend of
                                  Evolution Despite Extensive Lateral
                                  Genetic Transfer: a Probabilistic
                                  Analysis . . . . . . . . . . . . . . . . 93--112
          Armin Töpfer and   
            Osvaldo Zagordi and   
        Sandhya Prabhakaran and   
                Volker Roth and   
              Eran Halperin and   
              Niko Beerenwinkel   Probabilistic Inference of Viral
                                  Quasispecies Subject to Recombination    113--123
             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   Simultaneous Reconstruction of Multiple
                                  Signaling Pathways via the
                                  Prize-Collecting Steiner Forest Problem  124--136
                      Lu He and   
               Fabio Vandin and   
          Gopal Pandurangan and   
           Chris Bailey-Kellogg   Ballast: a Ball-based Algorithm for
                                  Structural Motifs  . . . . . . . . . . . 137--151
           Andrew S. Parker and   
               Yoonjoo Choi and   
           Karl E. Griswold and   
           Chris Bailey-Kellogg   Structure-Guided Deimmunization of
                                  Therapeutic Proteins . . . . . . . . . . 152--165

Journal of Computational Biology
Volume 20, Number 3, March, 2013

                  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   A Robust Method for Transcript
                                  Quantification with RNA-Seq Data . . . . 167--187
              Stefan Canzar and   
          Mohammed El-Kebir and   
           René Pool and   
          Khaled Elbassioni and   
       Alpeshkumar K. Malde and   
               Alan E. Mark and   
             Daan P. Geerke and   
               Leen Stougie and   
                 Gunnar W. Klau   Charge Group Partitioning in
                                  Biomolecular Simulation  . . . . . . . . 188--198
         Jesse M. Rodriguez and   
            Sivan Bercovici and   
               Megan Elmore and   
              Serafim Batzoglou   Ancestry Inference in Complex Admixtures
                                  via Variable-length Markov Chain Linkage
                                  Models . . . . . . . . . . . . . . . . . 199--211
              Daniel Holtby and   
             Shuai Cheng Li and   
                        Ming Li   LoopWeaver: Loop Modeling by the
                                  Weighted Scaling of Verified Proteins    212--223
              Zhanyong Wang and   
         Farhad Hormozdiari and   
               Wen-Yun Yang and   
              Eran Halperin and   
                  Eleazar Eskin   CNVeM: Copy Number Variation Detection
                                  Using Uncertainty of Read Mapping  . . . 224--236
              ZhiZhuo Zhang and   
            Cheng Wei Chang and   
                 Willy Hugo and   
               Edwin Cheung and   
                  Wing-Kin Sung   Simultaneously Learning DNA Motif Along
                                  with Its Position and Sequence Rank
                                  Preferences Through Expectation
                                  Maximization Algorithm . . . . . . . . . 237--248
               Roded Sharan and   
                Richard M. Karp   Reconstructing Boolean Models of
                                  Signaling  . . . . . . . . . . . . . . . 249--257

Journal of Computational Biology
Volume 20, Number 4, April, 2013

            John Kececioglu and   
                   Dan DeBlasio   Accuracy Estimation and Parameter
                                  Advising for Protein Multiple Sequence
                                  Alignment  . . . . . . . . . . . . . . . 259--279
           Patrick Holloway and   
            Krister Swenson and   
               David Ardell and   
               Nadia El-Mabrouk   Ancestral Genome Organization: an
                                  Alignment Approach . . . . . . . . . . . 280--295
            Babak Alipanahi and   
            Nathan Krislock and   
                 Ali Ghodsi and   
            Henry Wolkowicz and   
            Logan Donaldson and   
                        Ming Li   Determining Protein Structures from
                                  NOESY Distance Constraints by
                                  Semidefinite Programming . . . . . . . . 296--310
                 Imran Rauf and   
             Florian Rasche and   
    François Nicolas and   
          Sebastian Böcker   Finding Maximum Colorful Subtrees in
                                  Practice . . . . . . . . . . . . . . . . 311--321
                   Hua Wang and   
                 Heng Huang and   
                     Chris Ding   Function--Function Correlated
                                  Multi-label Protein Function Prediction
                                  over Interaction Networks  . . . . . . . 322--343
                   Hua Wang and   
                 Heng Huang and   
                 Chris Ding and   
                    Feiping Nie   Predicting Protein--Protein Interactions
                                  from Multimodal Biological Data Sources
                                  via Nonnegative Matrix Tri-Factorization 344--358
                Son K. Pham and   
             Dmitry Antipov and   
         Alexander Sirotkin and   
               Glenn Tesler and   
           Pavel A. Pevzner and   
               Max A. Alekseyev   Pathset Graphs: a Novel Approach for
                                  Comprehensive Utilization of Paired
                                  Reads in Genome Assembly . . . . . . . . 359--371

Journal of Computational Biology
Volume 20, Number 5, May, 2013

            Andrea Califano and   
             Manolis Kellis and   
            Gustavo Stolovitzky   Preface: RECOMB Systems Biology,
                                  Regulatory Genomics, and DREAM 2012
                                  Special Issue  . . . . . . . . . . . . . 373--374
            Yaron Orenstein and   
                  Eran Mick and   
                     Ron Shamir   RAP: Accurate and Fast Motif Finding
                                  Based on Protein-Binding Microarray Data 375--382
         Roberto Pagliarini and   
              Diego di Bernardo   A Genome-Scale Modeling Approach to
                                  Study Inborn Errors of Liver Metabolism:
                                  Toward an In Silico Patient  . . . . . . 383--397
     Andreas Tjärnberg and   
Torbjörn E. M. Nordling and   
            Matthew Studham and   
          Erik L. L. Sonnhammer   Optimal Sparsity Criteria for Network
                                  Inference  . . . . . . . . . . . . . . . 398--408
      Christopher L. Poirel and   
       Richard R. Rodrigues and   
          Katherine C. Chen and   
              John J. Tyson and   
                   T. M. Murali   Top-Down Network Analysis to Drive
                                  Bottom-Up Modeling of Physiological
                                  Processes  . . . . . . . . . . . . . . . 409--418

Journal of Computational Biology
Volume 20, Number 6, June, 2013

             Emmanuel Faure and   
          Isabelle S. Peter and   
               Eric H. Davidson   A New Software Package for Predictive
                                  Gene Regulatory Network Modeling and
                                  Redesign . . . . . . . . . . . . . . . . 419--423
            Franco P. Preparata   On Contigs and Coverage  . . . . . . . . 424--432
             Michael Antosh and   
                  David Fox and   
             Leon N. Cooper and   
                 Nicola Neretti   CORaL: Comparison of Ranked Lists for
                                  Analysis of Gene Expression Data . . . . 433--443
              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   Bioinformatics Method to Analyze the
                                  Mechanism of Pancreatic Cancer Disorder  444--452
         Shruthi Prabhakara and   
            Raunaq Malhotra and   
                Raj Acharya and   
                      Mary Poss   Mutant-Bin: Unsupervised Haplotype
                                  Estimation of Viral Population Diversity
                                  Without Reference Genome . . . . . . . . 453--463
               Huilan Chang and   
                Hung-Lin Fu and   
                 ChiH-Huai Shih   Threshold Group Testing on Inhibitor
                                  Model  . . . . . . . . . . . . . . . . . 464--470

Journal of Computational Biology
Volume 20, Number 7, July, 2013

               Ehsan Behnam and   
        Michael S. Waterman and   
                Andrew D. Smith   A Geometric Interpretation for Local
                                  Alignment-Free Sequence Comparison . . . 471--485
          Hamidreza Chitsaz and   
     Elmirasadat Forouzmand and   
             Gholamreza Haffari   An Efficient Algorithm for Upper Bound
                                  on the Partition Function of Nucleic
                                  Acids  . . . . . . . . . . . . . . . . . 486--494
                   Jing Qin and   
            Christian M. Reidys   On Topological RNA Interaction
                                  Structures . . . . . . . . . . . . . . . 495--513
                   Yalu Wen and   
                    Ming Li and   
                 Wenjiang J. Fu   Catching the Genomic Wave in
                                  Oligonucleotide Single-Nucleotide
                                  Polymorphism Arrays by Modeling Sequence
                                  Binding  . . . . . . . . . . . . . . . . 514--523
                 Jaejik Kim and   
                   Jiaxu Li and   
Srirangapatnam G. Venkatesh and   
         Douglas S. Darling and   
            Grzegorz A. Rempala   Model Discrimination in Dynamic
                                  Molecular Systems: Application to
                                  Parotid De-differentiation Network . . . 524--539
          Henry C. M. Leung and   
               Siu-Ming Yiu and   
             John Parkinson and   
             Francis Y. L. Chin   IDBA-MT: \em De Novo Assembler for
                                  Metatranscriptomic Data Generated from
                                  Next-Generation Sequencing Technology    540--550

Journal of Computational Biology
Volume 20, Number 8, August, 2013

                Hoyt Koepke and   
             Elizabeth Thompson   Efficient Identification of Equivalences
                                  in Dynamic Graphs and Pedigree
                                  Structures . . . . . . . . . . . . . . . 551--570
           Mitsunori Kayano and   
                Seiya Imoto and   
              Rui Yamaguchi and   
                  Satoru Miyano   Multi-omics Approach for Estimating
                                  Metabolic Networks Using Low-Order
                                  Partial Correlations . . . . . . . . . . 571--582
             Steven Flygare and   
           Michael Campbell and   
           Robert Mars Ross and   
                Barry Moore and   
                   Mark Yandell   ImagePlane: an Automated Image Analysis
                                  Pipeline for High-Throughput Screens
                                  Using the Planarian \bionameSchmidtea
                                  mediterranea . . . . . . . . . . . . . . 583--592
         Emanuele Giaquinta and   
                    Laura Pozzi   An Effective Exact Algorithm and a New
                                  Upper Bound for the Number of Contacts
                                  in the Hydrophobic-Polar Two-Dimensional
                                  Lattice Model  . . . . . . . . . . . . . 593--609
            Lyamine Hedjazi and   
    Marie-Veronique Le Lann and   
          Tatiana Kempowsky and   
            Florence Dalenc and   
      Joseph Aguilar-Martin and   
                   Gilles Favre   Symbolic Data Analysis to Defy Low
                                  Signal-to-Noise Ratio in Microarray Data
                                  for Breast Cancer Prognosis  . . . . . . 610--620

Journal of Computational Biology
Volume 20, Number 9, September, 2013

         Emanuele Giaquinta and   
           Szymon Grabowski and   
                   Esko Ukkonen   Fast Matching of Transcription Factor
                                  Motifs Using Generalized Position Weight
                                  Matrix Models  . . . . . . . . . . . . . 621--630
           Janusz Dutkowski and   
                   Jerzy Tiuryn   A Probabilistic Model of Neutral and
                                  Selective Dynamics of Protein Network
                                  Evolution  . . . . . . . . . . . . . . . 631--642
           Sandro Andreotti and   
               Knut Reinert and   
                  Stefan Canzar   The Duplication-Loss Small Phylogeny
                                  Problem: From Cherries to Trees  . . . . 643--659
         Hervé Seligmann   Triplex DNA:RNA, 3'-to-5' Inverted RNA
                                  and Protein Coding in Mitochondrial
                                  Genomes  . . . . . . . . . . . . . . . . 660--671
          Guillaume Chapuis and   
            Olivier Filangi and   
          Jean-Michel Elsen and   
         Dominique Lavenier and   
                 Pascale Le Roy   Graphics Processing Unit--Accelerated
                                  Quantitative Trait Loci Detection  . . . 672--686
            Carl Nettelblad and   
            Behrang Mahjani and   
               Sverker Holmgren   Fast and Accurate Detection of Multiple
                                  Quantitative Trait Loci  . . . . . . . . 687--702
                  Xiayu Rao and   
                 Dejian Lai and   
                   Xuelin Huang   A New Method for Quantitative Real-Time
                                  Polymerase Chain Reaction Data Analysis  703--711

Journal of Computational Biology
Volume 20, Number 10, October, 2013

                    Fengzhu Sun   Preface: Research in Computational
                                  Molecular Biology (RECOMB 2013)  . . . . 713--713
                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   Assembling Single-Cell Genomes and
                                  Mini-Metagenomes From Chimeric MDA
                                  Products . . . . . . . . . . . . . . . . 714--737
            Mukul S. Bansal and   
                Eric J. Alm and   
                 Manolis Kellis   Reconciliation Revisited: Handling
                                  Multiple Optima when Reconciling with
                                  Duplication, Transfer, and Loss  . . . . 738--754
          William A. Bryant and   
              Ali A. Faruqi and   
                 John W. Pinney   Analysis of Metabolic Evolution in
                                  Bacteria Using Whole-Genome Metabolic
                                  Models . . . . . . . . . . . . . . . . . 755--764
                    Fei Guo and   
             Shuai Cheng Li and   
                   Wenji Ma and   
                   Lusheng Wang   Detecting Protein Conformational Changes
                                  in Interactions via Scaling Known
                                  Structures . . . . . . . . . . . . . . . 765--779
                     Dan He and   
              Zhanyong Wang and   
                   Buhm Han and   
               Laxmi Parida and   
                  Eleazar Eskin   IPED: Inheritance Path-based Pedigree
                                  Reconstruction Algorithm Using Genotype
                                  Data . . . . . . . . . . . . . . . . . . 780--791
                      Yufeng Wu   An Algorithm for Constructing
                                  Parsimonious Hybridization Networks with
                                  Multiple Phylogenetic Trees  . . . . . . 792--804
                    Dong Xu and   
                     Hua Li and   
                     Yang Zhang   Protein Depth Calculation and the Use
                                  for Improving Accuracy of Protein Fold
                                  Recognition  . . . . . . . . . . . . . . 805--816
               Emrah Kostem and   
                  Eleazar Eskin   Efficiently Identifying Significant
                                  Associations in Genome-wide Association
                                  Studies  . . . . . . . . . . . . . . . . 817--830

Journal of Computational Biology
Volume 20, Number 11, November, 2013

              ZhiZhuo Zhang and   
                Guoliang Li and   
              Kim-Chuan Toh and   
                  Wing-Kin Sung   $3$D Chromosome Modeling with
                                  Semi-Definite Programming and Hi-C Data  831--846
               Shijian Chen and   
                  Anqi Wang and   
                      Lei M. Li   SEME: a Fast Mapper of Illumina
                                  Sequencing Reads with Statistical
                                  Evaluation . . . . . . . . . . . . . . . 847--860
               Itamar Eskin and   
         Farhad Hormozdiari and   
                Lucia Conde and   
               Jacques Riby and   
       Christine F. Skibola and   
              Eleazar Eskin and   
                  Eran Halperin   eALPS: Estimating Abundance Levels in
                                  Pooled Sequencing Using Available
                                  Genotyping Data  . . . . . . . . . . . . 861--877
                   Lei Deng and   
                Jihong Guan and   
               Xiaoming Wei and   
                    Yuan Yi and   
      Qiangfeng Cliff Zhang and   
                  Shuigeng Zhou   Boosting Prediction Performance of
                                  Protein--Protein Interaction Hot Spots
                                  by Using Structural Neighborhood
                                  Properties . . . . . . . . . . . . . . . 878--891
             Kriti Puniyani and   
                   Eric P. Xing   NP-MuScL: Unsupervised Global Prediction
                                  of Interaction Networks from Multiple
                                  Data Sources . . . . . . . . . . . . . . 892--904
          Vladimir Reinharz and   
                 Yann Ponty and   
Jérôme Waldispühl   Using Structural and Evolutionary
                                  Information to Detect and Correct
                                  Pyrosequencing Errors in Noncoding RNAs  905--919
          Mohammad J. Sadeh and   
                Giusi Moffa and   
                   Rainer Spang   Considering Unknown Unknowns:
                                  Reconstruction of Nonconfoundable Causal
                                  Relations in Biological Networks . . . . 920--932
             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   Inference of Tumor Phylogenies with
                                  Improved Somatic Mutation Discovery  . . 933--944

Journal of Computational Biology
Volume 20, Number 12, December, 2013

                 Dima Blokh and   
                Danny Segev and   
                   Roded Sharan   The Approximability of Shortest
                                  Path-Based Graph Orientations of
                                  Protein--Protein Interaction Networks    945--957
         Avraham A. Melkman and   
                 Tatsuya Akutsu   An Improved Satisfiability Algorithm for
                                  Nested Canalyzing Functions and its
                                  Application to Determining a Singleton
                                  Attractor of a Boolean Network . . . . . 958--969
             Steven N. Hart and   
          Terry M. Therneau and   
                 Yuji Zhang and   
          Gregory A. Poland and   
             Jean-Pierre Kocher   Calculating Sample Size Estimates for
                                  RNA Sequencing Data  . . . . . . . . . . 970--978
                  Paul Kirk and   
             Aviva Witkover and   
      Charles R. M. Bangham and   
          Sylvia Richardson and   
         Alexandra M. Lewin and   
           Michael P. H. Stumpf   Balancing the Robustness and Predictive
                                  Performance of Biomarkers  . . . . . . . 979--989
                  Yuval Nov and   
           Alexander Fulton and   
              Karl-Erich Jaeger   Optimal Scanning of All Single-Point
                                  Mutants of a Protein . . . . . . . . . . 990--997


Journal of Computational Biology
Volume 21, Number 1, January, 2014

           Jakub Ková\vc   On the Complexity of Rearrangement
                                  Problems under the Breakpoint Distance   1--15
            Stefano Beretta and   
            Paola Bonizzoni and   
      Gianluca Della Vedova and   
                Yuri Pirola and   
                Raffaella Rizzi   Modeling Alternative Splicing Variants
                                  from RNA-Seq Data with Isoform Graphs    16--40
           Conrad J. Burden and   
              Paul Leopardi and   
            Sylvain Forêt   The Distribution of Word Matches Between
                                  Markovian Sequences with Periodic
                                  Boundary Conditions  . . . . . . . . . . 41--63
         A\"\ida Ouangraoua and   
               Mathieu Raffinot   On the Identification of Conflicting
                                  Contiguities in Ancestral Genome
                                  Reconstruction . . . . . . . . . . . . . 64--79
                Chuan-Xi Li and   
               Ru-Jing Wang and   
                  Peng Chen and   
                   He Huang and   
                       Ya-Ru Su   Interaction Relation Ontology Learning   80--88
      Pawe\l Górecki and   
              Oliver Eulenstein   DrML: Probabilistic Modeling of Gene
                                  Duplications . . . . . . . . . . . . . . 89--98

Journal of Computational Biology
Volume 21, Number 2, February, 2014

       Francesco Bartolucci and   
                Silvia Pandolfi   A New Constant Memory Recursion for
                                  Hidden Markov Models . . . . . . . . . . 99--117
             David J. Galas and   
       Nikita A. Sakhanenko and   
           Alexander Skupin and   
                   Tomasz Ignac   Describing the Complexity of Systems:
                                  Multivariable ``Set Complexity'' and the
                                  Information Basis of Systems Biology . . 118--140
               Junshan Wang and   
                 Ajay Jasra and   
                 Maria De Iorio   Computational Methods for a Class of
                                  Network Models . . . . . . . . . . . . . 141--161
               Wajdi Dhifli and   
                Rabie Saidi and   
         Engelbert Mephu Nguifo   Smoothing $3$D Protein Structure Motifs
                                  Through Graph Mining and Amino Acid
                                  Similarities . . . . . . . . . . . . . . 162--172
              Nissan Levtov and   
           Sandeep Amberkar and   
        Zakharia M. Frenkel and   
              Lars Kaderali and   
                 Zeev Volkovich   Detecting Non-Uniform Clusters in
                                  Large-Scale Interaction Graphs . . . . . 173--183

Journal of Computational Biology
Volume 21, Number 3, March, 2014

              Chaozhi Zheng and   
             Mary K. Kuhner and   
          Elizabeth A. Thompson   Joint Inference of Identity by Descent
                                  Along Multiple Chromosomes from
                                  Population Samples . . . . . . . . . . . 185--200
                  Yang Ding and   
          William A. Lorenz and   
                  Ivan Dotu and   
                Evan Senter and   
                    Peter Clote   Computing the Probability of RNA Hairpin
                                  and Multiloop Formation  . . . . . . . . 201--218
                Heewook Lee and   
               Ellen Popodi and   
         Patricia L. Foster and   
                     Haixu Tang   Detection of Structural Variants
                                  Involving Repetitive Regions in the
                                  Reference Genome . . . . . . . . . . . . 219--233
               Mu-Fen Hsieh and   
                   Sing-Hoi Sze   Finding Alignments of Conserved
                                  Graphlets in Protein Interaction
                                  Networks . . . . . . . . . . . . . . . . 234--246
        Dariusz Plewczynski and   
               Anna Philips and   
       Marcin Von Grotthuss and   
          Leszek Rychlewski and   
             Krzysztof Ginalski   HarmonyDOCK: The Structural Analysis of
                                  Poses in Protein-Ligand Docking  . . . . 247--256
            Guillermo Peris and   
           Andrés Marzal   Statistical Significance of Normalized
                                  Global Alignment . . . . . . . . . . . . 257--268
              Andrew F. Neuwald   A Bayesian Sampler for Optimization of
                                  Protein Domain Hierarchies . . . . . . . 269--286

Journal of Computational Biology
Volume 21, Number 4, April, 2014

              Andrew F. Neuwald   Evaluating, Comparing, and Interpreting
                                  Protein Domain Hierarchies . . . . . . . 287--302
             Lavanya Kannan and   
                Ward C. Wheeler   Exactly Computing the Parsimony Scores
                                  on Phylogenetic Networks Using Dynamic
                                  Programming  . . . . . . . . . . . . . . 303--319
                   Xun Wang and   
                  Ying Miao and   
                  Minquan Cheng   Finding Motifs in DNA Sequences Using
                                  Low-Dispersion Sequences . . . . . . . . 320--329
               Matteo Comin and   
                Montse Farreras   Parallel Continuous Flow: a Parallel
                                  Suffix Tree Construction Tool for Whole
                                  Genomes  . . . . . . . . . . . . . . . . 330--344
                Seyoung Kim and   
                   Eric P. Xing   Exploiting Genome Structure in
                                  Association Analysis . . . . . . . . . . 345--360
            Robert Hochberg and   
            Treena Larrew Milam   Data Structures for Parsimony
                                  Correlation and Biosequence Co-Evolution 361--369

Journal of Computational Biology
Volume 21, Number 5, May, 2014

            Andrea Califano and   
             Manolis Kellis and   
            Gustavo Stolovitzky   RECOMB/ISCB Systems Biology, Regulatory
                                  Genomics, and DREAM 2013 Special Issue   371--372
         Patrick K. O'Neill and   
              Robert Forder and   
                     Ivan Erill   Informational Requirements for
                                  Transcriptional Regulation . . . . . . . 373--384
               Zhiyong Wang and   
                   Jinbo Xu and   
                    Xinghua Shi   Finding Alternative Expression
                                  Quantitative Trait Loci by Exploring
                                  Sparse Model Space . . . . . . . . . . . 385--393
                Arnon Mazza and   
              Irit Gat-Viks and   
                   Roded Sharan   Elucidating Influenza Inhibition
                                  Pathways via Network Reconstruction  . . 394--404

Journal of Computational Biology
Volume 21, Number 6, June, 2014

             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   Joint Variant and \em De Novo Mutation
                                  Identification on Pedigrees from
                                  High-Throughput Sequencing Data  . . . . 405--419
                     Wei Hu and   
                        John Hu   Prediction of siRNA Potency Using Sparse
                                  Logistic Regression  . . . . . . . . . . 420--427
             Sebastian Klie and   
            Zoran Nikoloski and   
                 Joachim Selbig   Biological Cluster Evaluation for Gene
                                  Function Prediction  . . . . . . . . . . 428--445
              Vamsi Kundeti and   
    Sanguthevar Rajasekaran and   
                      Hieu Dinh   Border Length Minimization Problem on a
                                  Square Array . . . . . . . . . . . . . . 446--455
                 Nivit Gill and   
           Shailendra Singh and   
                Trilok C. Aseri   Computational Disease Gene
                                  Prioritization: An Appraisal . . . . . . 456--465
                Abdul Arif Khan   \em In Silico Prediction of
                                  \bionameEscherichia coli Proteins
                                  Targeting the Host Cell Nucleus, with
                                  Special Reference to Their Role in Colon
                                  Cancer Etiology  . . . . . . . . . . . . 466--475
                      Anonymous   Correction: \booktitleJournal of
                                  Computational Biology: 2014; \bf
                                  21/4:303--319  . . . . . . . . . . . . . 476--476

Journal of Computational Biology
Volume 21, Number 7, July, 2014

Jérôme Waldispühl and   
       Charles W. O'Donnell and   
             Sebastian Will and   
           Srinivas Devadas and   
              Rolf Backofen and   
                  Bonnie Berger   Simultaneous Alignment and Folding of
                                  Protein Sequences  . . . . . . . . . . . 477--491
          M. Muksitul Haque and   
         Michael K. Skinner and   
             Lawrence B. Holder   Imbalanced Class Learning in Epigenetics 492--507
           Daniel Gamermann and   
            Arnaud Montagud and   
        J. Alberto Conejero and   
Javier F. Urchueguía and   
Pedro Fernández de Córdoba   New Approach for Phylogenetic Tree
                                  Recovery Based on Genome-Scale Metabolic
                                  Networks . . . . . . . . . . . . . . . . 508--519
      Fabien de Montgolfier and   
           Mathieu Raffinot and   
                     Irena Rusu   Easy Identification of Generalized
                                  Common and Conserved Nested Intervals    520--533
               Anna Zhukova and   
            David James Sherman   Knowledge-based Generalization of
                                  Metabolic Models . . . . . . . . . . . . 534--547
            Wen-Shyong Tzou and   
              Ying-Tsang Lo and   
                Tun-Wen Pai and   
                Chin-Hwa Hu and   
                   Chung-Hao Li   Stochastic Simulation of Notch Signaling
                                  Reveals Novel Factors That Mediate the
                                  Differentiation of Neural Stem Cells . . 548--567

Journal of Computational Biology
Volume 21, Number 8, August, 2014

           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   Chromatin Properties of Regulatory DNA
                                  Probed by Manipulation of Transcription
                                  Factors  . . . . . . . . . . . . . . . . 569--577
                   Yu Zheng and   
                   Louxin Zhang   Are the Duplication Cost and
                                  Robinson--Foulds Distance Equivalent?    578--590
          Hillary S. W. Han and   
            Thomas J. X. Li and   
            Christian M. Reidys   Combinatorics of $ \gamma $-Structures   591--608
              Cuncong Zhong and   
                  Shaojie Zhang   Simultaneous Folding of Alternative RNA
                                  Structures with Mutual Constraints: an
                                  Application to Next-Generation
                                  Sequencing-based RNA Structure Probing   609--621
             Nikita Alexeev and   
                   Peter Zograf   Random Matrix Approach to the
                                  Distribution of Genomic Distance . . . . 622--631
        Ponne Saravanaraman and   
      Raj Kumar Chinnadurai and   
              Rathanam Boopathy   A New Role for the Nonpathogenic
                                  Nonsynonymous Single-Nucleotide
                                  Polymorphisms of Acetylcholinesterase in
                                  the Treatment of Alzheimer's Disease: a
                                  Computational Study  . . . . . . . . . . 632--647

Journal of Computational Biology
Volume 21, Number 9, September, 2014

          Benjamin M. M. Fu and   
            Christian M. Reidys   Shapes of Interacting RNA Complexes  . . 649--664
      Maria Brigida Ferraro and   
             Marco Savarese and   
      Giuseppina Di Fruscio and   
             Vincenzo Nigro and   
       Mario Rosario Guarracino   Prediction of Rare Single-Nucleotide
                                  Causative Mutations for Muscular
                                  Diseases in Pooled Next-Generation
                                  Sequencing Experiments . . . . . . . . . 665--675
                 Jan Irvahn and   
              Vladimir N. Minin   Phylogenetic Stochastic Mapping Without
                                  Matrix Exponentiation  . . . . . . . . . 676--690
               Yunzhang Huo and   
                        Ping Ji   Continuous-Time Markov Chain--Based Flux
                                  Analysis in Metabolism . . . . . . . . . 691--698
           Alexandru Agapie and   
              Anca Andreica and   
                 Marius Giuclea   Probabilistic Cellular Automata  . . . . 699--708
              Albert Vexler and   
                 Xiwei Chen and   
                     Jihnhee Yu   Evaluations and Comparisons of Treatment
                                  Effects Based on Best Combinations of
                                  Biomarkers with Applications to
                                  Biomedical Studies . . . . . . . . . . . 709--721

Journal of Computational Biology
Volume 21, Number 10, October, 2014

                  Josh Voorkamp   Maximal Acyclic Agreement Forests  . . . 723--731
           Loni Philip Tabb and   
                   Wei Zhao and   
               Jingyu Huang and   
                  Gail L. Rosen   Characterizing the Empirical
                                  Distribution of Prokaryotic Genome
                                  $n$-mers in the Presence of Nullomers    732--740
           \vZiva Stepan\vci\vc   Enhancing Gibbs Sampling Method for
                                  Motif Finding in DNA with Initial Graph
                                  Representation of Sequences  . . . . . . 741--752
                   Hari Ram and   
                 Alok Kumar and   
               Lebin Thomas and   
                  Ved Pal Singh   \em In silico Approach to Study Adaptive
                                  Divergence in Nucleotide Composition of
                                  the 16S rRNA Gene Among Bacteria
                                  Thriving Under Different Temperature
                                  Regimes  . . . . . . . . . . . . . . . . 753--759
                  Alex Radu and   
             Michael Charleston   Node Fingerprinting: an Efficient
                                  Heuristic for Aligning Biological
                                  Networks . . . . . . . . . . . . . . . . 760--770
                 Peican Zhu and   
                        Jie Han   Asynchronous Stochastic Boolean Networks
                                  as Gene Network Models . . . . . . . . . 771--783

Journal of Computational Biology
Volume 21, Number 11, November, 2014

          Takanori Hasegawa and   
                Tomoya Mori and   
              Rui Yamaguchi and   
                Seiya Imoto and   
              Satoru Miyano and   
                 Tatsuya Akutsu   An Efficient Data Assimilation Schema
                                  for Restoration and Extension of Gene
                                  Regulatory Networks Using Time-Course
                                  Observation Data . . . . . . . . . . . . 785--798
                Amir Carmel and   
            Noa Musa-Lempel and   
                 Dekel Tsur and   
             Michal Ziv-Ukelson   The Worst Case Complexity of Maximum
                                  Parsimony  . . . . . . . . . . . . . . . 799--808
         Bogumil M. Konopka and   
               Tomasz Golda and   
           Ma\lgorzata Kotulska   Evaluating the Significance of Protein
                                  Functional Similarity Based on Gene
                                  Ontology . . . . . . . . . . . . . . . . 809--822
         José Santos and   
               Pablo Villot and   
          Martin Diéguez   Emergent Protein Folding Modeled with
                                  Evolved Neural Cellular Automata Using
                                  the $3$D HP Model  . . . . . . . . . . . 823--845
                 Nha Nguyen and   
                      An Vo and   
                 Kyoung-Jae Won   A Wavelet Approach to Detect Enriched
                                  Regions and Explore Epigenomic
                                  Landscapes . . . . . . . . . . . . . . . 846--854
              Katrin Illner and   
           Christiane Fuchs and   
                Fabian J. Theis   Bayesian Blind Source Separation for
                                  Data with Network Structure  . . . . . . 855--865

Journal of Computational Biology
Volume 21, Number 12, December, 2014

             Changchuan Yin and   
             Xuemeng E. Yin and   
                   Jiasong Wang   A Novel Method for Comparative Analysis
                                  of DNA Sequences by Ramanujan-Fourier
                                  Transform  . . . . . . . . . . . . . . . 867--879
                  Eman Badr and   
               Lenwood S. Heath   Identifying Splicing Regulatory Elements
                                  with de Bruijn Graphs  . . . . . . . . . 880--897
            Alexia Kakourou and   
                Werner Vach and   
                   Bart Mertens   Combination Approaches Improve
                                  Predictive Performance of Diagnostic
                                  Rules for Mass-Spectrometry Proteomic
                                  Data . . . . . . . . . . . . . . . . . . 898--914
         William Y. C. Chen and   
              Qiang-Hui Guo and   
                Lisa H. Sun and   
                      Jian Wang   Zigzag Stacks and $m$-Regular Linear
                                  Stacks . . . . . . . . . . . . . . . . . 915--935
           Huda A. Maghawry and   
      Mostafa G. M. Mostafa and   
                Tarek F. Gharib   A New Protein Structure Representation
                                  for Efficient Protein Function
                                  Prediction . . . . . . . . . . . . . . . 936--946
         Laurent Noé and   
            Donald E. K. Martin   A Coverage Criterion for Spaced Seeds
                                  and Its Applications to Support Vector
                                  Machine String Kernels and $k$-Mer
                                  Distances  . . . . . . . . . . . . . . . 947--963
                 Lizhen Liu and   
                 Xuemin Dai and   
                Hanshi Wang and   
                   Wei Song and   
                      Jingli Lu   A Weighted Multipath Measurement Based
                                  on Gene Ontology for Estimating Gene
                                  Products Similarity  . . . . . . . . . . 964--974


Journal of Computational Biology
Volume 22, Number 1, January, 2015

               Sunita Yadav and   
                   D. Swati and   
      Hariharan Chandrasekharan   Thiamine Pyrophosphate Riboswitch in
                                  Some Representative Plant Species: a
                                  Bioinformatics Study . . . . . . . . . . 1--9
               Adam Persing and   
                 Ajay Jasra and   
          Alexandros Beskos and   
              David Balding and   
                 Maria De Iorio   A Simulation Approach for Change-Points
                                  on Phylogenetic Trees  . . . . . . . . . 10--24
           Frederic Y. Bois and   
              Ghislaine Gayraud   Probabilistic Generation of Random
                                  Networks Taking into Account Information
                                  on Motifs Occurrence . . . . . . . . . . 25--36
              Derek E. Chen and   
          Darryl L. Willick and   
           Joseph B. Ruckel and   
               Wely B. Floriano   Principal Component Analysis of Binding
                                  Energies for Single-Point Mutants of
                                  hT2R16 Bound to an Agonist Correlate
                                  with Experimental Mutant Cell Response   37--53
        Dhammika Amaratunga and   
             Javier Cabrera and   
                  Yung-Seop Lee   Resampling-Based Similarity Measures for
                                  High-Dimensional Data  . . . . . . . . . 54--62
               Tuantuan Gui and   
                  Xiao Dong and   
                  Rudong Li and   
                   Yixue Li and   
                      Zhen Wang   Identification of Hepatocellular
                                  Carcinoma--Related Genes with a Machine
                                  Learning and Network Analysis  . . . . . 63--71

Journal of Computational Biology
Volume 22, Number 2, February, 2015

                Heewon Park and   
               Atushi Niida and   
              Satoru Miyano and   
                    Seiya Imoto   Sparse Overlapping Group Lasso for
                                  Integrative Multi-Omics Analysis . . . . 73--84
                     Wei Lu and   
            Takeyuki Tamura and   
             Jiangning Song and   
                 Tatsuya Akutsu   Computing Smallest Intervention
                                  Strategies for Multiple Metabolic
                                  Networks in a Boolean Model  . . . . . . 85--110
                  Quan Chen and   
          Xianghong J. Zhou and   
                    Fengzhu Sun   Finding Genetic Overlaps Among Diseases
                                  Based on Ranked Gene Lists . . . . . . . 111--123
                Evan Senter and   
                    Peter Clote   Fast, Approximate Kinetics of RNA
                                  Folding  . . . . . . . . . . . . . . . . 124--144
                 Aditya Rao and   
                 Deepthi P. and   
          C. H. Renumadhavi and   
          M. Girish Chandra and   
            Rajgopal Srinivasan   Compressed Sensing Methods for DNA
                                  Microarrays, RNA Interference, and
                                  Metagenomics . . . . . . . . . . . . . . 145--158
                   Xuan Guo and   
                    Ning Yu and   
               Xiaojun Ding and   
               Jianxin Wang and   
                         Yi Pan   DIME: a Novel Framework for \em De Novo
                                  Metagenomic Sequence Assembly  . . . . . 159--177
  Fatemeh Zamanzad Ghavidel and   
        Jürgen Claesen and   
             Tomasz Burzykowski   A Nonhomogeneous Hidden Markov Model for
                                  Gene Mapping Based on Next-Generation
                                  Sequencing Data  . . . . . . . . . . . . 178--188

Journal of Computational Biology
Volume 22, Number 3, March, 2015

           Fabrice Jossinet and   
                 Yann Ponty and   
Jérôme Waldispühl   Preface  . . . . . . . . . . . . . . . . 189--189
           Azadeh Saffarian and   
             Mathieu Giraud and   
         Hél\`ene Touzet   Modeling Alternate RNA Structures in
                                  Genomic Sequences  . . . . . . . . . . . 190--204
         Laetitia Bourgeade and   
       Cédric Chauve and   
                  Julien Allali   Chaining Sequence/Structure Seeds for
                                  Computing RNA Similarity . . . . . . . . 205--217
             Mattia Petroni and   
              Nikolaj Zimic and   
                  Miha Mraz and   
                  Miha Mo\vskon   Stochastic Simulation Algorithm for Gene
                                  Regulatory Networks with Multiple
                                  Binding Sites  . . . . . . . . . . . . . 218--226
  Meltem Gölgeli Matur and   
       Johannes Müller and   
          Christina Kuttler and   
              Burkhard A. Hense   An Approximative Approach for Single
                                  Cell Spatial Modeling of Quorum Sensing  227--235
                 Nha Nguyen and   
                      An Vo and   
                Inchan Choi and   
                 Kyoung-Jae Won   A Stationary Wavelet Entropy-Based
                                  Clustering Approach Accurately Predicts
                                  Gene Expression  . . . . . . . . . . . . 236--249

Journal of Computational Biology
Volume 22, Number 4, April, 2015

            AnDrea Califano and   
             Manolis Kellis and   
            Gustavo Stolovitzky   Preface: RECOMB/ISCB Systems Biology,
                                  Regulatory Genomics, and DREAM 2014
                                  Special Issue  . . . . . . . . . . . . . 251--252
               Anagha Joshi and   
                Yvonne Beck and   
                    Tom Michoel   Multi-Species Network Inference Improves
                                  Gene Regulatory Network Reconstruction
                                  for Early Embryonic Development in
                                  \bionameDrosophila . . . . . . . . . . . 253--265
                 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   A Scalable Method for Molecular Network
                                  Reconstruction Identifies Properties of
                                  Targets and Mutations in Acute Myeloid
                                  Leukemia . . . . . . . . . . . . . . . . 266--288
              Brittany Baur and   
                  Serdar Bozdag   A Canonical Correlation Analysis-Based
                                  Dynamic Bayesian Network Prior to Infer
                                  Gene Regulatory Networks from Multiple
                                  Types of Biological Data . . . . . . . . 289--299
                 Xueling Li and   
                    Min Zhu and   
           Allan R. Brasier and   
            Andrzej S. Kudlicki   Inferring Genome-Wide Functional
                                  Modulatory Network: a Case Study on NF-$
                                  \kappa $B/RelA Transcription Factor  . . 300--312
               Bingqing Xie and   
                  Gady Agam and   
    Sandhya Balasubramanian and   
                   Jinbo Xu and   
          T. Conrad Gilliam and   
            Natalia Maltsev and   
          Daniela Börnigen   Disease Gene Prioritization Using
                                  Network and Feature  . . . . . . . . . . 313--323
                 Aaron Wise and   
                 Ziv Bar-Joseph   cDREM: Inferring Dynamic Combinatorial
                                  Gene Regulation  . . . . . . . . . . . . 324--333

Journal of Computational Biology
Volume 22, Number 5, May, 2015

                   Roded Sharan   Preface  . . . . . . . . . . . . . . . . 335--335
               Rayan Chikhi and   
           Antoine Limasset and   
              Shaun Jackman and   
           Jared T. Simpson and   
                  Paul Medvedev   On the Representation of de Bruijn
                                  Graphs . . . . . . . . . . . . . . . . . 336--352
             Adrian Guthals and   
          Christina Boucher and   
                  Nuno Bandeira   The Generating Function Approach for
                                  Peptide Identification in Spectral
                                  Networks . . . . . . . . . . . . . . . . 353--366
          Henry C. M. Leung and   
               Siu-Ming Yiu and   
             Francis Y. L. Chin   IDBA-MTP: a Hybrid Metatranscriptomic
                                  Assembler Based on Protein Information   367--376
            Siavash Mirarab and   
                 Nam Nguyen and   
                  Sheng Guo and   
                Li-San Wang and   
               Junhyong Kim and   
                   Tandy Warnow   PASTA: Ultra-Large Multiple Sequence
                                  Alignment for Nucleotide and Amino-Acid
                                  Sequences  . . . . . . . . . . . . . . . 377--386
                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   Building a Pan-Genome Reference for a
                                  Population . . . . . . . . . . . . . . . 387--401
                 Keith Noto and   
               Saeed Majidi and   
            Andrea G. Edlow and   
            Heather C. Wick and   
           Diana W. Bianchi and   
                Donna K. Slonim   CSAX: Characterizing Systematic
                                  Anomalies in eXpression Data . . . . . . 402--413
            Arne C. Reimers and   
         Frank J. Bruggeman and   
           Brett G. Olivier and   
                   Leen Stougie   Fast Flux Module Detection Using Matroid
                                  Theory . . . . . . . . . . . . . . . . . 414--424
                Mingfu Shao and   
                     Yu Lin and   
            Bernard M. E. Moret   An Exact Algorithm to Compute the
                                  Double-Cut-and-Join Distance for Genomes
                                  with Duplicate Genes . . . . . . . . . . 425--435
                  Shutan Xu and   
                 Shuxue Zou and   
                   Lincong Wang   A Geometric Clustering Algorithm with
                                  Applications to Structural Data  . . . . 436--450
               Wen-Yun Yang and   
         Farhad Hormozdiari and   
              Eleazar Eskin and   
                Bogdan Pasaniuc   A Spatial Haplotype Copying Model with
                                  Applications to Genotype Imputation  . . 451--462

Journal of Computational Biology
Volume 22, Number 6, June, 2015

          Hamidreza Chitsaz and   
       Mohammad Aminisharifabad   Exact Learning of RNA Energy Parameters
                                  From Structure . . . . . . . . . . . . . 463--473
       Hetunandan Kamisetty and   
              Bornika Ghosh and   
 Christopher James Langmead and   
           Chris Bailey-Kellogg   Learning Sequence Determinants of
                                  Protein:Protein Interaction Specificity
                                  with Sparse Graphical Models . . . . . . 474--486
         Arun S. Konagurthu and   
           Parthan Kasarapu and   
              Lloyd Allison and   
           James H. Collier and   
                 Arthur M. Lesk   On Sufficient Statistics of
                                  Least-Squares Superposition of Vector
                                  Sets . . . . . . . . . . . . . . . . . . 487--497
           Murray Patterson and   
           Tobias Marschall and   
              Nadia Pisanti and   
             Leo van Iersel and   
               Leen Stougie and   
             Gunnar W. Klau and   
       Alexander Schönhuth   WhatsHap: Weighted Haplotype Assembly
                                  for Future-Generation Sequencing Reads   498--509
        Benjamin J. Raphael and   
                   Fabio Vandin   Simultaneous Inference of Cancer
                                  Pathways and Tumor Progression from
                                  Cross-Sectional Mutation Data  . . . . . 510--527
              Yana Safonova and   
            Anton Bankevich and   
               Pavel A. Pevzner   dipSPAdes: Assembler for Highly
                                  Polymorphic Diploid Genomes  . . . . . . 528--545
                   Hua Wang and   
                 Heng Huang and   
                     Chris Ding   Correlated Protein Function Prediction
                                  via Maximization of Data-Knowledge
                                  Consistency  . . . . . . . . . . . . . . 546--562
              Zhanyong Wang and   
               Jae Hoon Sul and   
                  Sagi Snir and   
             Jose A. Lozano and   
                  Eleazar Eskin   Gene--Gene Interactions Detection Using
                                  a Two-stage Model  . . . . . . . . . . . 563--576
                 Shay Zakov and   
                   Vineet Bafna   Reconstructing Breakage Fusion Bridge
                                  Architectures Using Noisy Copy Numbers   577--594
           Marinka \vZitnik and   
                   Bla\vz Zupan   Data Imputation in Epistatic MAPs by
                                  Network-Guided Matrix Completion . . . . 595--608

Journal of Computational Biology
Volume 22, Number 7, July, 2015

                     Yuzhen Guo   The Noncompacted Folding of Proteins by
                                  Modified Elastic Net Algorithm . . . . . 609--618
         Robert Müller and   
                Markus E. Nebel   Combinatorics of RNA Secondary
                                  Structures with Base Triples . . . . . . 619--648
           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   Estimation of Tumor Size Evolution Using
                                  Particle Filters . . . . . . . . . . . . 649--665
                 Zhexue Wei and   
                 Daming Zhu and   
                   Lusheng Wang   A Dynamic Programming Algorithm For
                                  (1,2)-Exemplar Breakpoint Distance . . . 666--676
               Huilan Chang and   
              Yi-Chang Chiu and   
                    Yi-Lin Tsai   A Variation of Cover-Free Families and
                                  Its Applications . . . . . . . . . . . . 677--686
                  Alex Radu and   
             Michael Charleston   Node Handprinting: a Scalable and
                                  Accurate Algorithm for Aligning Multiple
                                  Biological Networks  . . . . . . . . . . 687--697
             Florian Kaiser and   
           Alexander Eisold and   
                   Dirk Labudde   A Novel Algorithm for Enhanced
                                  Structural Motif Matching in Proteins    698--713

Journal of Computational Biology
Volume 22, Number 8, August, 2015

               Sean Simmons and   
                  Jian Peng and   
         Jadwiga Bienkowska and   
                  Bonnie Berger   Discovering What Dimensionality
                                  Reduction Really Tells Us About RNA-Seq
                                  Data . . . . . . . . . . . . . . . . . . 715--728
              Peter Zörnig   Reduced-Size Integer Linear Programming
                                  Models for String Selection Problems:
                                  Application to the Farthest String
                                  Problem  . . . . . . . . . . . . . . . . 729--742
             Kaisa Koskinen and   
              Petri Auvinen and   
  K. Johanna Björkroth and   
                  Jenni Hultman   Inconsistent Denoising and Clustering
                                  Algorithms for Amplicon Sequence Data    743--751
                 Chia-Hui Huang   Medical Reasoning with Rough-Set
                                  Influence Diagrams . . . . . . . . . . . 752--764
                   Miao Sun and   
                 Dejian Lai and   
                   Li Zhang and   
                   Xuelin Huang   Modified SuperCurve Method for Analysis
                                  of Reverse-Phase Protein Array Data  . . 765--769
                  Oliver Serang   A Fast Numerical Method for
                                  Max-Convolution and the Application to
                                  Efficient Max-Product Inference in
                                  Bayesian Networks  . . . . . . . . . . . 770--783

Journal of Computational Biology
Volume 22, Number 9, September, 2015

                    Jing He and   
               Amarda Shehu and   
               Nurit Haspel and   
                     Brian Chen   The 7th Computational Structural
                                  Bioinformatics Workshop  . . . . . . . . 785--786
                   Hui Dong and   
               Jin Seob Kim and   
          Gregory S. Chirikjian   Computational Analysis of SAXS Data
                                  Acquisition  . . . . . . . . . . . . . . 787--805
               Irina Hashmi and   
                   Amarda Shehu   idDock+: Integrating Machine Learning in
                                  Probabilistic Search for
                                  Protein--Protein Docking . . . . . . . . 806--822
        Hsin-Yi (Cindy) Yeh and   
              Aaron Lindsey and   
               Chih-Peng Wu and   
              Shawna Thomas and   
                 Nancy M. Amato   Decoy Database Improvement for Protein
                                  Folding  . . . . . . . . . . . . . . . . 823--836
            Abhishek Biswas and   
                Desh Ranjan and   
            Mohammad Zubair and   
                        Jing He   A Dynamic Programming Algorithm for
                                  Finding the Optimal Placement of a
                                  Secondary Structure Topology in Cryo-EM
                                  Data . . . . . . . . . . . . . . . . . . 837--843
               Rudy Clausen and   
                   Amarda Shehu   A Data-Driven Evolutionary Algorithm for
                                  Mapping Multibasin Protein Energy
                                  Landscapes . . . . . . . . . . . . . . . 844--860
                   Ziyi Guo and   
                Brian Yuan Chen   Conformational Sampling Reveals Amino
                                  Acids with a Steric Influence on
                                  Specificity  . . . . . . . . . . . . . . 861--875
                  Ping Zhou and   
                 Ning Zhang and   
              Ruth Nussinov and   
                      Buyong Ma   Defining the Domain Arrangement of the
                                  Mammalian Target of Rapamycin Complex
                                  Component Rictor Protein . . . . . . . . 876--886
                  Kelin Xia and   
              Zhixiong Zhao and   
                    Guo-Wei Wei   Multiresolution Topological
                                  Simplification . . . . . . . . . . . . . 887--891
        Bahar Akbal-Delibas and   
               Marc Pomplun and   
                   Nurit Haspel   Accurate Prediction of Docked Protein
                                  Structure Similarity . . . . . . . . . . 892--904

Journal of Computational Biology
Volume 22, Number 10, October, 2015

                 Yael Baran and   
                  Eran Halperin   A Note on the Relations Between
                                  Spatio-Genetic Models  . . . . . . . . . 905--917
            Filippo Disanto and   
              Noah A. Rosenberg   Coalescent Histories for Lodgepole
                                  Species Trees  . . . . . . . . . . . . . 918--929
              Alexa Pragman and   
           Richard Issacson and   
            Christine Wendt and   
                   Cavan Reilly   A Method for Determining Taxonomical
                                  Contributions to Group Differences in
                                  Microbiomic Investigations . . . . . . . 930--939
                Tim Wallace and   
                 Ali Sekmen and   
                   Xiaofei Wang   Application of Subspace Clustering in
                                  DNA Sequence Analysis  . . . . . . . . . 940--952
Alexandre Wagner Chagas Faria and   
   Alisson Marques da Silva and   
  Thiago de Souza Rodrigues and   
      Marcelo Azevedo Costa and   
            Antonio Padua Braga   A Ranking Approach for Probe Selection
                                  and Classification of Microarray Data
                                  with Artificial Neural Networks  . . . . 953--961
                      Bo Li and   
             Xianfang Zheng and   
                Chuancui Hu and   
                     Yunxia Cao   Human Papillomavirus Genome-Wide
                                  Identification of T-Cell Epitopes for
                                  Peptide Vaccine Development Against
                                  Cervical Cancer: an Integration of
                                  Computational Analysis and Experimental
                                  Assay  . . . . . . . . . . . . . . . . . 962--974

Journal of Computational Biology
Volume 22, Number 11, November, 2015

                   Chin Lung Lu   An Efficient Algorithm for the Contig
                                  Ordering Problem under Algebraic
                                  Rearrangement Distance . . . . . . . . . 975--987
                  Ping Chen and   
                   Xuelin Huang   Comparison of Analytic Methods for
                                  Quantitative Real-Time Polymerase Chain
                                  Reaction Data  . . . . . . . . . . . . . 988--996
                 Anthony O'Hare   Inference in High-Dimensional Parameter
                                  Space  . . . . . . . . . . . . . . . . . 997--1004
       Nikita A. Sakhanenko and   
                 David J. Galas   Biological Data Analysis as an
                                  Information Theory Problem:
                                  Multivariable Dependence Measures and
                                  the Shadows Algorithm  . . . . . . . . . 1005--1024
                 Ajay Jasra and   
               Adam Persing and   
          Alexandros Beskos and   
                 Kari Heine and   
                 Maria De Iorio   Bayesian Inference for
                                  Duplication--Mutation with
                                  Complementarity Network Models . . . . . 1025--1033
                   Sera Kim and   
              Kyeongjun Lee and   
                     Hokeun Sun   Statistical Selection Strategy for Risk
                                  and Protective Rare Variants Associated
                                  with Complex Traits  . . . . . . . . . . 1034--1043
Luís Felipe I. Cunha and   
     Luis Antonio B. Kowada and   
       Rodrigo de A. Hausen and   
     Celina M. H. de Figueiredo   A Faster 1.375-Approximation Algorithm
                                  for Sorting by Transpositions* . . . . . 1044--1056

Journal of Computational Biology
Volume 22, Number 12, December, 2015

               Marco Frasca and   
            Alberto Bertoni and   
              Giorgio Valentini   UNIPred: Unbalance-Aware Network
                                  Integration and Prediction of Protein
                                  Functions  . . . . . . . . . . . . . . . 1057--1074
           Ahmed T. Soliman and   
                   Tao Meng and   
             Shu-Ching Chen and   
              S. S. Iyengar and   
            Puneeth Iyengar and   
                 John Yordy and   
                  Mei-Ling Shyu   Driver Missense Mutation Identification
                                  Using Feature Selection and Model Fusion 1075--1085
              Tuan-Anh Tran and   
                 Nam Tri Vo and   
           Hoang Duc Nguyen and   
                   Bao The Pham   A Novel Method to Predict Highly
                                  Expressed Genes Based on Radius
                                  Clustering and Relative Synonymous Codon
                                  Usage  . . . . . . . . . . . . . . . . . 1086--1096
            Kyoung-Tak Kang and   
              Sung-Hwan Kim and   
                 Juhyun Son and   
              Young Han Lee and   
                Heoung-Jae Chun   Probabilistic Approach for Determining
                                  the Material Properties of Meniscal
                                  Attachments \em In Vivo Using Magnetic
                                  Resonance Imaging and a Finite Element
                                  Model  . . . . . . . . . . . . . . . . . 1097--1107
               Shu-Yuan Niu and   
              Ming-Yuan Xin and   
                   Jian Luo and   
               Ming-Yao Liu and   
                 Zhen-Ran Jiang   DSEP: a Tool Implementing Novel Method
                                  to Predict Side Effects of Drugs . . . . 1108--1117
                 Anas Al-Okaily   Error Tree: a Tree Structure for Hamming
                                  and Edit Distances and Wildcards
                                  Matching . . . . . . . . . . . . . . . . 1118--1128
             Olga Chernomor and   
             Bui Quang Minh and   
             Arndt von Haeseler   Consequences of Common Topological
                                  Rearrangements for Partition Trees in
                                  Phylogenomic Inference . . . . . . . . . 1129--1142


Journal of Computational Biology
Volume 23, Number 1, January, 2016

               Feilong Deng and   
                    Shi-Yi Chen   dbHT-Trans: an Efficient Tool for
                                  Filtering the Protein-Encoding
                                  Transcripts Assembled by RNA-Seq
                                  According to Search for Homologous
                                  Proteins . . . . . . . . . . . . . . . . 1--9
              Sabeur Aridhi and   
         Ha\"\itham Sghaier and   
             Manel Zoghlami and   
           Mondher Maddouri and   
         Engelbert Mephu Nguifo   Prediction of Ionizing Radiation
                                  Resistance in Bacteria Using a Multiple
                                  Instance Learning Model  . . . . . . . . 10--20
    Christopher Girdlestone and   
                 Steven Hayward   The DynDom3D Webserver for the Analysis
                                  of Domain Movements in Multimeric
                                  Proteins . . . . . . . . . . . . . . . . 21--26
            Cesar M. Camilo and   
         Gustavo M. A. Lima and   
          Fernando V. Maluf and   
         Rafael V. C. Guido and   
                Igor Polikarpov   HTP-OligoDesigner: an Online Primer
                                  Design Tool for High-Throughput Gene
                                  Cloning and Site-Directed Mutagenesis    27--29
               Fabio Vandin and   
        Benjamin J. Raphael and   
                      Eli Upfal   On the Sample Complexity of Cancer
                                  Pathways Identification  . . . . . . . . 30--41
              Ya-Chun Hsiao and   
                Li-Yu Daisy Liu   A Stepwise Approach of Finding Dependent
                                  Variables via Coefficient of Intrinsic
                                  Dependence . . . . . . . . . . . . . . . 42--55
                 Yucheng Hu and   
              John S. Lowengrub   Collective Properties of a Transcription
                                  Initiation Model Under Varying
                                  Environment  . . . . . . . . . . . . . . 56--66

Journal of Computational Biology
Volume 23, Number 2, February, 2016

            Yaron Orenstein and   
                  Bonnie Berger   Efficient Design of Compact Unstructured
                                  RNA Libraries Covering All $k$-mers  . . 67--79
               Leyla Rohani and   
          Derrick J. Morton and   
             Xiao-Qian Wang and   
              Jaideep Chaudhary   Relative Stability of Wild-Type and
                                  Mutant p53 Core Domain: a Molecular
                                  Dynamic Study  . . . . . . . . . . . . . 80--89
               Daniele Pepe and   
                    Jin Hwan Do   Comparison of Perturbed Pathways in Two
                                  Different Cell Models for Parkinson's
                                  Disease with Structural Equation Model   90--101
              Xiaoling Peng and   
                    Gang Li and   
                    Zhenqiu Liu   Zero-Inflated Beta Regression for
                                  Differential Abundance Analysis with
                                  Metagenomics Data  . . . . . . . . . . . 102--110
        Xiujun (Sylvia) Zhu and   
                   Monnie McGee   Metagenomic Classification Using an
                                  Abstraction Augmented Markov Model . . . 111--122
                   Haiou Li and   
                     Lu Sun and   
                  Sheng Luo and   
                Xiaoyan Xia and   
                      Qiang Lyu   Modeling Protein Loop Structure by
                                  Cyclic Coordinate Descent-based Approach 123--136

Journal of Computational Biology
Volume 23, Number 3, March, 2016

            Paola Bonizzoni and   
      Gianluca Della Vedova and   
                Yuri Pirola and   
            Marco Previtali and   
                Raffaella Rizzi   LSG: an External-Memory Tool to Compute
                                  String Graphs for Next-Generation
                                  Sequencing Data Assembly . . . . . . . . 137--149
              Pavel Avdeyev and   
                Shuai Jiang and   
            Sergey Aganezov and   
                     Fei Hu and   
               Max A. Alekseyev   Reconstruction of Ancestral Genomes in
                                  Presence of Gene Gain and Loss . . . . . 150--164
                 Ilan Smoly and   
                Amir Carmel and   
          Yonat Shemer-Avni and   
           Esti Yeger-Lotem and   
             Michal Ziv-Ukelson   Algorithms for Regular Tree Grammar
                                  Network Search and Their Application to
                                  Mining Human--viral Infection Patterns   165--179
      Deeparnab Chakrabarty and   
             Sampath Kannan and   
                     Kevin Tian   Detecting Character Dependencies in
                                  Stochastic Models of Evolution . . . . . 180--191
                Zhenqiu Liu and   
                  Shili Lin and   
                   Nan Deng and   
      Dermot P. B. McGovern and   
              Steven Piantadosi   Sparse Inverse Covariance Estimation
                                  with $L$$_0$ Penalty for Network
                                  Construction with Omics Data . . . . . . 192--202
              Stefan Canzar and   
          Khaled Elbassioni and   
             Mitchell Jones and   
           Julián Mestre   Resolving Conflicting Predictions from
                                  Multimapping Reads . . . . . . . . . . . 203--217
        Benjamin Drinkwater and   
          Michael A. Charleston   RASCAL: a Randomized Approach for
                                  Coevolutionary Analysis  . . . . . . . . 218--227

Journal of Computational Biology
Volume 23, Number 4, April, 2016

                Shi-Yi Chen and   
               Feilong Deng and   
                 Ying Huang and   
                 Xianbo Jia and   
                Yi-Ping Liu and   
                   Song-Jia Lai   bioOTU: an Improved Method for
                                  Simultaneous Taxonomic Assignments and
                                  Operational Taxonomic Units Clustering
                                  of 16s rRNA Gene Sequences . . . . . . . 229--238
                 Arfa Anjum and   
                Seema Jaggi and   
             Eldho Varghese and   
              Shwetank Lall and   
              Arpan Bhowmik and   
                       Anil Rai   Identification of Differentially
                                  Expressed Genes in RNA-seq Data of
                                  \bionameArabidopsis thaliana: a Compound
                                  Distribution Approach  . . . . . . . . . 239--247
        Nelson Pérez and   
           Miguel Gutierrez and   
                    Nelson Vera   Computational Performance Assessment of
                                  $k$-mer Counting Algorithms  . . . . . . 248--255
             Abdoulaye Sarr and   
       Anya Désilles and   
        Alexandra Fronville and   
                  Vincent Rodin   A Viability Approach for Robustness
                                  Measurement, Organizational Autopoiesis,
                                  and Cell Turnover in a Multicellular
                                  System . . . . . . . . . . . . . . . . . 256--269
                 Pablo Mier and   
      Miguel A. Andrade-Navarro   FastaHerder2: Four Ways to Research
                                  Protein Function and Evolution with
                                  Clustering and Clustered Databases . . . 270--278
        Michael Laimighofer and   
               Jan Krumsiek and   
           Florian Buettner and   
                Fabian J. Theis   Unbiased Prediction and Feature
                                  Selection in High-Dimensional Survival
                                  Regression . . . . . . . . . . . . . . . 279--290
                Daniel Lobo and   
         Jennifer Hammelman and   
                  Michael Levin   MoCha: Molecular Characterization of
                                  Unknown Pathways . . . . . . . . . . . . 291--297

Journal of Computational Biology
Volume 23, Number 5, May, 2016

               Teresa Przytycka   Preface  . . . . . . . . . . . . . . . . 299--299
               Huichao Gong and   
                  Sai Zhang and   
             Jiangdian Wang and   
               Haipeng Gong and   
                  Jianyang Zeng   Constructing Structure Ensembles of
                                  Intrinsically Disordered Proteins from
                                  Chemical Shift Data  . . . . . . . . . . 300--310
             Mark A. Hallen and   
                Bruce R. Donald   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 311--321
                  Yifeng Li and   
               Chih-Yu Chen and   
             Wyeth W. Wasserman   Deep Feature Selection: Theory and
                                  Application to Identify Enhancers and
                                  Promoters  . . . . . . . . . . . . . . . 322--336
                Mingfu Shao and   
            Bernard M. E. Moret   A Fast and Exact Algorithm for the
                                  Exemplar Breakpoint Distance . . . . . . 337--346
              Leena Salmela and   
          Kristoffer Sahlin and   
          Veli Mäkinen and   
           Alexandru I. Tomescu   Gap Filling as Exact Path Length Problem 347--361
             Rasmus Fonseca and   
        Henry van den Bedem and   
                 Julie Bernauer   Probing RNA Native Conformational
                                  Ensembles with Structural Constraints    362--371
               Seunghak Lee and   
      Aurélie Lozano and   
        Prabhanjan Kambadur and   
                   Eric P. Xing   An Efficient Nonlinear Regression
                                  Approach for Genome-wide Detection of
                                  Marginal and Interacting Genetic
                                  Variations . . . . . . . . . . . . . . . 372--389
                Arnon Mazza and   
               Allon Wagner and   
               Eytan Ruppin and   
                   Roded Sharan   Functional Alignment of Metabolic
                                  Networks . . . . . . . . . . . . . . . . 390--399
       Sumudu P. Leelananda and   
         Robert L. Jernigan and   
            Andrzej Kloczkowski   Predicting Designability of Small
                                  Proteins from Graph Features of Contact
                                  Maps . . . . . . . . . . . . . . . . . . 400--411

Journal of Computational Biology
Volume 23, Number 6, June, 2016

            Jonathan D. Jou and   
                 Swati Jain and   
         Ivelin S. Georgiev and   
                Bruce R. Donald   BWM*: a Novel, Provable, Ensemble-based
                                  Dynamic Programming Algorithm for Sparse
                                  Approximations of Computational Protein
                                  Design . . . . . . . . . . . . . . . . . 413--424
                 Emre Sefer and   
                Geet Duggal and   
                 Carl Kingsford   Deconvolution of Ensemble Chromatin
                                  Interaction Data Reveals the Latent
                                  Mixing Structures in Cell Subpopulations 425--438
                Yichao Zhou and   
                  Yuexin Wu and   
                  Jianyang Zeng   Computational Protein Design Using
                                  AND/OR Branch-and-Bound Search . . . . . 439--451
       Sharma V. Thankachan and   
     Sriram P. Chockalingam and   
               Yongchao Liu and   
         Alberto Apostolico and   
                 Srinivas Aluru   ALFRED: a Practical Method for
                                  Alignment-Free Distance Computation  . . 452--460
            Ilan Ben-Bassat and   
                     Benny Chor   CRISPR Detection From Short Reads Using
                                  Partial Overlap Graphs . . . . . . . . . 461--471
       Sharma V. Thankachan and   
         Alberto Apostolico and   
                 Srinivas Aluru   A Provably Efficient Algorithm for the
                                  $k$-Mismatch Average Common Substring
                                  Problem  . . . . . . . . . . . . . . . . 472--482
       Stefano R. Bonissone and   
               Pavel A. Pevzner   Immunoglobulin Classification Using the
                                  Colored Antibody Graph . . . . . . . . . 483--494
                  Shuo Yang and   
                 Shai Carmi and   
                    Itsik Pe'er   Rapidly Registering Identity-by-Descent
                                  Across Ancestral Recombination Graphs    495--507
              David Manescu and   
                      Uri Keich   A Symmetric Length-Aware Enrichment Test 508--525
             Surojit Biswas and   
          Meredith Mcdonald and   
          Derek S. Lundberg and   
           Jeffery L. Dangl and   
                 Vladimir Jojic   Learning Microbial Interaction Networks
                                  from Metagenomic Count Data  . . . . . . 526--535

Journal of Computational Biology
Volume 23, Number 7, July, 2016

             Zhi-Zhong Chen and   
                   Fei Deng and   
                  Chao Shen and   
                  Yiji Wang and   
                   Lusheng Wang   Better ILP-Based Approaches to Haplotype
                                  Assembly . . . . . . . . . . . . . . . . 537--552
                   Louxin Zhang   On Tree-Based Phylogenetic Networks  . . 553--565
                Jiawen Chen and   
               Zhong-Ru Xie and   
                     Yinghao Wu   Elucidating the Functional Roles of
                                  Spatial Organization in Cross-Membrane
                                  Signal Transduction by a Hybrid
                                  Simulation Method  . . . . . . . . . . . 566--584
                 Boxin Guan and   
           Changsheng Zhang and   
                     Jiaxu Ning   EDGA: a Population Evolution
                                  Direction-Guided Genetic Algorithm for
                                  Protein--Ligand Docking  . . . . . . . . 585--596
                    Yi Wang and   
          Shuangshuang Wang and   
               Dongjie Zhou and   
                 Shuai Yang and   
                Yongchao Xu and   
                  Chao Yang and   
                      Long Yang   CsSNP: a Web-Based Tool for the
                                  Detecting of Comparative Segments SNPs   597--602
             Fabrizio Serra and   
            Chiara Romualdi and   
              Federico Fogolari   Similarity Measures Based on the Overlap
                                  of Ranked Genes Are Effective for
                                  Comparison and Classification of
                                  Microarray Data  . . . . . . . . . . . . 603--614
             Anas Al-Okaily and   
                 Chun-Hsi Huang   ET-Motif: Solving the Exact $ (l,
                                  d)$-Planted Motif Problem Using Error
                                  Tree Structure . . . . . . . . . . . . . 615--623

Journal of Computational Biology
Volume 23, Number 8, August, 2016

      Jira Jindalertudomdee and   
         Morihiro Hayashida and   
                 Tatsuya Akutsu   Enumeration Method for Structural
                                  Isomers Containing User-Defined
                                  Structures Based on Breadth-First Search
                                  Approach . . . . . . . . . . . . . . . . 625--640
                    Eli Goz and   
                   Tamir Tuller   Evidence of a Direct Evolutionary
                                  Selection for Strong Folding and
                                  Mutational Robustness Within HIV Coding
                                  Regions  . . . . . . . . . . . . . . . . 641--650
               Ravi P. More and   
              Hemant J. Purohit   The Identification of Discriminating
                                  Patterns from 16S rRNA Gene to Generate
                                  Signature for Bacillus Genus . . . . . . 651--661
             Metodi Traykov and   
               Slav Angelov and   
                   Nicola Yanev   A New Heuristic Algorithm for Protein
                                  Folding in the HP Model  . . . . . . . . 662--668
                   Duo Chen and   
               Jiasong Wang and   
                   Ming Yan and   
              Forrest Sheng Bao   A Complex Prime Numerical Representation
                                  of Amino Acids for Protein Function
                                  Comparison . . . . . . . . . . . . . . . 669--677
Enrique J. deAndrés-Galiana and   
Juan Luis Fernández-Martínez and   
               Stephen T. Sonis   Design of Biomedical Robots for
                                  Phenotype Prediction Problems  . . . . . 678--692
                Yuandi Wang and   
                     Jinyu Cong   An Improved Model of Nonuniform
                                  Coleochaete Cell Division  . . . . . . . 693--709

Journal of Computational Biology
Volume 23, Number 9, September, 2016

             Sergey Pirogov and   
            Alexander Rybko and   
         Anastasia Kalinina and   
                Mikhail Gelfand   Recombination Processes and Nonlinear
                                  Markov Chains  . . . . . . . . . . . . . 711--717
            Paola Bonizzoni and   
             Riccardo Dondi and   
             Gunnar W. Klau and   
                Yuri Pirola and   
              Nadia Pisanti and   
                Simone Zaccaria   On the Minimum Error Correction Problem
                                  for Haplotype Assembly in Diploid and
                                  Polyploid Genomes  . . . . . . . . . . . 718--736
                 Yuchao Pan and   
                  Yuxi Dong and   
              Jingtian Zhou and   
                Mark Hallen and   
            Bruce R. Donald and   
              Jianyang Zeng and   
                         Wei Xu   cOSPREY: a Cloud-Based Distributed
                                  Algorithm for Large-Scale Computational
                                  Protein Design . . . . . . . . . . . . . 737--749
               Andy S. Alic and   
               Ignacio Blanquer   MuffinInfo: HTML5-Based Statistics
                                  Extractor from Next-Generation
                                  Sequencing Data  . . . . . . . . . . . . 750--755
       Kerstin Gärtner and   
               Andreas Futschik   Improved Versions of Common Estimators
                                  of the Recombination Rate  . . . . . . . 756--768
                   Eduard Fomin   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 . . . . . . . . . . . . . . . . . 769--775
             Martin McGrane and   
          Michael A. Charleston   Biological Network Edit Distance . . . . 776--788

Journal of Computational Biology
Volume 23, Number 10, October, 2016

             Eliza O'Reilly and   
   François Baccelli and   
         Gustavo De Veciana and   
                   Haris Vikalo   End-to-End Optimization of
                                  High-Throughput DNA Sequencing . . . . . 789--800
       Sergio Gálvez and   
               Adis Ferusic and   
       Francisco J. Esteban and   
     Pilar Hernández and   
          Juan A. Caballero and   
                 Gabriel Dorado   Speeding-up Bioinformatics Algorithms
                                  with Heterogeneous Architectures: Highly
                                  Heterogeneous Smith-Waterman (HHeterSW)  801--809
             Troy Hernandez and   
                       Jie Yang   Descriptive Statistics of the Genome:
                                  Phylogenetic Classification of Viruses   810--820
               Shufang Zhao and   
                  Yichao He and   
                Xinlu Zhang and   
                     Wen Xu and   
                   Weili Wu and   
                    Suogang Gao   Group Testing with Multiple Inhibitor
                                  Sets and Error-Tolerant and Its Decoding
                                  Algorithms . . . . . . . . . . . . . . . 821--829
                 Yucheng Hu and   
                  Gongrong Yang   Sequence Evolution Under Constraints:
                                  Lessons Learned from Sudoku  . . . . . . 830--840
               Morgan Madec and   
    François Pecheux and   
             Yves Gendrault and   
               Elise Rosati and   
       Christophe Lallement and   
                 Jacques Haiech   GeNeDA: an Open-Source Workflow for
                                  Design Automation of Gene Regulatory
                                  Networks Inspired from Microelectronics  841--855

Journal of Computational Biology
Volume 23, Number 11, November, 2016

     Christopher L. Barrett and   
            Thomas J. X. Li and   
            Christian M. Reidys   RNA Secondary Structures Having a
                                  Compatible Sequence of Certain
                                  Nucleotide Ratios  . . . . . . . . . . . 857--873
                 Strahil Ristov   A Fast and Simple Pattern Matching with
                                  Hamming Distance on Large Alphabets  . . 874--876
               Wenchuan Guo and   
                Zhenqiu Liu and   
                      Shujie Ma   Nonparametric Regularized Regression for
                                  Phenotype-Associated Taxa Selection and
                                  Network Construction with Metagenomic
                                  Count Data . . . . . . . . . . . . . . . 877--890
Mariana Buongermino Pereira and   
            Mikael Wallroth and   
          Erik Kristiansson and   
            Marina Axelson-Fisk   HattCI: Fast and Accurate \bionameattC
                                  site Identification Using Hidden Markov
                                  Models . . . . . . . . . . . . . . . . . 891--902
          Somaye Hashemifar and   
               Qixing Huang and   
                       Jinbo Xu   Joint Alignment of Multiple
                                  Protein--Protein Interaction Networks
                                  via Convex Optimization  . . . . . . . . 903--911
             Lamiaa A. Amar and   
             Nahla A. Belal and   
               Shaheera Rashwan   Comparing Unlabeled Pedigree Graphs via
                                  Covering with Bipartite and Path . . . . 912--922

Journal of Computational Biology
Volume 23, Number 12, December, 2016

               Manca Bizjak and   
              Nikolaj Zimic and   
                  Miha Mraz and   
                  Miha Mo\vskon   Computational Framework for Modeling
                                  Multiple Noncooperative Transcription
                                  Factor Binding and Its Application to
                                  the Analysis of Nuclear Factor Kappa B
                                  Oscillatory Response . . . . . . . . . . 923--933
                   Eduard Fomin   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  . . . . . . . . . . . . . . . 934--942
              Qiang-Hui Guo and   
                Lisa H. Sun and   
                      Jian Wang   Enumeration of Extended $m$-Regular
                                  Linear Stacks  . . . . . . . . . . . . . 943--956
Enrique J. Deandrés-Galiana and   
Juan Luis Fernández-Martínez and   
          Leorey N. Saligan and   
               Stephen T. Sonis   Impact of Microarray Preprocessing
                                  Techniques in Unraveling Biological
                                  Pathways . . . . . . . . . . . . . . . . 957--968
           Sean B. Johnston and   
               Ronald T. Raines   PTENpred: a Designer Protein Impact
                                  Predictor for PTEN-related Disorders . . 969--975
            Stefano Pirr\`o and   
         Antonella Minutolo and   
             Andrea Galgani and   
           Marina Potest\`a and   
           Vittorio Colizzi and   
                Carla Montesano   Bioinformatics Prediction and
                                  Experimental Validation of MicroRNAs
                                  Involved in Cross-Kingdom Interaction    976--989


Journal of Computational Biology
Volume 24, Number 1, January, 2017

                    Jing He and   
               Nurit Haspel and   
                     Brian Chen   Preface: Selected Articles from 2015
                                  Computational Structural Bioinformatics
                                  Workshop . . . . . . . . . . . . . . . . 1--1
                     Hu Cao and   
                    Yonggang Lu   Using Variable-Length Aligned Fragment
                                  Pairs and an Improved Transition
                                  Function for Flexible Protein Structure
                                  Alignment  . . . . . . . . . . . . . . . 2--12
               Jin Seob Kim and   
               Bijan Afsari and   
          Gregory S. Chirikjian   Cross-Validation of Data Compatibility
                                  Between Small Angle X-ray Scattering and
                                  Cryo-Electron Microscopy . . . . . . . . 13--30
                  Wen Cheng and   
                   Changhui Yan   A Graph Approach to Mining Biological
                                  Patterns in the Binding Interfaces . . . 31--39
          Roshanak Farhoodi and   
        Bahar Akbal-Delibas and   
                   Nurit Haspel   Machine Learning Approaches for
                                  Predicting Protein Complex Similarity    40--51
             Stephanie Zeil and   
               Julio Kovacs and   
             Willy Wriggers and   
                        Jing He   Comparing an Atomic Model or Structure
                                  to a Corresponding Cryo-electron
                                  Microscopy Image at the Central Axis of
                                  a Helix  . . . . . . . . . . . . . . . . 52--67
           Bridget E. Nolan and   
             Emily Levenson and   
                  Brian Y. Chen   Influential Mutations in the SMAD4
                                  Trimer Complex Can Be Detected from
                                  Disruptions of Electrostatic
                                  Complementarity  . . . . . . . . . . . . 68--78
       Anastasia Novinskaya and   
             Didier Devaurs and   
                  Mark Moll and   
               Lydia E. Kavraki   Defining Low-Dimensional Projections to
                                  Guide Protein Conformational Sampling    79--89

Journal of Computational Biology
Volume 24, Number 2, February, 2017

         Adrian-Horia Dediu and   
      Carlos Martín-Vide   Preface: Selected Articles of the Second
                                  International Conference on Algorithms
                                  for Computational Biology (AlCoB 2015)   91--92
             Nikita Alexeev and   
              Anna Pologova and   
               Max A. Alekseyev   Generalized Hultman Numbers and Cycle
                                  Structures of Breakpoint Graphs  . . . . 93--105
             Jesper Jansson and   
                  Ramesh Rajaby   A More Practical Algorithm for the
                                  Rooted Triplet Distance  . . . . . . . . 106--126
                  Ron Zeira and   
                     Ron Shamir   Sorting by Cuts, Joins, and Whole
                                  Chromosome Duplications  . . . . . . . . 127--137
                Heewon Park and   
              Atsushi Niida and   
                Seiya Imoto and   
                  Satoru Miyano   Interaction-Based Feature Selection for
                                  Uncovering Cancer Driver Genes Through
                                  Copy Number-Driven Expression Level  . . 138--152
        Elizabeth S. Allman and   
             John A. Rhodes and   
                 Seth Sullivant   Statistically Consistent $k$-mer Methods
                                  for Phylogenetic Tree Reconstruction . . 153--171
                   Xin Tian and   
               Mingyuan Xin and   
                   Jian Luo and   
                Mingyao Liu and   
                  Zhenran Jiang   Identification of Genes Involved in
                                  Breast Cancer Metastasis by Integrating
                                  Protein--Protein Interaction Information
                                  with Expression Data . . . . . . . . . . 172--182
                       Jie Zhou   Effect of Protein Repetitiveness on
                                  Protein--Protein Interaction Prediction
                                  Results Using Support Vector Machines    183--192

Journal of Computational Biology
Volume 24, Number 3, March, 2017

          Bartek Wilczynski and   
                   Jerzy Tiuryn   FastBill: an Improved Tool for
                                  Prediction of \em Cis-Regulatory Modules 193--199
             Celine Prakash and   
             Arndt Von Haeseler   An Enumerative Combinatorics Model for
                                  Fragmentation Patterns in RNA Sequencing
                                  Provides Insights into Nonuniformity of
                                  the Expected Fragment Starting-Point and
                                  Coverage Profile . . . . . . . . . . . . 200--212
               David Budden and   
                 Mitchell Jones   Cautionary Tales of Inapproximability    213--216
                   Li Zhang and   
                   Han Wang and   
                    Lun Yan and   
                 Lingtao Su and   
                        Dong Xu   OMPcontact: an Outer Membrane Protein
                                  Inter-Barrel Residue Contact Prediction
                                  Method . . . . . . . . . . . . . . . . . 217--228
                  Marc Cole and   
         Steffen Eikenberry and   
              Takahide Kato and   
           Roman A. Sandler and   
       Stanley M. Yamashiro and   
          Vasilis Z. Marmarelis   Nonparametric Model of Smooth Muscle
                                  Force Production During Electrical
                                  Stimulation  . . . . . . . . . . . . . . 229--237
              James Gigrich and   
           Shahryar Sarkani and   
                  Thomas Holzer   A New Approach in Applying Systems
                                  Engineering Tools and Analysis to
                                  Determine Hepatocyte Toxicogenomics Risk
                                  Levels to Human Health . . . . . . . . . 238--254
            Bruno Borguesan and   
      Mario Inostroza-Ponta and   
             Márcio Dorn   NIAS-Server: Neighbors Influence of
                                  Amino acids and Secondary Structures in
                                  Proteins . . . . . . . . . . . . . . . . 255--265

Journal of Computational Biology
Volume 24, Number 4, April, 2017

             Serge Sverdlov and   
             Elizabeth Thompson   Combinatorial Methods for Epistasis and
                                  Dominance  . . . . . . . . . . . . . . . 267--279
             Anas Al-Okaily and   
              Badar Almarri and   
             Sultan Al Yami and   
                 Chun-Hsi Huang   Toward a Better Compression for DNA
                                  Sequences Using Huffman Encoding . . . . 280--288
                   Doo Yang and   
                 Ilya Ioshikhes   \bionameDrosophila H2A and H2A.Z
                                  Nucleosome Sequences Reveal Different
                                  Nucleosome Positioning Sequence Patterns 289--298
              Lianping Yang and   
                   Weilin Zhang   A Multiresolution Graphical
                                  Representation for Similarity
                                  Relationship and Multiresolution
                                  Clustering for Biological Sequences  . . 299--310
             Viktor Jonsson and   
      Tobias Österlund and   
                Olle Nerman and   
              Erik Kristiansson   Variability in Metagenomic Count Data
                                  and Its Influence on the Identification
                                  of Differentially Abundant Genes . . . . 311--326
            Priya S. Venkat and   
       Krishna R. Narayanan and   
                Aniruddha Datta   A Bayesian Network-Based Approach to
                                  Selection of Intervention Points in the
                                  Mitogen-Activated Protein Kinase Plant
                                  Defense Response Pathway . . . . . . . . 327--339
          Grigoriy Gogoshin and   
            Eric Boerwinkle and   
                Andrei S. Rodin   New Algorithm and Software (BNOmics) for
                                  Inferring and Visualizing Bayesian
                                  Networks from Heterogeneous Big
                                  Biological and Genetic Data  . . . . . . 340--356
         Audrone Jakaitiene and   
              Mariano Avino and   
       Mario Rosario Guarracino   Beta-Binomial Model for the Detection of
                                  Rare Mutations in Pooled Next-Generation
                                  Sequencing Experiments . . . . . . . . . 357--367
                  Ying Wang and   
                  Haiyan Hu and   
                     Xiaoman Li   rRNAFilter: a Fast Approach for
                                  Ribosomal RNA Read Removal Without a
                                  Reference Database . . . . . . . . . . . 368--375

Journal of Computational Biology
Volume 24, Number 5, May, 2017

                 Amrit Dhar and   
              Vladimir N. Minin   Calculating Higher-Order Moments of
                                  Phylogenetic Stochastic Mapping
                                  Summaries in Linear Time . . . . . . . . 377--399
                   Gira Lee and   
                     Hokeun Sun   Selection Probability for Rare Variant
                                  Association Studies  . . . . . . . . . . 400--411
               Nicola Yanev and   
             Metodi Traykov and   
              Peter Milanov and   
               Borislav Yurukov   Protein Folding Prediction in a Cubic
                                  Lattice in Hydrophobic-Polar Model . . . 412--421
         Damian Bogdanowicz and   
                Krzysztof Giaro   Comparing Phylogenetic Trees by Matching
                                  Nodes Using the Transfer Distance
                                  Between Partitions . . . . . . . . . . . 422--435
                 Sihai Yang and   
                Xianhua Han and   
             Yukako Tohsato and   
                 Koji Kyoda and   
              Shuichi Onami and   
            Ikuko Nishikawa and   
                    Yenwei Chen   Phenotype Analysis Method for
                                  Identification of Gene Functions
                                  Involved in Asymmetric Division of
                                  \bionameCaenorhabditis elegans . . . . . 436--446
              David Barrios and   
                  Carlos Prieto   D3GB: an Interactive Genome Browser for
                                  R, Python, and WordPress . . . . . . . . 447--449
           Ngoc Tam L. Tran and   
                 Chun-Hsi Huang   Cloud-based MOTIFSIM: Detecting
                                  Similarity in Large DNA Motif Data Sets  450--459
                Rajat Anand and   
              Samrat Chatterjee   Extracting Genes Involved in Disease
                                  from a Connected Network of Perturbed
                                  Biological Processes . . . . . . . . . . 460--469

Journal of Computational Biology
Volume 24, Number 6, June, 2017

                      Anonymous   Preface: Selected Papers from RECOMB
                                  2016 . . . . . . . . . . . . . . . . . . 471--471
               Chandler Zuo and   
                Kailei Chen and   
       Sündüz Kele\cs   A MAD-Bayes Algorithm for State-Space
                                  Inference and Clustering with
                                  Application to Querying Large
                                  Collections of ChIP-Seq Data Sets  . . . 472--485
                   Hao Wang and   
               Joel McManus and   
                 Carl Kingsford   Accurate Recovery of Ribosome Positions
                                  Reveals Slow Translation of
                                  Wobble-Pairing Codons in Yeast . . . . . 486--500
         Meghana Kshirsagar and   
       Keerthiram Murugesan and   
         Jaime G. Carbonell and   
       Judith Klein-Seetharaman   Multitask Matrix Completion for Learning
                                  Protein Interactions Across Diseases . . 501--514
              Nilgun Donmez and   
              Salem Malikic and   
         Alexander W. Wyatt and   
           Martin E. Gleave and   
           Colin C. Collins and   
               S. Cenk Sahinalp   Clonality Inference from Single Tumor
                                  Samples Using Low-Coverage Sequence Data 515--523
                Nicolo Fusi and   
            Jennifer Listgarten   Flexible Modeling of Genetic Effects on
                                  Function-Valued Traits . . . . . . . . . 524--535
             Mark A. Hallen and   
            Jonathan D. Jou and   
                Bruce R. Donald   LUTE (Local Unpruned Tuple Expansion):
                                  Accurate Continuously Flexible Protein
                                  Design with General Energy Functions and
                                  Rigid Rotamer-Like Efficiency  . . . . . 536--546
               David Pellow and   
            Darya Filippova and   
                 Carl Kingsford   Improving Bloom Filter Performance on
                                  Sequence Data Using $k$-mer Bloom
                                  Filters  . . . . . . . . . . . . . . . . 547--557
       Alexander Artyomenko and   
             Nicholas C. Wu and   
             Serghei Mangul and   
              Eleazar Eskin and   
                    Ren Sun and   
                Alex Zelikovsky   Long Single-Molecule Reads Can Resolve
                                  the Complexity of the Influenza Virus
                                  Composed of Rare, Closely Related Mutant
                                  Variants . . . . . . . . . . . . . . . . 558--570
                Mingfu Shao and   
            Bernard M. E. Moret   On Computing Breakpoint Distances for
                                  Genomes with Duplicate Genes . . . . . . 571--580
          Kristoffer Sahlin and   
     Mattias Frånberg and   
                  Lars Arvestad   Structural Variation Detection with Read
                                  Pair Information: an Improved Null
                                  Hypothesis Reduces Bias  . . . . . . . . 581--589
       Alexandru I. Tomescu and   
                  Paul Medvedev   Safe and Complete Contig Assembly
                                  Through Omnitigs . . . . . . . . . . . . 590--602
             Simona Cristea and   
               Jack Kuipers and   
              Niko Beerenwinkel   pathTiMEx: Joint Inference of Mutually
                                  Exclusive Cancer Pathways and Their
                                  Progression Dynamics . . . . . . . . . . 603--615
               Daniel Doerr and   
     Luis Antonio B. Kowada and   
                Eloi Araujo and   
           Shachi Deshpande and   
              Simone Dantas and   
        Bernard M. E. Moret and   
                     Jens Stoye   New Genome Similarity Measures based on
                                  Conserved Gene Adjacencies . . . . . . . 616--634

Journal of Computational Biology
Volume 24, Number 7, July, 2017

               Haiyan Huang and   
                   Hua Tang and   
                 Jing Huang and   
                   Bin Chen and   
                Ruixiao Liu and   
           Rui (Sammi) Tang and   
                    Ying Lu and   
                      Peng Yang   Special Issue: Selected Papers of the
                                  Inaugural DahShu Data Science Symposium:
                                  Computational Precision Health (CPH
                                  2017)  . . . . . . . . . . . . . . . . . 635--636
               Yangyang Hao and   
              Xiaoling Xuei and   
                    Lang Li and   
      Harikrishna Nakshatri and   
         Howard J. Edenberg and   
                    Yunlong Liu   RareVar: a Framework for Detecting
                                  Low-Frequency Single-Nucleotide Variants 637--646
                Tianzhou Ma and   
               Faming Liang and   
         Steffi Oesterreich and   
                George C. Tseng   A Joint Bayesian Model for Integrating
                                  Microarray and RNA Sequencing
                                  Transcriptomic Data  . . . . . . . . . . 647--662
                  Funan Shi and   
                   Haiyan Huang   Identifying Cell Subpopulations and
                                  Their Genetic Drivers from Single-Cell
                                  RNA-Seq Data Using a Biclustering
                                  Approach . . . . . . . . . . . . . . . . 663--674
            Sara M. Clifton and   
              Chaeryon Kang and   
          Jingyi Jessica Li and   
                    Qi Long and   
               Nirmish Shah and   
               Daniel M. Abrams   Hybrid Statistical and Mechanistic
                                  Mathematical Model Guides Mobile Health
                                  Intervention for Chronic Pain  . . . . . 675--688
                    Hu Yang and   
                    Xiaoqin Liu   Studies on the Clustering Algorithm for
                                  Analyzing Gene Expression Data with a
                                  Bidirectional Penalty  . . . . . . . . . 689--698
               Huaying Fang and   
           Chengcheng Huang and   
                Hongyu Zhao and   
                   Minghua Deng   gCoda: Conditional Dependence Network
                                  Inference for Compositional Data . . . . 699--708
               Minhyeok Lee and   
                Junhee Seok and   
               Donghyun Tae and   
                  Hua Zhong and   
                   Sung Won Han   A Comparison of Two-Stage Approaches
                                  Based on Penalized Regression for
                                  Estimating Gene Networks . . . . . . . . 709--720
                Yoonha Choi and   
                 Marc Coram and   
                   Jie Peng and   
                       Hua Tang   A Poisson Log-Normal Model for
                                  Constructing Gene Covariation Network
                                  Using RNA-seq Data . . . . . . . . . . . 721--731

Journal of Computational Biology
Volume 24, Number 8, August, 2017

Abdoulaye Baniré Diallo and   
     Engelbert Mephu Nguifo and   
               Mohammed J. Zaki   Preface: Selected Papers from the
                                  Workshop Bioinformatics and Artificial
                                  Intelligence Joined with the
                                  International Joint Conference on
                                  Artificial Intelligence  . . . . . . . . 733--733
             Vincent Picard and   
                Anne Siegel and   
  Jérémie Bourdon   A Logic for Checking the Probabilistic
                                  Steady-State Properties of Reaction
                                  Networks . . . . . . . . . . . . . . . . 734--745
      Abedalrhman Alkhateeb and   
                     Luis Rueda   Zseq: an Approach for Preprocessing
                                  Next-Generation Sequencing Data  . . . . 746--755
        Forough Firoozbakht and   
              Iman Rezaeian and   
          Michele D'agnillo and   
                Lisa Porter and   
                 Luis Rueda and   
                   Alioune Ngom   An Integrative Approach for Identifying
                                  Network Biomarkers of Breast Cancer
                                  Subtypes Using Genomic, Interactomic,
                                  and Transcriptomic Data  . . . . . . . . 756--766
             Ieva Vasiljeva and   
          Ognjen Arandjelovi\'c   Diagnosis Prediction from Electronic
                                  Health Records Using the Binary
                                  Diagnosis History Vector Representation  767--786
              Ham Ching Lam and   
                    Xuan Bi and   
         Srinand Sreevatsan and   
                   Daniel Boley   Evolution and Vaccination of Influenza
                                  Virus  . . . . . . . . . . . . . . . . . 787--798
              Ahmed Halioui and   
             Petko Valtchev and   
 Abdoulaye Baniré Diallo   T-GOWler: Discovering Generalized
                                  Process Models Within Texts  . . . . . . 799--808
  Ricardo De Souza Jacomini and   
  David Correa Martins, Jr. and   
       Felipe Leno Da Silva and   
        Anna Helena Reali Costa   GeNICE: a Novel Framework for Gene
                                  Network Inference by Clustering,
                                  Exhaustive Search, and Multivariate
                                  Analysis . . . . . . . . . . . . . . . . 809--830

Journal of Computational Biology
Volume 24, Number 9, September, 2017

            Filippo Disanto and   
              Noah A. Rosenberg   Enumeration of Ancestral Configurations
                                  for Matching Gene Trees and Species
                                  Trees  . . . . . . . . . . . . . . . . . 831--850
                  Zheng Dai and   
              David Becerra and   
Jérôme Waldispühl   On Stable States in a Topologically
                                  Driven Protein Folding Model . . . . . . 851--862
              Doaa Altarawy and   
         Fatma-Elzahraa Eid and   
               Lenwood S. Heath   PEAK: Integrating Curated and Noisy
                                  Prior Knowledge in Gene Regulatory
                                  Network Inference  . . . . . . . . . . . 863--873
            Daniel J. White and   
                  Jing Wang and   
                Richard J. Hall   Assessing the Impact of Assemblers on
                                  Virus Detection in a De Novo Metagenomic
                                  Analysis Pipeline  . . . . . . . . . . . 874--881
             Radhika Khanna and   
            Sangeeta Mittal and   
                 Sujata Mohanty   Development of Computer Algorithm for
                                  Editing of Next Generation Sequencing
                                  Metagenome Data  . . . . . . . . . . . . 882--894
           Ngoc Tam L. Tran and   
                 Chun-Hsi Huang   MOTIFSIM 2.1: an Enhanced Software
                                  Platform for Detecting Similarity in
                                  Multiple DNA Motif Data Sets . . . . . . 895--905
                  Noa Godin and   
                  Jerry Eichler   The Mitochondrial Protein Atlas: a
                                  Database of Experimentally Verified
                                  Information on the Human Mitochondrial
                                  Proteome . . . . . . . . . . . . . . . . 906--916
           Byeonghyeok Park and   
             Min-Jeong Baek and   
              Byoungnam Min and   
                   In-Geol Choi   Prokaryotic Contig Annotation Pipeline
                                  Server: Web Application for a
                                  Prokaryotic Genome Annotation Pipeline
                                  Based on the \pkgShiny App Package . . . 917--922
                   Xiuli Ma and   
               Guangyu Zhou and   
               Jingbo Shang and   
              Jingjing Wang and   
                  Jian Peng and   
                     Jiawei Han   Detection of Complexes in Biological
                                  Networks Through Diversified Dense
                                  Subgraph Mining  . . . . . . . . . . . . 923--941
                   Yu Zheng and   
                Xiaoyang Li and   
             Lydia C. Manor and   
                Hongbao Cao and   
                  Qiusheng Chen   An Integrative Computational Approach to
                                  Evaluate Genetic Markers for Chronic
                                  Lymphocytic Leukemia . . . . . . . . . . 942--952

Journal of Computational Biology
Volume 24, Number 10, October, 2017

            Paola Bonizzoni and   
      Gianluca Della Vedova and   
                Yuri Pirola and   
            Marco Previtali and   
                Raffaella Rizzi   FSG: Fast String Graph Construction for
                                  De Novo Assembly . . . . . . . . . . . . 953--968
               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   EpiGeNet: a Graph Database of
                                  Interdependencies Between Genetic and
                                  Epigenetic Events in Colorectal Cancer   969--980
            Cheng-Hong Yang and   
               Yu-Shiun Lin and   
              Li-Yeh Chuang and   
                Hsueh-Wei Chang   A Particle Swarm Optimization-Based
                                  Approach with Local Search for
                                  Predicting Protein Folding . . . . . . . 981--994
Pedro P. González-Pérez and   
             Daniel J. Orta and   
         Irving Peña and   
          Eduardo C. Flores and   
José U. Ramírez and   
    Hiram I. Beltrán and   
         Salomón J. Alas   A Computational Approach to Studying
                                  Protein Folding Problems Considering the
                                  Crucial Role of the Intracellular
                                  Environment  . . . . . . . . . . . . . . 995--1013
          Marek C. Milewski and   
                Karol Kamel and   
   Anna Kurzynska-Kokorniak and   
      Marcin K. Chmielewski and   
              Marek Figlerowicz   EvOligo: a Novel Software to Design and
                                  Group Libraries of Oligonucleotides
                                  Applicable for Nucleic Acid-Based
                                  Experiments  . . . . . . . . . . . . . . 1014--1028
               Lebin Thomas and   
                   Hari Ram and   
                  Ved Pal Singh   Evolutionary Relationships and
                                  Taxa-Specific Conserved Signature Indels
                                  Among Cellulases of Archaea, Bacteria,
                                  and Eukarya  . . . . . . . . . . . . . . 1029--1042
  Rajashekar Varma Kadumuri and   
            Ramakrishna Vadrevu   LoopX: a Graphical User Interface-Based
                                  Database for Comprehensive Analysis and
                                  Comparative Evaluation of Loops from
                                  Protein Structures . . . . . . . . . . . 1043--1049
                  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   pSuc-PseRat: Predicting Lysine
                                  Succinylation in Proteins by Exploiting
                                  the Ratios of Sequence Coupling and
                                  Properties . . . . . . . . . . . . . . . 1050--1059
               Feilong Deng and   
                Shi-Yi Chen and   
                Zhou-Lin Wu and   
                Yongsong Hu and   
                 Xianbo Jia and   
                   Song-Jia Lai   GFFview: a Web Server for Parsing and
                                  Visualizing Annotation Information of
                                  Eukaryotic Genome  . . . . . . . . . . . 1060--1064
                 Aldona Krupska   Influence of Oscillatory Enzyme Activity
                                  on the Reaction Kinetics: Mathematical
                                  Model  . . . . . . . . . . . . . . . . . 1065--1070

Journal of Computational Biology
Volume 24, Number 11, November, 2017

        Christina J. Castro and   
               Terry Fei Fan Ng   U$_{50}$: a New Metric for Measuring
                                  Assembly Output Based on
                                  Non-Overlapping, Target-Specific Contigs 1071--1080
Mahmut \cSam\.il Sa\ugiro\uglu and   
    M. O\uguzhan Külekc\.i   A System Architecture for Efficient
                                  Transmission of Massive DNA Sequencing
                                  Data . . . . . . . . . . . . . . . . . . 1081--1088
           Pawe\l B\la\.zej and   
     Ma\lgorzata Wn\ketrzak and   
    Ma\lgorzata Grabi\'nska and   
              Pawe\l Mackiewicz   Representations of Search Spaces in the
                                  Problem of Mutational Pressure
                                  Optimization According to Protein-Coding
                                  Sequences  . . . . . . . . . . . . . . . 1089--1098
                   Yan Zhou and   
               Baoxue Zhang and   
                 Gaorong Li and   
                Tiejun Tong and   
                      Xiang Wan   GD-RDA: a New Regularized Discriminant
                                  Analysis for High-Dimensional Data . . . 1099--1111
               Shengqing Lv and   
                 Yimin Chen and   
                    Zeyu Li and   
                  Jiahui Lu and   
                 Mingke Gao and   
                    Rongrong Lu   Application of Time-Frequency Domain
                                  Transform to Three-Dimensional
                                  Interpolation of Medical Images  . . . . 1112--1124
Gesiele Almeida Barros-Carvalho and   
       Marie-Anne Van Sluys and   
         Fabricio Martins Lopes   An Efficient Approach to Explore and
                                  Discriminate Anomalous Regions in
                                  Bacterial Genomes Based on Maximum
                                  Entropy  . . . . . . . . . . . . . . . . 1125--1133
           Natacha Cerisier and   
               Leslie Regad and   
                Dhoha Triki and   
       Anne-Claude Camproux and   
               Michel Petitjean   Cavity Versus Ligand Shape Descriptors:
                                  Application to Urokinase Binding Pockets 1134--1137
              Andrey Kechin and   
          Uljana Boyarskikh and   
              Alexander Kel and   
                Maxim Filipenko   cutPrimers: a New Tool for Accurate
                                  Cutting of Primers from Reads of
                                  Targeted Next Generation Sequencing  . . 1138--1143
  Álvaro Rubio-Largo and   
         Leonardo Vanneschi and   
             Mauro Castelli and   
Miguel A. Vega-Rodríguez   Reducing Alignment Time Complexity of
                                  Ultra-Large Sets of Sequences  . . . . . 1144--1152

Journal of Computational Biology
Volume 24, Number 12, December, 2017

       Nikita A. Sakhanenko and   
          James Kunert-Graf and   
                 David J. Galas   The Information Content of Discrete
                                  Functions and Their Application in
                                  Genetic Data Analysis  . . . . . . . . . 1153--1178
                  Ron Zeira and   
              Meirav Zehavi and   
                     Ron Shamir   A Linear-Time Algorithm for the Copy
                                  Number Transformation Problem  . . . . . 1179--1194
                Wenbin Chen and   
            William Hendrix and   
             Nagiza F. Samatova   The Application of the Weighted
                                  $k$-Partite Graph Problem to the
                                  Multiple Alignment for Metabolic
                                  Pathways . . . . . . . . . . . . . . . . 1195--1211
            Cheng-Hong Yang and   
                  Yu-Da Lin and   
              Li-Yeh Chuang and   
               Jin-Bor Chen and   
                Hsueh-Wei Chang   Joint Analysis of SNP--SNP-Environment
                                  Interactions for Chronic Dialysis by an
                                  Improved Branch and Bound Algorithm  . . 1212--1225
         Haitham Elmarakeby and   
           Mostafa Arefiyan and   
               Elijah Myers and   
                    Song Li and   
                 Ruth Grene and   
               Lenwood S. Heath   Beacon Editor: Capturing Signal
                                  Transduction Pathways Using the Systems
                                  Biology Graphical Notation Activity Flow
                                  Language . . . . . . . . . . . . . . . . 1226--1229
                   Wenhe Su and   
               Xiangke Liao and   
                  Yutong Lu and   
                   Quan Zou and   
                 Shaoliang Peng   Multiple Sequence Alignment Based on a
                                  Suffix Tree and Center-Star Strategy: a
                                  Linear Method for Multiple Nucleotide
                                  Sequence Alignment on Spark Parallel
                                  Framework  . . . . . . . . . . . . . . . 1230--1242
                   Chao Pei and   
               Shu-Lin Wang and   
               Jianwen Fang and   
                      Wei Zhang   GSMC: Combining Parallel Gibbs Sampling
                                  with Maximal Cliques for Hunting DNA
                                  Motif  . . . . . . . . . . . . . . . . . 1243--1253
               Shin-Fu Tsai and   
              Chih-Wei Tung and   
               Chen-An Tsai and   
                  Chen-Tuo Liao   An Exhaustive Scan Method for SNP Main
                                  Effects and SNP $ \times $ SNP
                                  Interactions Over Highly Homozygous
                                  Genomes  . . . . . . . . . . . . . . . . 1254--1264
            Samana Shrestha and   
               Adam Vanasse and   
             Leon N. Cooper and   
              Michael P. Antosh   Gene Expression as a Dosimeter in
                                  Irradiated \bionameDrosophila
                                  melanogaster . . . . . . . . . . . . . . 1265--1274
           Md Shahinuzzaman and   
                    Dipak Barua   A Multiscale Algorithm for
                                  Spatiotemporal Modeling of Multivalent
                                  Protein--Protein Interaction . . . . . . 1275--1283


Journal of Computational Biology
Volume 25, Number 1, January, 2018

                    Jing He and   
              Kamal Al Nasr and   
                 Weitao Sun and   
                    Yonggang Lu   \em Special Issue Preface: The 9th
                                  Computational Structural Bioinformatics
                                  Workshop . . . . . . . . . . . . . . . . 1--2
           Jayvee R. Abella and   
                  Mark Moll and   
               Lydia E. Kavraki   Maintaining and Enhancing Diversity of
                                  Sampled Protein Conformations in
                                  Robotics-Inspired Methods  . . . . . . . 3--20
              Kamal Al Nasr and   
          Christopher Jones and   
               Feras Yousef and   
                    Ruba Jebril   PEM-fitter: a Coarse-Grained Method to
                                  Validate Protein Candidate Models  . . . 21--32
           Tatiana Maximova and   
               Zijing Zhang and   
             Daniel B. Carr and   
                Erion Plaku and   
                   Amarda Shehu   Sample-Based Models of Protein Energy
                                  Landscapes and Slow Structural
                                  Rearrangements . . . . . . . . . . . . . 33--50
             Nathan Clement and   
            Muhibur Rasheed and   
           Chandrajit Lal Bajaj   Viral Capsid Assembly: a Quantified
                                  Uncertainty Approach . . . . . . . . . . 51--71
               Jin Seob Kim and   
          Gregory S. Chirikjian   Symmetrical Parameterization of Rigid
                                  Body Transformations for Biomolecular
                                  Structures . . . . . . . . . . . . . . . 72--88
           Michael Siderius and   
              Filip Jagodzinski   Mutation Sensitivity Maps: Identifying
                                  Residue Substitutions That Impact
                                  Protein Structure Via a Rigidity
                                  Analysis In Silico Mutation Approach . . 89--102
                     Weitao Sun   The Relationship Between Low-Frequency
                                  Motions and Community Structure of
                                  Residue Network in Protein Molecules . . 103--113
            Tunazzina Islam and   
             Michael Poteat and   
                        Jing He   Quantification of Twist from the Central
                                  Lines of $ \beta $-Strands . . . . . . . 114--120

Journal of Computational Biology
Volume 25, Number 2, February, 2018

        Stephen F. Altschul and   
              Andrew F. Neuwald   Initial Cluster Analysis . . . . . . . . 121--129
                Heewon Park and   
           Teppei Shimamura and   
                Seiya Imoto and   
                  Satoru Miyano   Adaptive NetworkProfiler for Identifying
                                  Cancer Characteristic-Specific Gene
                                  Regulatory Networks  . . . . . . . . . . 130--145
                 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   Analyzing the LncRNA, miRNA, and mRNA
                                  Regulatory Network in Prostate Cancer
                                  with Bioinformatics Software . . . . . . 146--157
            Cheng-Hong Yang and   
            Yi-Cheng Chiang and   
              Li-Yeh Chuang and   
                      Yu-Da Lin   A CpGCluster-Teaching--Learning-Based
                                  Optimization for Prediction of CpG
                                  Islands in the Human Genome  . . . . . . 158--169
            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   In Silico Approach to Investigate the
                                  Structural and Functional Attributes of
                                  Familial Hypercholesterolemia Variants
                                  Reported in the Saudi Population . . . . 170--181
         Mohammad S. Rahman and   
           Ann E. Nicholson and   
             Gholamreza Haffari   HetFHMM: a Novel Approach to Infer Tumor
                                  Heterogeneity Using Factorial Hidden
                                  Markov Models  . . . . . . . . . . . . . 182--193
           Evaldo Bezerra Costa   MELC Genomics: a Framework for De Novo
                                  Genome Assembly  . . . . . . . . . . . . 194--199
            Jordi Vilaplana and   
                  Rui Alves and   
           Francesc Solsona and   
                Jordi Mateo and   
        Ivan Teixidó and   
            Marc Pifarré   MetReS, an Efficient Database for
                                  Genomic Applications . . . . . . . . . . 200--213
            Arnon Benshahar and   
        Vered Chalifa-Caspi and   
             Danny Hermelin and   
             Michal Ziv-Ukelson   A Biclique Approach to
                                  Reference-Anchored Gene Blocks and Its
                                  Applications to Genomic Islands  . . . . 214--235
                Sawsan Kanj and   
          Thomas Brüls and   
          Stéphane Gazut   Shared Nearest Neighbor Clustering in a
                                  Locality Sensitive Hashing Framework . . 236--250

Journal of Computational Biology
Volume 25, Number 3, March, 2018

                Zhipeng Cai and   
                Pavel Skums and   
           Alexander Zelikovsky   \em Special Issue Preface: 13th
                                  International Symposium on
                                  Bioinformatics Research and Applications
                                  (ISBRA 2017) . . . . . . . . . . . . . . 251--252
             Kuang-Yu Chang and   
                    Yun Cui and   
               Siu-Ming Yiu and   
                   Wing-Kai Hon   Reconstructing One-Articulated Networks
                                  with Distance Matrices . . . . . . . . . 253--269
                 Zihao Wang and   
                    Yu Chen and   
             Jingrong Zhang and   
                     Lun Li and   
                Xiaohua Wan and   
                Zhiyong Liu and   
                    Fei Sun and   
                       Fa Zhang   ICON-MIC: Implementing a CPU/MIC
                                  Collaboration Parallel Framework for
                                  ICON on Tianhe-2 Supercomputer . . . . . 270--281
   Micha\l Aleksander Ciach and   
 Mateusz Krzysztof \L\kacki and   
       B\la\.zej Miasojedow and   
           Frederik Lermyte and   
            Dirk Valkenborg and   
               Frank Sobott and   
                    Anna Gambin   Estimation of Rates of Reactions
                                  Triggered by Electron Transfer in
                                  Top-Down Mass Spectrometry . . . . . . . 282--301
                 Ruofan Xia and   
                     Yu Lin and   
                   Jun Zhou and   
                  Bing Feng and   
                     Jijun Tang   A Median Solver and Phylogenetic
                                  Inference Based on Double-Cut-and-Join
                                  Sorting  . . . . . . . . . . . . . . . . 302--312
             Rashika Mishra and   
              Ovidiu Daescu and   
             Patrick Leavey and   
             Dinesh Rakheja and   
                 Anita Sengupta   Convolutional Neural Network for
                                  Histopathological Analysis of
                                  Osteosarcoma . . . . . . . . . . . . . . 313--325
                  Albert Ng and   
                        Dong Si   Beta-Barrel Detection for Medium
                                  Resolution Cryo-Electron Microscopy
                                  Density Maps Using Genetic Algorithms
                                  and Ray Tracing  . . . . . . . . . . . . 326--336
               Xiuchun Xiao and   
                   Bing Liu and   
                 Jing Zhang and   
                 Xueli Xiao and   
                         Yi Pan   An Optimized Method for Bayesian
                                  Connectivity Change Point Model  . . . . 337--347
                Bruno Fosso and   
            Graziano Pesole and   
   Francesc Rosselló and   
               Gabriel Valiente   Unbiased Taxonomic Annotation of
                                  Metagenomic Samples  . . . . . . . . . . 348--360
                   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   A Computational-Based Method for
                                  Predicting Drug-Target Interactions by
                                  Using Stacked Autoencoder Deep Neural
                                  Network  . . . . . . . . . . . . . . . . 361--373

Journal of Computational Biology
Volume 25, Number 4, April, 2018

             Ana M. Jelovic and   
             Nenad S. Mitic and   
             Samira Eshafah and   
             Milos V. Beljanski   Finding Statistically Significant
                                  Repeats in Nucleic Acids and Proteins    375--387
                  Hong Wang and   
               Xiaolin Chen and   
                        Gang Li   Survival Forests with $R$-Squared
                                  Splitting Rules  . . . . . . . . . . . . 388--395
                Lingling Li and   
               Tianhai Tian and   
                    Xinan Zhang   Mutation Mechanisms of Human Breast
                                  Cancer . . . . . . . . . . . . . . . . . 396--404
          Hsin-Hsiung Huang and   
         Senthil B. Girimurugan   A Novel Real-Time Genome Comparison
                                  Method Using Discrete Wavelet Transform  405--416
                  Jaeil Ahn and   
            Brian Conkright and   
             Simina M. Boca and   
                 Subha Madhavan   POPSTR: Inference of Admixed Population
                                  Structure Based on Single-Nucleotide
                                  Polymorphisms and Copy Number Variations 417--429
            Andreas M. Kist and   
           Angelika Lampert and   
            Andrias O. O'Reilly   DIsulfide Mapping PLanner Software Tool  430--434
                    Jun Fan and   
                  Jing Yang and   
                  Zhenran Jiang   Prediction of Central Nervous System
                                  Side Effects Through Drug Permeability
                                  to Blood--Brain Barrier and
                                  Recommendation Algorithm . . . . . . . . 435--443
            Andrey Minarsky and   
             Nadya Morozova and   
              Robert Penner and   
        Christophe Soulé   Theory of Morphogenesis  . . . . . . . . 444--450
      Rodrigo Ligabue-Braun and   
            Bruno Borguesan and   
                 Hugo Verli and   
          Mathias J. Krause and   
             Márcio Dorn   Everyone Is a Protagonist: Residue
                                  Conformational Preferences in
                                  High-Resolution Protein Structures . . . 451--465

Journal of Computational Biology
Volume 25, Number 5, May, 2018

                   Chen Sun and   
           Robert S. Harris and   
               Rayan Chikhi and   
                  Paul Medvedev   AllSome Sequence Bloom Trees . . . . . . 467--479
Néli J. Fonseca-Júnior and   
       Marcelo Q. L. Afonso and   
          Lucas C. Oliveira and   
                 Lucas Bleicher   PFstats: a Network-Based Open Tool for
                                  Protein Family Analysis  . . . . . . . . 480--486
               Qianghui Guo and   
                  Jian Wang and   
                        Zhao Xu   Approximation Algorithms for Protein
                                  Folding in the Hydrophobic-Polar Model
                                  on $3$D Hexagonal Prism Lattice  . . . . 487--498
                    Yang Xu and   
                  Xiao-Chun Luo   PyPathway: Python Package for Biological
                                  Network Analysis and Visualization . . . 499--504
              Miha Mo\vskon and   
              Nikolaj Zimic and   
                      Miha Mraz   Grohar: Automated Visualization of
                                  Genome-Scale Metabolic Models and Their
                                  Pathways . . . . . . . . . . . . . . . . 505--508
              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   REDO: RNA Editing Detection in Plant
                                  Organelles Based on Variant Calling
                                  Results  . . . . . . . . . . . . . . . . 509--516
          Carlos N. Fischer and   
         Victor De A.Campos and   
              Victor H. Barella   On the Search for Retrotransposons:
                                  Alternative Protocols to Obtain
                                  Sequences to Learn Profile Hidden Markov
                                  Models . . . . . . . . . . . . . . . . . 517--527

Journal of Computational Biology
Volume 25, Number 6, June, 2018

                Yongan Zhao and   
              Xiaofeng Wang and   
                     Haixu Tang   A Secure Alignment Algorithm for Mapping
                                  Short Reads to Human Genome  . . . . . . 529--540
              Albert Vexler and   
                     Jihnhee Yu   To $t$-Test or Not to $t$-Test? A
                                  $p$-Values-Based Point of View in the
                                  Receiver Operating Characteristic Curve
                                  Framework  . . . . . . . . . . . . . . . 541--550
                    Lu Zeng and   
        Stephen M. Pederson and   
                Danfeng Cao and   
                 Zhipeng Qu and   
                Zhiqiang Hu and   
           David L. Adelson and   
                   Chaochun Wei   Genome-Wide Analysis of the Association
                                  of Transposable Elements with Gene
                                  Regulation Suggests that \bionameAlu
                                  Elements Have the Largest Overall
                                  Regulatory Impact  . . . . . . . . . . . 551--562
              Xiaodong Wang and   
                       Lei Wang   A Simple Linear Space Algorithm for
                                  Computing Nonoverlapping Inversion and
                                  Transposition Distance in Quadratic
                                  Average Time . . . . . . . . . . . . . . 563--575
                   Yan Dong and   
                Hongbao Cao and   
                  Zhigang Liang   A Curated Target Gene Pool Assisting
                                  Early Disease Prediction and
                                  Patient-Specific Treatment for Small
                                  Cell Lung Cancer . . . . . . . . . . . . 576--585
                 Lizhen Liu and   
                 Xiaowu Sun and   
                   Wei Song and   
                        Chao Du   A Method for Predicting Protein
                                  Complexes from Dynamic Weighted
                                  Protein--Protein Interaction Networks    586--605
         Chelsea M. Lawhorn and   
           Rachel Schomaker and   
         Jonathan T. Rowell and   
                  Olav Rueppell   Simple Comparative Analyses of
                                  Differentially Expressed Gene Lists May
                                  Overestimate Gene Overlap  . . . . . . . 606--612
                   Markus Boenn   ShRangeSim: Simulation of Single
                                  Nucleotide Polymorphism Clusters in
                                  Next-Generation Sequencing Data  . . . . 613--622

Journal of Computational Biology
Volume 25, Number 7, July, 2018

                  Cenk Sahinalp   Preface: Selected Articles from RECOMB
                                  2017 . . . . . . . . . . . . . . . . . . 623--623
            Ashok Rajaraman and   
                        Jian Ma   Toward Recovering Allele-specific Cancer
                                  Genome Graphs  . . . . . . . . . . . . . 624--636
                 Soyeon Ahn and   
                   Haris Vikalo   aBayesQR: a Bayesian Method for
                                  Reconstruction of Viral Populations
                                  Characterized by Low Diversity . . . . . 637--648
             Benedict Paten and   
          Jordan M. Eizenga and   
             Yohei M. Rosen and   
              Adam M. Novak and   
              Erik Garrison and   
                   Glenn Hickey   Superbubbles, Ultrabubbles, and Cacti    649--663
             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   A Flow Procedure for Linearization of
                                  Genome Sequence Graphs . . . . . . . . . 664--676
             Victoria Popic and   
         Volodymyr Kuleshov and   
             Michael Snyder and   
              Serafim Batzoglou   Fast Metagenomic Binning via Hashing and
                                  Bayesian Clustering  . . . . . . . . . . 677--688
            Simone Zaccaria and   
          Mohammed El-Kebir and   
             Gunnar W. Klau and   
            Benjamin J. Raphael   Phylogenetic Copy-Number Factorization
                                  of Multiple Tumor Samples  . . . . . . . 689--708
             Robert O. Ness and   
                Karen Sachs and   
              Parag Mallick and   
                     Olga Vitek   A Bayesian Active Learning Experimental
                                  Design for Inferring Signaling Networks  709--725
         Adegoke A. Ojewole and   
            Jonathan D. Jou and   
            Vance G. Fowler and   
                Bruce R. Donald   \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  . . . . . . . . . 726--739
             Jesper Jansson and   
             Andrzej Lingas and   
              Ramesh Rajaby and   
                  Wing-Kin Sung   Determining the Consistency of Resolved
                                  Triplets and Fan Triplets  . . . . . . . 740--754
               Brad Solomon and   
                 Carl Kingsford   Improved Search of Large Transcriptomic
                                  Sequencing Databases Using Split
                                  Sequence Bloom Trees . . . . . . . . . . 755--765
                Chirag Jain and   
          Alexander Dilthey and   
               Sergey Koren and   
             Srinivas Aluru and   
              Adam M. Phillippy   A Fast Approximate Algorithm for Mapping
                                  Long Reads to Large Reference Databases  766--779
               Dan DeBlasio and   
                John Kececioglu   Adaptive Local Realignment of Protein
                                  Sequences  . . . . . . . . . . . . . . . 780--793
            Regev Schweiger and   
                Eyal Fisher and   
              Elior Rahmani and   
               Liat Shenhav and   
             Saharon Rosset and   
                  Eran Halperin   Using Stochastic Approximation
                                  Techniques to Efficiently Construct
                                  Confidence Intervals for Heritability    794--808
              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   Longitudinal Genotype--Phenotype
                                  Association Study through Temporal
                                  Structure Auto-Learning Predictive Model 809--824
           Guillaume Holley and   
             Roland Wittler and   
                 Jens Stoye and   
                     Faraz Hach   Dynamic Alignment-Free and
                                  Reference-Free Read Compression  . . . . 825--836

Journal of Computational Biology
Volume 25, Number 8, August, 2018

Miguel A. Vega-Rodríguez and   
  José M. Granado-Criado   \em Preface to the Special Issue:
                                  Parallel Computing in Computational
                                  Biology: a Technological Point of View   837--840
Esteban Pérez-Wohlfeil and   
                Oswaldo Trelles   Precise and Parallel Pairwise
                                  Metagenomic Comparisons  . . . . . . . . 841--849
     Andreia Sofia Teixeira and   
          Pedro T. Monteiro and   
João A. Carriço and   
        Francisco C. Santos and   
         Alexandre P. Francisco   Large-Scale Simulations of Bacterial
                                  Populations Over Complex Networks  . . . 850--861
Héctor Martínez and   
          Sergio Barrachina and   
           Maribel Castillo and   
Enrique S. Quintana-Ortí and   
     Jordi Rambla de Argila and   
        Xavier Farré and   
                 Arcadi Navarro   FaST-LMM for Two-Way Epistasis Tests on
                                  High-Performance Clusters  . . . . . . . 862--870
              Marek Nowicki and   
             Davit Bzhalava and   
                    Piotr Ba\la   Massively Parallel Implementation of
                                  Sequence Alignment with Basic Local
                                  Alignment Search Tool Using Parallel
                                  Computing in Java Library  . . . . . . . 871--881
   Juan José Escobar and   
               Julio Ortega and   
Antonio Francisco Díaz and   
Jesús González and   
                   Miguel Damas   A Power--Performance Perspective to
                                  Multiobjective Electroencephalogram
                                  Feature Selection on Heterogeneous
                                  Parallel Platforms . . . . . . . . . . . 882--893
        Jordi Lladós and   
             Fernando Cores and   
               Fernando Guirado   Scalable Consistency in T-Coffee Through
                                  Apache Spark and Cassandra Database  . . 894--906
               Jian-Xin Wen and   
                Xiao-Qin Li and   
                       Yu Chang   Signature Gene Identification of Cancer
                                  Occurrence and Pattern Recognition . . . 907--916
               Elise Rosati and   
               Morgan Madec and   
     Jean-Baptiste Kammerer and   
         Luc Hébrard and   
       Christophe Lallement and   
                 Jacques Haiech   Efficient Modeling and Simulation of
                                  Space-Dependent Biological Systems . . . 917--933
              Fengqian Pang and   
                    Heng Li and   
               Yonggang Shi and   
                     Zhiwen Liu   Computational Analysis of Cell Dynamics
                                  in Videos with Hierarchical-Pooled
                                  Deep-Convolutional Features  . . . . . . 934--953
                Tatsuhiko Naito   Human Splice-Site Prediction with Deep
                                  Neural Networks  . . . . . . . . . . . . 954--961

Journal of Computational Biology
Volume 25, Number 9, September, 2018

                  Jian Zhao and   
               Jiasong Wang and   
                  Hongmei Jiang   Detecting Periodicities in Eukaryotic
                                  Genomes by Ramanujan Fourier Transform   963--975
           Tsukasa Fukunaga and   
                Michiaki Hamada   A Novel Method for Assessing the
                                  Statistical Significance of RNA-RNA
                                  Interactions Between Two Long RNAs . . . 976--986
                 Yoonji Kim and   
                     Jaejik Kim   Estimation of Dynamic Systems for Gene
                                  Regulatory Networks from Dependent
                                  Time-Course Data . . . . . . . . . . . . 987--996
             Bandana Kumari and   
             Ravindra Kumar and   
                   Manish Kumar   Prediction of Rare Palmitoylation Events
                                  in Proteins  . . . . . . . . . . . . . . 997--1008
  Álvaro Rubio-Largo and   
             Mauro Castelli and   
         Leonardo Vanneschi and   
Miguel A. Vega-Rodríguez   A Parallel Multiobjective Metaheuristic
                                  for Multiple Sequence Alignment  . . . . 1009--1022
              Komlan Atitey and   
               Pavel Loskot and   
                      Paul Rees   Determining the Transcription Rates
                                  Yielding Steady-State Production of mRNA
                                  in the \bionameLac Genetic Switch of
                                  \bionameEscherichia coli . . . . . . . . 1023--1039
         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   Improving Single-Nucleotide
                                  Polymorphism-Based Fetal Fraction
                                  Estimation of Maternal Plasma
                                  Circulating Cell-Free DNA Using Bayesian
                                  Hierarchical Models  . . . . . . . . . . 1040--1049
               Xinrui Huang and   
                     Sha Li and   
                       Song Gao   Applying a Modified Wavelet Shrinkage
                                  Filter to Improve Cryo-Electron
                                  Microscopy Imaging . . . . . . . . . . . 1050--1058
              Joonyeon Park and   
               Myeongji Cho and   
                   Hyeon S. Son   Simulation Model of Bacterial Resistance
                                  to Antibiotics Using Individual-Based
                                  Modeling . . . . . . . . . . . . . . . . 1059--1070

Journal of Computational Biology
Volume 25, Number 10, October, 2018

                     Yu Bao and   
         Morihiro Hayashida and   
                 Pengyu Liu and   
         Masayuki Ishitsuka and   
             Jose C. Nacher and   
                 Tatsuya Akutsu   Analysis of Critical and Redundant
                                  Vertices in Controlling Directed Complex
                                  Networks Using Feedback Vertex Sets  . . 1071--1090
            Stefano Beretta and   
             Mauro Castelli and   
       Ivo Gonçalves and   
                   Ivan Kel and   
        Valentina Giansanti and   
                   Ivan Merelli   Improving eQTL Analysis Using a Machine
                                  Learning Approach for Data Integration:
                                  a Logistic Model Tree Solution . . . . . 1091--1105
            Marek Palkowski and   
           Wlodzimierz Bielecki   Parallel Tiled Codes Implementing the
                                  Smith--Waterman Alignment Algorithm for
                                  Two and Three Sequences  . . . . . . . . 1106--1119
       \.Irfan Kösesoy and   
             Murat Gök and   
                  Cemil Öz   PROSES: a Web Server for Sequence-Based
                                  Protein Encoding . . . . . . . . . . . . 1120--1122
              Shisheng Wang and   
                  Wen Zheng and   
                 Liqiang Hu and   
                  Meng Gong and   
                       Hao Yang   MixProTool: a Powerful and Comprehensive
                                  Web Tool for Analyzing and Visualizing
                                  Multigroup Proteomics Data . . . . . . . 1123--1127
                   Jie Chen and   
                   Shirong Deng   Detection of Copy Number Variation
                                  Regions Using the DNA-Sequencing Data
                                  from Multiple Profiles with Correlated
                                  Structure  . . . . . . . . . . . . . . . 1128--1140
                  Jan Voges and   
                Ali Fotouhi and   
        Jörn Ostermann and   
Muhammed O\uguzhan Külekci   A Two-Level Scheme for Quality Score
                                  Compression  . . . . . . . . . . . . . . 1141--1151
                    Qie Liu and   
                    Min Liu and   
                       Wenfa Wu   Strong/Weak Feature Recognition of
                                  Promoters Based on Position Weight
                                  Matrix and Ensemble Set-Valued Models    1152--1160
               Xuedong Wang and   
               Wenhui Shang and   
                   Yu Chang and   
                     Xiaoqin Li   Methylation Signature Genes
                                  Identification of the Lung Squamous Cell
                                  Carcinoma Occurrence and Recognition
                                  Research . . . . . . . . . . . . . . . . 1161--1169

Journal of Computational Biology
Volume 25, Number 11, November, 2018

            Yaron Orenstein and   
             Yun William Yu and   
                  Bonnie Berger   Joker de Bruijn: Covering $k$-Mers Using
                                  Joker Characters . . . . . . . . . . . . 1171--1178
        Christopher Barrett and   
                   Qijun He and   
             Fenix W. Huang and   
            Christian M. Reidys   An Efficient Dual Sampling Algorithm
                                  with Hamming Distance Filtration . . . . 1179--1192
                Xinrui Zhou and   
               Amihood Amir and   
          Concettina Guerra and   
                Gadi Landau and   
                Jarek Rossignac   EDoP Distance Between Sets of Incomplete
                                  Permutations: Application to Bacteria
                                  Classification Based on Gene Order . . . 1193--1202
             Nikita Alexeev and   
               Max A. Alekseyev   Combinatorial Scoring of Phylogenetic
                                  Trees and Networks Based on
                                  Homoplasy-Free Characters  . . . . . . . 1203--1219
        Theodore Alexandrov and   
            Nina Golyandina and   
             David Holloway and   
               Alex Shlemov and   
               Alexander Spirov   Two-Exponential Models of Gene
                                  Expression Patterns for Noisy
                                  Experimental Data  . . . . . . . . . . . 1220--1230
      Siamak K. Sorooshyari and   
          Matthew P. Taylor and   
                H. Vincent Poor   Probabilistic Modeling of Pseudorabies
                                  Virus Infection in a Neural Circuit  . . 1231--1246
         Ali Yousefian-Jazi and   
                   Jinwook Choi   Sequential Integration of Fuzzy
                                  Clustering and Expectation Maximization
                                  for Transcription Factor Binding Site
                                  Identification . . . . . . . . . . . . . 1247--1256
             Tiago Tambonis and   
            Marcelo Boareto and   
              Vitor B. P. Leite   Differential Expression Analysis in
                                  RNA-seq Data Using a Geometric Approach  1257--1265
                   Hui Yang and   
                     Hao Lv and   
                   Hui Ding and   
                   Wei Chen and   
                        Hao Lin   iRNA-2OM: a Sequence-Based Predictor for
                                  Identifying 2'-O-Methylation Sites in
                                  \bionameHomo sapiens . . . . . . . . . . 1266--1277
           Dinko Osmankovic and   
                Semir Doric and   
              Naris Pojskic and   
              Lada Lukic Bilela   New Approach to Detect Coiled Coil and
                                  Leucine Zipper Motifs in Protein
                                  Sequences  . . . . . . . . . . . . . . . 1278--1283

Journal of Computational Biology
Volume 25, Number 12, December, 2018

    José M. J. Costa and   
       Helcio R. B. Orlande and   
        Viviane O. F. Lione and   
         Antonio G. F. Lima and   
 Tayná C. S. Cardoso and   
    Leonardo A. B. Varón   Simultaneous Model Selection and Model
                                  Calibration for the Proliferation of
                                  Tumor and Normal Cells During In Vitro
                                  Chemotherapy Experiments . . . . . . . . 1285--1300
 Vijaya Raghavan Rangamaran and   
          Bharathram Uppili and   
              Dharani Gopal and   
         Kirubagaran Ramalingam   EasyQC: Tool with Interactive User
                                  Interface for Efficient Next-Generation
                                  Sequencing Data Quality Control  . . . . 1301--1311
               Xiaoping Yan and   
                   Yu Huang and   
                      Jiabin Wu   Identify Cross Talk Between Circadian
                                  Rhythm and Coronary Heart Disease by
                                  Multiple Correlation Analysis  . . . . . 1312--1327
              Caio Santiago and   
             Vivian Pereira and   
           Luciano Digiampietri   Homology Detection Using Multilayer
                                  Maximum Clustering Coefficient . . . . . 1328--1338
            Matthias Werner and   
               Pascal Fieth and   
             Alexander Hartmann   Large-Deviation Properties of Sequence
                                  Alignment of Correlated Sequences  . . . 1339--1346
              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   Machine Learning-Based Method for
                                  Obesity Risk Evaluation Using
                                  Single-Nucleotide Polymorphisms Derived
                                  from Next-Generation Sequencing  . . . . 1347--1360
                  Ming Yang and   
                  Louis Z. Yang   Determining a Reasonable Range of
                                  Relative Numerical Tolerance Values for
                                  Simulating Deterministic Models of
                                  Biochemical Reactions  . . . . . . . . . 1361--1364
             Snehalika Lall and   
            Debajyoti Sinha and   
  Sanghamitra Bandyopadhyay and   
               Debarka Sengupta   Structure-Aware Principal Component
                                  Analysis for Single-Cell RNA-seq Data    1365--1373
         Jeonifer M. Garren and   
                     Jaejik Kim   Bootstrapping Time-Course Gene
                                  Expression Data for Gene Networks:
                                  Application to Gene Relevance Networks   1374--1384
                    Yue Liu and   
               Shu-Lin Wang and   
                 Jun-Feng Zhang   Prediction of Microbe--Disease
                                  Associations by Graph Regularized
                                  Non-Negative Matrix Factorization  . . . 1385--1394


Journal of Computational Biology
Volume 26, Number 1, January, 2019

               Yanshen Yang and   
       Jeffrey A. Robertson and   
                   Zhen Guo and   
              Jake Martinez and   
            Christy Coghlan and   
               Lenwood S. Heath   MCAT: Motif Combining and Association
                                  Tool . . . . . . . . . . . . . . . . . . 1--15
              Defne Surujon and   
                 Yann Ponty and   
                    Peter Clote   Small-World Networks and RNA Secondary
                                  Structures . . . . . . . . . . . . . . . 16--26
                Eliran Avni and   
                      Sagi Snir   A New Quartet-Based Statistical Method
                                  for Comparing Sets of Gene Trees Is
                                  Developed Using a Generalized Hoeffding
                                  Inequality . . . . . . . . . . . . . . . 27--37
                  Dat Duong and   
           Wasi Uddin Ahmad and   
              Eleazar Eskin and   
              Kai-Wei Chang and   
              Jingyi Jessica Li   Word and Sentence Embedding Tools to
                                  Measure Semantic Similarity of Gene
                                  Ontology Terms by Their Definitions  . . 38--52
     Vaddadi Naga Sai Kavya and   
              Kshitij Tayal and   
        Rajgopal Srinivasan and   
               Naveen Sivadasan   Sequence Alignment on Directed Graphs    53--67
                   Eduard Fomin   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  . . . . . . 68--75
              Daniel Mellem and   
              Frank Fischer and   
         Sören Jaspers and   
                Horst Wenck and   
         Michael Rübhausen   Mitochondrial Morphologies Driven by
                                  Energy-Consuming Cell Sites in a
                                  Spatially and Time-Resolved Quality
                                  Model  . . . . . . . . . . . . . . . . . 76--85
             Shih-Chiang Lo and   
               Feng-You Liu and   
              Wun-Sin Jhang and   
                    Che-Chi Shu   The Insight into Protein-Ligand
                                  Interactions, a Novel Way of Buffering
                                  Protein Noise in Gene Expression . . . . 86--95
                 Michael Ta and   
             Changchuan Yin and   
             Gary Lee Smith and   
                       Wenbo Xu   A Workflow to Improve Variant Calling
                                  Accuracy in Molecular Barcoded
                                  Sequencing Reads . . . . . . . . . . . . 96--103

Journal of Computational Biology
Volume 26, Number 2, February, 2019

         Gopinath Samykannu and   
          Princy Vijayababu and   
Christian Bharathi Antonyraj and   
            Perumal Perumal and   
   Sundarabaalaji Narayanan and   
Syed Ibrahim Basheer Ahamed and   
            Jeyakumar Natarajan   In Silico Characterization of B Cell and
                                  T Cell Epitopes for Subunit Vaccine
                                  Design of \bionameSalmonella typhi PgtE:
                                  a Molecular Dynamics Simulation Approach 105--116
Filip Zavadil Koká\vs and   
Véronique Bergougnoux and   
Mária Majeská \vCudejková   SATrans: New Free Available Software for
                                  Annotation of Transcriptome and
                                  Functional Analysis of Differentially
                                  Expressed Genes  . . . . . . . . . . . . 117--123
              Vasily Ershov and   
              Artem Tarasov and   
               Alla Lapidus and   
             Anton Korobeynikov   IonHammer: Homopolymer-Space Hamming
                                  Clustering for IonTorrent Read Error
                                  Correction . . . . . . . . . . . . . . . 124--127
                 Sihai Yang and   
                Xianhua Han and   
                    Yenwei Chen   Three-Dimensional Embryonic Image
                                  Segmentation and Registration Based on
                                  Shape Index and Ellipsoid-Fitting Method 128--142
                 Changchuan Yin   Encoding and Decoding DNA Sequences by
                                  Integer Chaos Game Representation  . . . 143--151
                 Lisa Uechi and   
             David J. Galas and   
           Nikita A. Sakhanenko   Multivariate Analysis of Data Sets with
                                  Missing Values: an Information
                                  Theory-Based Reliability Function  . . . 152--171

Journal of Computational Biology
Volume 26, Number 3, March, 2019

        Christopher Barrett and   
                   Qijun He and   
             Fenix W. Huang and   
            Christian M. Reidys   A Boltzmann Sampler for $1$-Pairs with
                                  Double Filtration  . . . . . . . . . . . 173--192
              Xiaodong Wang and   
                       Lei Wang   Computing Nonoverlapping Inversion
                                  Distance Between Two Strings in Linear
                                  Average Time . . . . . . . . . . . . . . 193--201
                Heewon Park and   
              Makoto Yamada and   
                Seiya Imoto and   
                  Satoru Miyano   Robust Sample-Specific Stability
                                  Selection with Effective Error Control   202--217
                Xiaodan Mao and   
                  Yichen Xu and   
                  Zhenran Jiang   HColonDB: a Database for Human Colon
                                  Cancer Research  . . . . . . . . . . . . 218--224
            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   INDEX-db: The Indian Exome Reference
                                  Database (Phase I) . . . . . . . . . . . 225--234
             Monika Piwowar and   
                 Tomasz Ku\laga   Directional Association Measurement in
                                  Contingency Tables: Genomic Case . . . . 235--240
                Yuandi Wang and   
                Qingmei Wen and   
               Zhigang Zhou and   
                     Nanjun Yan   Cell Modeling Based on Bubbles with
                                  Weighted Membranes . . . . . . . . . . . 241--265
              Roberto Solar and   
           Victor Sepulveda and   
    Alonso Inostrosa-Psijas and   
                Oscar Rojas and   
         Veronica Gil-Costa and   
                 Mauricio Marin   A Service-Oriented Platform for
                                  Approximate Bayesian Computation in
                                  Population Genetics  . . . . . . . . . . 266--279
                Baekdoo Kim and   
               Thahmina Ali and   
               Changsu Dong and   
             Carlos Lijeron and   
              Raja Mazumder and   
            Claudia Wultsch and   
           Konstantinos Krampis   \em miCloud: a Plug-n-Play, Extensible,
                                  On-Premises Bioinformatics Cloud for
                                  Seamless Execution of Complex
                                  Next-Generation Sequencing Data Analysis
                                  Pipelines  . . . . . . . . . . . . . . . 280--284
      Andreas D. M. Gunawan and   
                Hongwei Yan and   
                   Louxin Zhang   Compression of Phylogenetic Networks and
                                  Algorithm for the Tree Containment
                                  Problem  . . . . . . . . . . . . . . . . 285--294

Journal of Computational Biology
Volume 26, Number 4, April, 2019

               Soonweng Cho and   
              Hyun-Seok Kim and   
           Martha A. Zeiger and   
    Christopher B. Umbricht and   
                 Leslie M. Cope   Measuring DNA Copy Number Variation
                                  Using High-Density Methylation
                                  Microarrays  . . . . . . . . . . . . . . 295--304
          Rafa\l Zaborowski and   
            Bartek Wilczy\'nski   BPscore: an Effective Metric for
                                  Meaningful Comparisons of Structural
                                  Chromosome Segmentations . . . . . . . . 305--314
                    Yi Wang and   
                   Kun Tian and   
              Stephen S.-T. Yau   Protein Sequence Classification Using
                                  Natural Vector and Convex Hull Method    315--321
              Paulina Urban and   
               Vahid Rezaei and   
            Grzegorz Bokota and   
         Micha\l Denkiewicz and   
              Subhadip Basu and   
          Dariusz Plewczy\'nski   Dendritic Spines Taxonomy: The
                                  Functional and Structural Classification
                                  $ \bullet $ Time-Dependent Probabilistic
                                  Model of Neuronal Activation . . . . . . 322--335
                Kyu Min Lee and   
               Minhyeok Lee and   
                Junhee Seok and   
                   Sung Won Han   Regression-Based Network Estimation for
                                  High-Dimensional Genetic Data  . . . . . 336--349
                  Yusong Ye and   
               Zhuoqin Yang and   
                     Jinzhi Lei   Stochastic Telomere Shortening and the
                                  Route to Limitless Replicative Potential 350--363
                  Yuewen Qi and   
                  Haowen Qi and   
                 Zeyuan Liu and   
                 Peiyuan He and   
                    Bingqing Li   Bioinformatics Analysis of Key Genes and
                                  Pathways in Colorectal Cancer  . . . . . 364--375
  Bruno César Feltes and   
 Eduardo Bassani Chandelier and   
       Bruno Iochins Grisci and   
             Márcio Dorn   CuMiDa: an Extensively Curated
                                  Microarray Database for Benchmarking and
                                  Testing of Machine Learning Approaches
                                  in Cancer Research . . . . . . . . . . . 376--386
                   Huan Liu and   
                     Li Liu and   
                       Hong Zhu   The Role of Significantly Deregulated
                                  MicroRNAs in Recurrent Cervical Cancer
                                  Based on Bioinformatic Analysis of the
                                  Cancer Genome Atlas Data . . . . . . . . 387--395
             Luigi Marongiu and   
                 Heike Allgayer   Mingle: a Command Line Utility for
                                  Merging Multi-fasta Files  . . . . . . . 396--404

Journal of Computational Biology
Volume 26, Number 5, May, 2019

            Prachi Kothiyal and   
           Wendy S. W. Wong and   
             Dale L. Bodian and   
            John E. Niederhuber   Mendelian Inconsistent Signatures from
                                  1314 Ancestrally Diverse Family Trios
                                  Distinguish Biological Variation from
                                  Sequencing Error . . . . . . . . . . . . 405--419
   Andre Rodrigues Oliveira and   
        Klairton Lima Brito and   
                Zanoni Dias and   
                   Ulisses Dias   Sorting by Weighted Reversals and
                                  Transpositions . . . . . . . . . . . . . 420--431
               Jaegyoon Ahn and   
              Junhyeok Choi and   
                 Harrim Kim and   
                      Jibum Kim   RN$^+$: a Novel Biclustering Algorithm
                                  for Analysis of Gene Expression Data
                                  Using Protein--Protein Interaction
                                  Network  . . . . . . . . . . . . . . . . 432--441
    Guilherme Torres Castro and   
 Luis Enrique Zárate and   
       Cristiane Neri Nobre and   
          Henrique Cota Freitas   A Fast Parallel $K$-Modes Algorithm for
                                  Clustering Nucleotide Sequences to
                                  Predict Translation Initiation Sites . . 442--456
          Guru Raj Rao Ravi and   
           Jayashree Biswal and   
         Sureka Kanagarajan and   
          Jeyaraman Jeyakanthan   Exploration of N5-CAIR Mutase Novel
                                  Inhibitors from \bionamePyrococcus
                                  horikoshii OT3: a Computational Study    457--472
                      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   Classification of Metaphase Chromosomes
                                  Using Deep Convolutional Neural Network  473--484
                  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   Identification of Potential Key Genes
                                  for Hepatitis B Virus-Associated
                                  Hepatocellular Carcinoma by
                                  Bioinformatics Analysis  . . . . . . . . 485--494
                  Wei Liang and   
                Yuxiao Yang and   
                  Yusi Fang and   
             Zhongying Zhao and   
                         Jie Hu   Bayesian Detection of Abnormal
                                  Asynchrony of Division Between Sister
                                  Cells in Mutant \bionameCaenorhabditis
                                  elegans Embryos  . . . . . . . . . . . . 495--505

Journal of Computational Biology
Volume 26, Number 6, June, 2019

Abdoulaye Baniré Diallo and   
     Engelbert Mephu Nguifo and   
               Wajdi Dhifli and   
                Elham Azizi and   
        Sandhya Prabhakaran and   
                  Wesley Tansey   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 . . . . . . . . . . . . . 507--508
            Romain Menegaux and   
             Jean-Philippe Vert   Continuous Embeddings of DNA Sequencing
                                  Reads and Application to Metagenomics    509--518
            Dylan Lebatteux and   
            Amine M. Remita and   
 Abdoulaye Baniré Diallo   Toward an Alignment-Free Method for
                                  Feature Extraction and Accurate
                                  Classification of Viral Sequences  . . . 519--535
               Andreea Deac and   
       Petar Veli\vckovi\'c and   
                Pietro Sormanni   Attentive Cross-Modal Paratope
                                  Prediction . . . . . . . . . . . . . . . 536--545
            Antonio Moretti and   
               Andrew Stirn and   
              Gabriel Marks and   
                    Itsik Pe'er   Autoencoding Topographic Factors . . . . 546--560
                Rabie Saidi and   
               Wajdi Dhifli and   
           Mondher Maddouri and   
         Engelbert Mephu Nguifo   Efficiently Mining Recurrent
                                  Substructures from Protein
                                  Three-Dimensional Structure Graphs . . . 561--571
         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   DeepSNP: an End-to-End Deep Neural
                                  Network with Attention-Based
                                  Localization for Breakpoint Detection in
                                  Single-Nucleotide Polymorphism Array
                                  Genomic Data . . . . . . . . . . . . . . 572--596
        Brenden K. Petersen and   
               Jiachen Yang and   
          Will S. Grathwohl and   
             Chase Cockrell and   
           Claudio Santiago and   
                    Gary An and   
              Daniel M. Faissol   Deep Reinforcement Learning and
                                  Simulation as a Path Toward Precision
                                  Medicine . . . . . . . . . . . . . . . . 597--604
                Qingyu Chen and   
              Xiuzhen Zhang and   
                     Yu Wan and   
               Justin Zobel and   
                 Karin Verspoor   Search Effectiveness in Nonredundant
                                  Sequence Databases: Assessments and
                                  Solutions  . . . . . . . . . . . . . . . 605--617
            Alexandre Bazin and   
             Didier Debroas and   
         Engelbert Mephu Nguifo   A De Novo Robust Clustering Approach for
                                  Amplicon-Based Sequence Data . . . . . . 618--624

Journal of Computational Biology
Volume 26, Number 7, July, 2019

     Guest Editor Ute Deichmann   \em Special Issue: Genomic Regulation:
                                  Experiments, Computational Modeling, and
                                  Philosophy . . . . . . . . . . . . . . . 625--628
                 Michel Morange   A Time to Model and a Time to Experiment 629--636
                  Ute Deichmann   From Gregor Mendel to Eric Davidson:
                                  Mathematical Models and Basic Principles
                                  in Biology . . . . . . . . . . . . . . . 637--652
                  Sorin Istrail   Eric Davidson's Regulatory Genome for
                                  Computer Science: Causality, Logic, and
                                  Proof Principles of the Genomic \em
                                  cis-Regulatory Code  . . . . . . . . . . 653--684
              Sorin Istrail and   
              Isabelle S. Peter   How Does the Regulatory Genome Work? . . 685--695
                  James Briscoe   Understanding Pattern Formation in
                                  Embryos: Experiment, Theory, and
                                  Simulation . . . . . . . . . . . . . . . 696--702
            Ellen V. Rothenberg   Causal Gene Regulatory Network Modeling
                                  and Genomics: Second-Generation
                                  Challenges . . . . . . . . . . . . . . . 703--718
             Aldo Ciau-Uitz and   
                  Roger Patient   Gene Regulatory Networks Governing the
                                  Generation and Regeneration of Blood . . 719--725
              Anthony S. Travis   Chemical Modeling: From Paul Ehrlich's
                                  Dyes to $ \beta $-Blockers --- A Brief
                                  History  . . . . . . . . . . . . . . . . 726--734
               Douglas H. Erwin   Prospects for a General Theory of
                                  Evolutionary Novelty . . . . . . . . . . 735--744
             Jonathan Engel and   
    Isana Veksler-Lublinsky and   
             Michal Ziv-Ukelson   Constrained Gene Block Discovery and Its
                                  Application to Prokaryotic Genomes . . . 745--766

Journal of Computational Biology
Volume 26, Number 8, August, 2019

                Zhipeng Cai and   
                Pavel Skums and   
           Alexander Zelikovsky   Preface: 14th International Symposium on
                                  Bioinformatics Research and Applications
                                  (ISBRA 2018) . . . . . . . . . . . . . . 767--768
                   Huiyu Li and   
               Sheng-Jun Li and   
             Junliang Shang and   
               Jin-Xing Liu and   
                 Chun-Hou Zheng   A Dynamic Scale-Free Network Particle
                                  Swarm Optimization for Extracting
                                  Features on Multi-Omics Data . . . . . . 769--781
       Krzysztof Gogolewski and   
            Maciej Sykulski and   
      Neo Christopher Chung and   
                    Anna Gambin   Truncated Robust Principal Component
                                  Analysis and Noise Reduction for Single
                                  Cell RNA Sequencing Data . . . . . . . . 782--793
                  Ben Yohay and   
                      Sagi Snir   Extending the Evolvability Model to the
                                  Prokaryotic World: Simulations and
                                  Results on Real Data . . . . . . . . . . 794--805
                      Sagi Snir   Bounds on Identification of Genome
                                  Evolution Pacemakers . . . . . . . . . . 806--821
              Marmar Moussa and   
               Ion I. M\uandoiu   Locality Sensitive Imputation for Single
                                  Cell RNA-Seq Data  . . . . . . . . . . . 822--835
              Qingfeng Chen and   
              Canshang Deng and   
                    Wei Lan and   
                Zhixian Liu and   
              Ruiqing Zheng and   
                    Jin Liu and   
                   Jianxin Wang   Identifying Interactions Between Kinases
                                  and Substrates Based on Protein--Protein
                                  Interaction Network  . . . . . . . . . . 836--845
              Wolfgang Kopp and   
                 Martin Vingron   DNA Motif Match Statistics Without
                                  Poisson Approximation  . . . . . . . . . 846--865
          Juan Pablo Acosta and   
            Silvia Restrepo and   
           Juan David Henao and   
    Liliana López-Kleine   Multivariate Method for Inferential
                                  Identification of Differentially
                                  Expressed Genes in Gene Expression
                                  Experiments  . . . . . . . . . . . . . . 866--874
                Dahye Chung and   
              Kaiyuan Zhang and   
                    Jihoon Yang   Method for Identifying Cancer-Related
                                  Genes Using Gene Similarity-Based
                                  Collaborative Filtering  . . . . . . . . 875--881
             Shahid Hussain and   
              Javed Ferzund and   
                    Raza Ul-Haq   Prediction of Drug Target Sensitivity in
                                  Cancer Cell Lines Using Apache Spark . . 882--889

Journal of Computational Biology
Volume 26, Number 9, September, 2019

  Carlos Martín-Vide and   
Miguel A. Vega-Rodríguez   Preface  . . . . . . . . . . . . . . . . 891--892
             Jesper Jansson and   
              Ramesh Rajaby and   
                  Wing-Kin Sung   An Efficient Algorithm for the Rooted
                                  Triplet Distance Between Galled Trees    893--907
        Gabriel H. G. Silva and   
         Edans F. O. Sandes and   
             George Teodoro and   
             Alba C. M. A. Melo   Using Multiple Fickett Bands to
                                  Accelerate Biological Sequence
                                  Comparisons  . . . . . . . . . . . . . . 908--922
              Shuto Hayashi and   
            Takuya Moriyama and   
              Rui Yamaguchi and   
            Shinichi Mizuno and   
           Mitsuhiro Komura and   
              Satoru Miyano and   
          Hidewaki Nakagawa and   
                    Seiya Imoto   ALPHLARD-NT: Bayesian Method for Human
                                  Leukocyte Antigen Genotyping and
                                  Mutation Calling through Simultaneous
                                  Analysis of Normal and Tumor
                                  Whole-Genome Sequence Data . . . . . . . 923--937
              Xiaodong Wang and   
                   Lei Wang and   
                      Daxin Zhu   Efficient Computation of Longest Common
                                  Subsequences with Multiple Substring
                                  Inclusive Constraints  . . . . . . . . . 938--947
            Paola Bonizzoni and   
      Gianluca Della Vedova and   
                Yuri Pirola and   
            Marco Previtali and   
                Raffaella Rizzi   Multithread Multistring Burrows--Wheeler
                                  Transform and Longest Common Prefix
                                  Array  . . . . . . . . . . . . . . . . . 948--961
              Muslum Yildiz and   
               Abdulkadir Kocak   Molecular Dynamics Studies of
                                  Histo-Blood Group Antigen Blocking Human
                                  Immunoglobulin A Antibody and Escape
                                  Mechanism in Noroviruses Upon Mutation   962--974
              Yushuang Yang and   
                   Wei Yang and   
                       Ling Jin   The Role of Long Non-coding RNA Prostate
                                  Cancer-Associated Transcript 1 in
                                  Prostate Cancer  . . . . . . . . . . . . 975--984
         Mohammad S. Rahman and   
             Gholamreza Haffari   Analyzing Tumor Heterogeneity by
                                  Incorporating Long-Range Mutational
                                  Influences and Multiple Sample Data into
                                  Heterogeneity Factorial Hidden Markov
                                  Model  . . . . . . . . . . . . . . . . . 985--1002
          Jacques Demongeot and   
         Hervé Seligmann   Bias for 3$^\prime $-Dominant Codon
                                  Directional Asymmetry in Theoretical
                                  Minimal RNA Rings  . . . . . . . . . . . 1003--1012
                Fangfang Ge and   
                    Yi Wang and   
                 Huayang Li and   
                  Rui Zhang and   
              Xiaotong Wang and   
                 Qingyun Li and   
            Zhenchang Liang and   
                      Long Yang   Plant-GQ: an Integrative Database of
                                  G-Quadruplex in Plant  . . . . . . . . . 1013--1019
                Zhicheng Li and   
                 Shijian Li and   
                   Xian Wei and   
                      Qing Zhao   Scaled Alternating Steepest Descent
                                  Algorithm Applied for Protein Structure
                                  Determination from Nuclear Magnetic
                                  Resonance Data . . . . . . . . . . . . . 1020--1029
                    Guo Mao and   
               Shu-Lin Wang and   
                      Wei Zhang   Prediction of Potential Associations
                                  Between MicroRNA and Disease Based on
                                  Bayesian Probabilistic Matrix
                                  Factorization Model  . . . . . . . . . . 1030--1039

Journal of Computational Biology
Volume 26, Number 10, October, 2019

       Sergey A. Solodskikh and   
      Alexey S. Velikorondy and   
                Vasily N. Popov   Predictive Estimates of Risks Associated
                                  with Type 2 Diabetes Mellitus on the
                                  Basis of Biochemical Biomarkers and
                                  Derived Time-Dependent Parameters  . . . 1041--1049
              Louis Z. Yang and   
                      Ming Yang   Modeling Biological Oscillations:
                                  Integration of Short Reaction Pauses
                                  into a Stationary Model of a Negative
                                  Feedback Loop Generates Sustained Long
                                  Oscillations . . . . . . . . . . . . . . 1050--1066
                     Yan Ye and   
                 Chunde Bao and   
                        Wei Fan   Overexpression of miR-101 May Target
                                  DUSP1 to Promote the Cartilage
                                  Degradation in Rheumatoid Arthritis  . . 1067--1079
                      Qi Li and   
                 Zhengqiang Luo   Identification of Candidate Genes for
                                  Skeletal Muscle Injury Prevention in Two
                                  Different Types  . . . . . . . . . . . . 1080--1089
                      Qi Li and   
                 Zhengqiang Luo   Transcriptional Regulatory Network
                                  Analysis to Reveal the Key Genes
                                  Involved in Skeletal Muscle Injury . . . 1090--1099
          Neeraj Budhlakoti and   
     Dwijesh Chandra Mishra and   
                   Anil Rai and   
                  S. B. Lal and   
   Krishna Kumar Chaturvedi and   
            Rajeev Ranjan Kumar   A Comparative Study of Single-Trait and
                                  Multi-Trait Genomic Selection  . . . . . 1100--1112
                 Xiao Liang and   
         William Chad Young and   
             Ling-Hong Hung and   
          Adrian E. Raftery and   
                   Ka Yee Yeung   Integration of Multiple Data Sources for
                                  Gene Network Inference Using Genetic
                                  Perturbation Data  . . . . . . . . . . . 1113--1129
                   Chao Sun and   
                   Yifan Gu and   
               Guoqing Chen and   
                       Yibao Du   Bioinformatics Analysis of Stromal
                                  Molecular Signatures Associated with
                                  Breast and Prostate Cancer . . . . . . . 1130--1139
                 Liang Wang and   
                 Yuquan Pei and   
                 Shaolei Li and   
             Shanyuan Zhang and   
                       Yue Yang   Distinct Molecular Mechanisms Analysis
                                  of Three Lung Cancer Subtypes Based on
                                  Gene Expression Profiles . . . . . . . . 1140--1155
              Fatima Ghrifi and   
               Loubna Allam and   
             Lakhlili Wiame and   
              Azeddine Ibrahimi   Curcumin-Synthetic Analogs Library
                                  Screening by Docking and Quantitative
                                  Structure--Activity Relationship Studies
                                  for AXL Tyrosine Kinase Inhibition in
                                  Cancers  . . . . . . . . . . . . . . . . 1156--1167
               Yudong Zhang and   
                Wenxiang Wu and   
                         Hao Qu   Integrated Analysis of the Gene
                                  Expression Changes During Colorectal
                                  Cancer Progression by Bioinformatic
                                  Methods  . . . . . . . . . . . . . . . . 1168--1176
   Victor Hugo Urrutia-Baca and   
       Ricardo Gomez-Flores and   
Myriam Angélica De La Garza-Ramos and   
      Patricia Tamez-Guerra and   
Daniela Guadalupe Lucio-Sauceda and   
María Cristina Rodríguez-Padilla   Immunoinformatics Approach to Design a
                                  Novel Epitope-Based Oral Vaccine Against
                                  \bionameHelicobacter pylori  . . . . . . 1177--1190

Journal of Computational Biology
Volume 26, Number 11, November, 2019

          Michael Rosenthal and   
             Darshan Bryner and   
                Fred Huffer and   
                Shane Evans and   
            Anuj Srivastava and   
                 Nicola Neretti   Bayesian Estimation of Three-Dimensional
                                  Chromosomal Structure from Single-Cell
                                  Hi-C Data  . . . . . . . . . . . . . . . 1191--1202
                     Yue Wu and   
         Farhad Hormozdiari and   
            Jong Wha J. Joo and   
                  Eleazar Eskin   Improving Imputation Accuracy by
                                  Inferring Causal Variants in Genetic
                                  Studies  . . . . . . . . . . . . . . . . 1203--1213
Luís Felipe I. Cunha and   
            Fábio Protti   Genome Rearrangements on Multigenomic
                                  Models: Applications of Graph Convexity
                                  Problems . . . . . . . . . . . . . . . . 1214--1222
   Andre Rodrigues Oliveira and   
        Klairton Lima Brito and   
               Ulisses Dias and   
                    Zanoni Dias   On the Complexity of Sorting by
                                  Reversals and Transpositions Problems    1223--1229
               Chao-Kun Yan and   
               Wen-Xiu Wang and   
                   Ge Zhang and   
              Jian-Lin Wang and   
                 Ashutosh Patel   BiRWDDA: a Novel Drug Repositioning
                                  Method Based on Multisimilarity Fusion   1230--1242
              Chaoxuan Dong and   
              Xiao-Yan Chen and   
                   Chao-Yi Dong   Discerning Functional Connections in the
                                  Pulsed Neural Networks with the Dynamic
                                  Bayesian Network Structure Search Method
                                  Based on a Genetic Algorithm . . . . . . 1243--1252
          Yulia M. Suvorova and   
             Eugene V. Korotkov   New Method for Potential Fusions
                                  Detection in Protein-Coding Sequences    1253--1261
              Bao-Xinzi Liu and   
           Guan-Jiang Huang and   
                   Hai-Bo Cheng   Comprehensive Analysis of Core Genes and
                                  Potential Mechanisms in Rectal Cancer    1262--1277
                    Feng Li and   
                Peiyuan Guo and   
                 Keqin Dong and   
                   Peng Guo and   
               Haoyuan Wang and   
                   Xianqiang Lv   Identification of Key Biomarkers and
                                  Potential Molecular Mechanisms in Renal
                                  Cell Carcinoma by Bioinformatics
                                  Analysis . . . . . . . . . . . . . . . . 1278--1295
                Shangjie Ai and   
                Guanfei Lin and   
                   Yong Bai and   
                 Xiande Liu and   
                   Linghua Piao   QSAR Classification-Based Virtual
                                  Screening Followed by Molecular Docking
                                  Identification of Potential COX-2
                                  Inhibitors in a Natural Product Library  1296--1315
              Shunxin Zheng and   
               Liuhong Yang and   
                 Yisong Dai and   
               Lifang Jiang and   
                     Yi Wei and   
                Hongwei Wen and   
                    Yingfang Xu   Screening and Survival Analysis of Hub
                                  Genes in Gastric Cancer Based on
                                  Bioinformatics . . . . . . . . . . . . . 1316--1325
                  Yufang Li and   
                  Aoshen Wu and   
                   Gang Liu and   
                        Lei Liu   A Review of Methods to Quantify the
                                  Genomic Similarity of Topological
                                  Associating Domains  . . . . . . . . . . 1326--1338

Journal of Computational Biology
Volume 26, Number 12, December, 2019

          Denis Kazakiewicz and   
        Jürgen Claesen and   
   Katarzyna Górczak and   
        Dariusz Plewczynski and   
             Tomasz Burzykowski   A Multivariate Negative-Binomial Model
                                  with Random Effects for Differential
                                  Gene-Expression Analysis of Correlated
                                  mRNA Sequencing Data . . . . . . . . . . 1339--1348
             David Toubiana and   
                 Rami Puzis and   
                  Avi Sadka and   
               Eduardo Blumwald   A Genetic Algorithm to Optimize Weighted
                                  Gene Co-Expression Network Analysis  . . 1349--1366
                 Kexin Shen and   
              Shujuan Zhang and   
                 Shurong Ma and   
                  Haishan Zhang   Molecular Markers and Diagnostic Model
                                  Specific for Barrett's Esophagus . . . . 1367--1378
                   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   Exploration of the Differentially
                                  Expressed Long Noncoding RNAs and Genes
                                  of Morphine Tolerance via Bioinformatic
                                  Analysis . . . . . . . . . . . . . . . . 1379--1393
                     Jie Wu and   
               Yijian Zhang and   
                      Maolan Li   Identification of Methylation Markers
                                  and Differentially Expressed Genes with
                                  Prognostic Value in Breast Cancer  . . . 1394--1408
                     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   Identification of a Five-CpG Signature
                                  with Diagnostic Value in Thyroid Cancer  1409--1417
                Hengxi Chen and   
              Shuting Cheng and   
                  Chang Liu and   
                    Jing Fu and   
                      Wei Huang   Bioinformatics Analysis of
                                  Differentially Expressed Genes,
                                  Methylated Genes, and miRNAs in
                                  Unexplained Recurrent Spontaneous
                                  Abortion . . . . . . . . . . . . . . . . 1418--1426
           B. Sharan Sharma and   
          Prabodha K. Swain and   
                Ramtej J. Verma   A Systematic Bioinformatics Approach to
                                  Motif-Based Analysis of Human Locus
                                  Control Regions  . . . . . . . . . . . . 1427--1437
                 Xinxin Liu and   
                    Xinqiang Li   Key Genes Involved in Diabetic
                                  Nephropathy Investigated by Microarray
                                  Analysis . . . . . . . . . . . . . . . . 1438--1447
              Mingxiang Wen and   
                   Xiang Qu and   
                 Yanyan Zhu and   
              Lingfang Tian and   
              Zhongqin Shen and   
                Xiulin Yang and   
                   Xianqing Shi   Exploration of Novel Biomarkers in
                                  Vasculitis by Integrated Bioinfomatic
                                  Approaches . . . . . . . . . . . . . . . 1448--1457
Wilson Alberto Tárraga and   
      Horacio Alberto Garda and   
        Juan Domingo Toledo and   
        Marina Cecilia Gonzalez   Potential Inhibitors of the Activity of
                                  the Cholesterol-Ester Transfer Protein   1458--1469
             Avinash Mishra and   
                Megan Cross and   
            Andreas Hofmann and   
             Mark J. Coster and   
                Abdul Karim and   
                   Abdul Sattar   Identification of a Novel Scaffold for
                                  Inhibition of Dipeptidyl Peptidase-4 . . 1470--1486


Journal of Computational Biology
Volume 27, Number 1, January, 2020

               Rupeng Zhang and   
                 Leifeng Lv and   
                 Wenrui Ban and   
              Xiaoqian Dang and   
                     Chen Zhang   Identification of Hub Genes in Duchenne
                                  Muscular Dystrophy: Evidence from
                                  Bioinformatic Analysis . . . . . . . . . 1--8
                Yangchun Xu and   
                     Yan Mu and   
                  Ling Wang and   
                     Xuan Zhang   Detailed Analysis of Molecular
                                  Mechanisms in Primary and Metastatic
                                  Melanoma . . . . . . . . . . . . . . . . 9--19
                     Yaron Ilan   Advanced Tailored Randomness: a Novel
                                  Approach for Improving the Efficacy of
                                  Biological Systems . . . . . . . . . . . 20--29
                  Jing Zhao and   
                 Linlin Yin and   
                        Ling He   The MicroRNA Landscapes Profiling
                                  Reveals Potential Signatures of
                                  Necrotizing Enterocolitis in Infants . . 30--39
                   Bao Yang and   
                 Keqin Dong and   
                Peiyuan Guo and   
                   Peng Guo and   
                    Guo Jie and   
              Guanhua Zhang and   
                      Tianke Li   Identification of Key Biomarkers and
                                  Potential Molecular Mechanisms in Oral
                                  Squamous Cell Carcinoma by
                                  Bioinformatics Analysis  . . . . . . . . 40--54
               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   Identification and Functional Enrichment
                                  Analysis of Potential Diagnostic and
                                  Therapeutic Targets in Adamantinomatous
                                  Craniopharyngioma  . . . . . . . . . . . 55--68
               Mengwei Chen and   
               Chengqi Kong and   
              Zhiyuan Zheng and   
                         Yin Li   Identification of Biomarkers Associated
                                  with Septic Cardiomyopathy Based on
                                  Bioinformatics Analyses  . . . . . . . . 69--80
                Guozhang Hu and   
                   Rui Wang and   
                     Bo Wei and   
                    Le Wang and   
                    Qi Yang and   
               Daliang Kong and   
                        Chao Du   Prognostic Markers Identification in
                                  Glioma by Gene Expression Profile
                                  Analysis . . . . . . . . . . . . . . . . 81--90
     Partha Sarathi Mohanty and   
             Sandeep Sharma and   
                 Farah Naaz and   
                Dilip Kumar and   
            Archana Raikwar and   
               Shripad A. Patil   Inhibition of \bionameMycobacterium
                                  tuberculosis tRNA-Ligases Using
                                  siRNA-Based Gene Silencing Method: a
                                  Computational Approach . . . . . . . . . 91--99
               Shanshan Liu and   
               Wenjuan Tian and   
                      Burong Li   Integrative Bioinformatics Analysis
                                  Identifies NEK2 as a Potential Biomarker
                                  in Head and Neck Squamous Cell Carcinoma 100--108
                     Ke Shi and   
                 Meng-na Ge and   
                 Xiao-qiao Chen   Coordinated DNA Methylation and Gene
                                  Expression Data for Identification of
                                  the Critical Genes Associated with
                                  Childhood Atopic Asthma  . . . . . . . . 109--120
               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   Identification of Differentially
                                  Expressed Genes Associated with Lymph
                                  Node Tuberculosis by the Bioinformatic
                                  Analysis Based on a Microarray . . . . . 121--130

Journal of Computational Biology
Volume 27, Number 2, February, 2020

                Zhipeng Cai and   
                Pavel Skums and   
           Alexander Zelikovsky   Preface Special Issue: 15th
                                  International Symposium on
                                  Bioinformatics Research and Applications
                                  (ISBRA 2019) . . . . . . . . . . . . . . 131--132
               Ariel Bruner and   
                   Roded Sharan   A Robustness Analysis of Dynamic Boolean
                                  Models of Cellular Circuits  . . . . . . 133--143
             Filipe Gouveia and   
           Inês Lynce and   
              Pedro T. Monteiro   Revision of Boolean Models of Regulatory
                                  Networks Using Stable State Observations 144--155
        Klairton Lima Brito and   
      Géraldine Jean and   
           Guillaume Fertin and   
   Andre Rodrigues Oliveira and   
               Ulisses Dias and   
                    Zanoni Dias   Sorting by Genome Rearrangements on Both
                                  Gene Order and Intergenic Sizes  . . . . 156--174
             Zhi-zhong Chen and   
                Shohei Ueta and   
                  Jingyu Li and   
                   Lusheng Wang   Computing a Consensus Phylogeny via Leaf
                                  Removal  . . . . . . . . . . . . . . . . 175--188
          Francesco Delfino and   
               Yuri Porozov and   
            Eugene Stepanov and   
              Gaik Tamazian and   
              Valentina Tozzini   Evolutionary Switches Structural
                                  Transitions via Coarse-Grained Models    189--199
                  Lixin Liu and   
               Haitao Jiang and   
               Peiqiang Liu and   
                 Binhai Zhu and   
                     Daming Zhu   Maximum Stacking Base Pairs: Hardness
                                  and Approximation by Nonlinear Linear
                                  Programming-Rounding . . . . . . . . . . 200--211
                 Zihao Wang and   
             Jingrong Zhang and   
                Weifang Gao and   
                Zhiyong Liu and   
                Xiaohua Wan and   
                       Fa Zhang   A Consensus Framework of Distributed
                                  Multiple-Tilt Reconstruction in Electron
                                  Tomography . . . . . . . . . . . . . . . 212--222
            Enrico Petrucci and   
         Laurent Noé and   
               Cinzia Pizzi and   
                   Matteo Comin   Iterative Spaced Seed Hashing: Closing
                                  the Gap Between Spaced Seed Hashing and
                                  $k$-mer Hashing  . . . . . . . . . . . . 223--233
             Jelena Fiosina and   
            Maksims Fiosins and   
                    Stefan Bonn   Explainable Deep Learning for
                                  Augmentation of Small RNA Expression
                                  Profiles . . . . . . . . . . . . . . . . 234--247
              Heta P. Desai and   
     Anuja P. Parameshwaran and   
     Rajshekhar Sunderraman and   
                  Michael Weeks   Comparative Study Using Neural Networks
                                  for 16S Ribosomal Gene Classification    248--258
       Charles E. Wimberley and   
                  Steffen Heber   PeakPass: Automating ChIP-Seq Blacklist
                                  Creation . . . . . . . . . . . . . . . . 259--268
          Jakob L. Andersen and   
              Daniel Merkle and   
             Peter S. Rasmussen   Combining Graph Transformations and
                                  Semigroups for Isotopic Labeling Design  269--287
     Ana A. Hernandez-lopez and   
            Claudio Alberti and   
               Marco Mattavelli   Toward a Dynamic Threshold for Quality
                                  Score Distortion in Reference-Based
                                  Alignment  . . . . . . . . . . . . . . . 288--300

Journal of Computational Biology
Volume 27, Number 3, March, 2020

                  Sorin Istrail   Preface Special Issue: RECOMB 2018 . . . 301
      Édouard Bonnet and   
       Pawe\l Rz\ka\.zewski and   
                 Florian Sikora   Designing RNA Secondary Structures Is
                                  Hard . . . . . . . . . . . . . . . . . . 302--316
  Ali Ebrahimpour Boroojeny and   
             Akash Shrestha and   
         Ali Sharifi-Zarchi and   
   Suzanne Renick Gallagher and   
           S. Cenk Sahinalp and   
              Hamidreza Chitsaz   Graph Traversal Edit Distance and
                                  Extensions . . . . . . . . . . . . . . . 317--329
        Shounak Chakraborty and   
              Stefan Canzar and   
           Tobias Marschall and   
               Marcel H. Schulz   Chromatyping: Reconstructing Nucleosome
                                  Profiles from NOMe Sequencing Data . . . 330--341
     Franziska Görtler and   
          Marian Schön and   
               Jakob Simeth and   
             Stefan Solbrig and   
                Tilo Wettig and   
            Peter J. Oefner and   
               Rainer Spang and   
         Michael Altenbuchinger   Loss-Function Learning for Digital
                                  Tissue Deconvolution . . . . . . . . . . 342--355
                 Jan Hoinka and   
                 Yijie Wang and   
            Teresa M. Przytycka   AptaBlocks Online: a Web-Based Toolkit
                                  for the In Silico Design of
                                  Oligonucleotide Sticky Bridges . . . . . 356--360
                Gary Larson and   
          Jeffrey L. Thorne and   
                Scott Schmidler   Incorporating Nearest-Neighbor Site
                                  Dependence into Protein Evolution Models 361--375
                Yaron Orenstein   Reverse de Bruijn: Utilizing Reverse
                                  Peptide Synthesis to Cover All Amino
                                  Acid $k$-mers  . . . . . . . . . . . . . 376--385
          Marian Schön and   
               Jakob Simeth and   
              Paul Heinrich and   
     Franziska Görtler and   
             Stefan Solbrig and   
                Tilo Wettig and   
            Peter J. Oefner and   
     Michael Altenbuchinger and   
                   Rainer Spang   DTD: an R Package for Digital Tissue
                                  Deconvolution  . . . . . . . . . . . . . 386--389
       Antoine Soulé and   
         Jean-Marc Steyaert and   
Jérôme Waldispühl   A Nested $2$-Level Cross-Validation
                                  Ensemble Learning Pipeline Suggests a
                                  Negative Pressure Against Crosstalk
                                  snoRNA-mRNA Interactions in \em
                                  Saccharomyces cerevisiae . . . . . . . . 390--402
            Yuriy Sverchkov and   
                Yi-hsuan Ho and   
               Audrey Gasch and   
                    Mark Craven   Context-Specific Nested Effects Models   403--417
                     Yue Wu and   
              Eleazar Eskin and   
            Sriram Sankararaman   A Unifying Framework for Imputing
                                  Summary Statistics in Genome-Wide
                                  Association Studies  . . . . . . . . . . 418--428
               Naomi Yamada and   
     Prashant Kumar Kuntala and   
           B. Franklin Pugh and   
                   Shaun Mahony   ChExMix: a Method for Identifying and
                                  Classifying Protein--DNA Interaction
                                  Subtypes . . . . . . . . . . . . . . . . 429--435
  Ali Ebrahimpour Boroojeny and   
             Akash Shrestha and   
         Ali Sharifi-zarchi and   
   Suzanne Renick Gallagher and   
Süleyman Cenk Sahinalp and   
              Hamidreza Chitsaz   PyGTED: Python Application for Computing
                                  Graph Traversal Edit Distance  . . . . . 436--439

Journal of Computational Biology
Volume 27, Number 4, April, 2020

                Lenore J. Cowen   Preface Special Issue: RECOMB 2019 . . . 441
             Philipp Benner and   
                 Martin Vingron   ModHMM: a Modular Supra-Bayesian Genome
                                  Segmentation Method  . . . . . . . . . . 442--457
                Boying Gong and   
               Elizabeth Purdom   MethCP: Differentially Methylated Region
                                  Detection with Change Point Models . . . 458--471
          Kristoffer Sahlin and   
                  Paul Medvedev   De Novo Clustering of Long-Read
                                  Transcriptome Data Using a Greedy,
                                  Quality Value-Based Algorithm  . . . . . 472--484
         Fatemeh Almodaresi and   
            Prashant Pandey and   
            Michael Ferdman and   
                Rob Johnson and   
                      Rob Patro   An Efficient, Scalable, and Exact
                                  Representation of High-Dimensional Color
                                  Information Enabled Using de Bruijn
                                  Graph Search . . . . . . . . . . . . . . 485--499
                Alan Kuhnle and   
                  Taher Mun and   
          Christina Boucher and   
               Travis Gagie and   
               Ben Langmead and   
               Giovanni Manzini   Efficient Construction of a Complete
                                  Index for Pan-Genomics Read Alignment    500--513
                  Taher Mun and   
                Alan Kuhnle and   
          Christina Boucher and   
               Travis Gagie and   
               Ben Langmead and   
               Giovanni Manzini   Matching Reads to Many Genomes with the
                                  $r$-Index  . . . . . . . . . . . . . . . 514--518
                 Weihua Pan and   
                  Tao Jiang and   
                Stefano Lonardi   OMGS: Optical Map-Based Genome
                                  Scaffolding  . . . . . . . . . . . . . . 519--533
        Leonardo Pellegrina and   
               Cinzia Pizzi and   
                   Fabio Vandin   Fast Approximation of Frequent $k$-Mers
                                  and Applications to Metagenomics . . . . 534--549
            Jonathan D. Jou and   
             Graham T. Holt and   
           Anna U. Lowegard and   
                Bruce R. Donald   Minimization-Aware Recursive $ K* $: a
                                  Novel, Provable Algorithm that
                                  Accelerates Ensemble-Based Protein
                                  Design and Provably Approximates the
                                  Energy Landscape . . . . . . . . . . . . 550--564
                 Haoyun Lei and   
                Bochuan Lyu and   
           E. Michael Gertz and   
 Alejandro A. Schäffer and   
                 Xulian Shi and   
                     Kui Wu and   
                   Guibo Li and   
                   Liqin Xu and   
                   Yong Hou and   
               Michael Dean and   
               Russell Schwartz   Tumor Copy Number Deconvolution
                                  Integrating Bulk and Single-Cell
                                  Sequencing Data  . . . . . . . . . . . . 565--598
               Joel Mefford and   
                 Danny Park and   
                Zhili Zheng and   
                  Arthur Ko and   
           Mika Ala-Korpela and   
              Markku Laakso and   
       Päivi Pajukanta and   
                  Jian Yang and   
                 John Witte and   
                   Noah Zaitlen   Efficient Estimation and Applications of
                                  Cross-Validated Genetic Predictions to
                                  Polygenic Risk Scores and Linear Mixed
                                  Models . . . . . . . . . . . . . . . . . 599--612
                Younhun Kim and   
           Frederic Koehler and   
               Ankur Moitra and   
            Elchanan Mossel and   
              Govind Ramnarayan   How Many Subpopulations Is Too Many?
                                  Exponential Lower Bounds for Inferring
                                  Population Histories . . . . . . . . . . 613--625
          Mikhail Karasikov and   
              Harun Mustafa and   
               Amir Joudaki and   
         Sara Javadzadeh-no and   
         Gunnar Rätsch and   
            André Kahles   Sparse Binary Relation Representations
                                  for Genome Graph Annotation  . . . . . . 626--639
                Chirag Jain and   
               Haowen Zhang and   
                     Yu Gao and   
                 Srinivas Aluru   On the Complexity of Sequence-to-Graph
                                  Alignment  . . . . . . . . . . . . . . . 640--654
             Lodewijk Brand and   
                   Xue Yang and   
                    Kai Liu and   
             Saad Elbeleidy and   
                   Hua Wang and   
                  Hao Zhang and   
                    Feiping Nie   Learning Robust Multilabel Sample
                                  Specific Distances for Identifying HIV-1
                                  Drug Resistance  . . . . . . . . . . . . 655--672
                      Anonymous   \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) . . . . . . . . . 673

Journal of Computational Biology
Volume 27, Number 5, May, 2020

                 Yury Gusev and   
         Svyatoslav Mazilov and   
            Irina Volokhina and   
               Mikhail Chumakov   Agrobacterial, Single-Stranded
                                  DNA-Binding Protein VirE2 and Its
                                  Complexes  . . . . . . . . . . . . . . . 675--682
  Brenda Ivette Garcia-Maya and   
               Nikolaos Limnios   Identification of Words in Biological
                                  Sequences Under the Semi-Markov
                                  Hypothesis . . . . . . . . . . . . . . . 683--697
                Lixia Zhang and   
      Leonardo O. Rodrigues and   
            Niven R. Narain and   
          Viatcheslav R. Akmaev   \em bAIcis: a Novel Bayesian Network
                                  Structural Learning Algorithm and Its
                                  Comprehensive Performance Evaluation
                                  Against Open-Source Software . . . . . . 698--708
                Zhicheng Li and   
                 Shijian Li and   
                   Xian Wei and   
                Xubiao Peng and   
                      Qing Zhao   Recovering the Missing Regions in
                                  Crystal Structures from the Nuclear
                                  Magnetic Resonance Measurement Data
                                  Using Matrix Completion Method . . . . . 709--717
               Jingwei Zhao and   
                    Le Wang and   
               Daliang Kong and   
                Guozhang Hu and   
                         Bo Wei   Construction of Novel DNA
                                  Methylation-Based Prognostic Model to
                                  Predict Survival in Glioblastoma . . . . 718--728
                     Lei Li and   
               Linhua Jiang and   
                     Sihua Peng   Protein Network Analysis of the Fifth
                                  Chromosome of Zebrafish  . . . . . . . . 729--737
       Rahul Singh Jasrotia and   
             Sarika Jaiswal and   
         Pramod Kumar Yadav and   
               Mustafa Raza and   
           Mir Asif Iquebal and   
                   Anil Rai and   
                   Dinesh Kumar   Genome-Wide Analysis of HSP70 Family
                                  Protein in \bionameVigna radiata and
                                  Coexpression Analysis Under Abiotic and
                                  Biotic Stress  . . . . . . . . . . . . . 738--754
              Lopamudra Dey and   
           Anirban Mukhopadhyay   A Graph-Based Approach for Finding the
                                  Dengue Infection Pathways in Humans
                                  Using Protein--Protein Interactions  . . 755--768
                    Ying Lu and   
                   Qixiu Lu and   
                 Houlin Liu and   
                 Jixiang Yu and   
                Chunlei Xin and   
               Yingping Liu and   
                Yanfang Liu and   
                     Linlin Fan   Time-Series Expression Analysis of
                                  Epidermal Stem Cells from High Fat Diet
                                  Mice . . . . . . . . . . . . . . . . . . 769--778
             Guochang Zhang and   
                    Juan Li and   
                   Hong Sun and   
                 Guanzheng Yang   Screening for the Biomarkers Associated
                                  with Myocardial Infarction by
                                  Bioinformatics Analysis  . . . . . . . . 779--785
          Hanadi M. Baeissa and   
            Frances M. G. Pearl   Identifying the Impact of Inframe
                                  Insertions and Deletions on Protein
                                  Function in Cancer . . . . . . . . . . . 786--795
                Jack Hanson and   
          Kuldip K. Paliwal and   
              Thomas Litfin and   
               Yuedong Yang and   
                     Yaoqi Zhou   Getting to Know Your Neighbor: Protein
                                  Structure Prediction Comes of Age with
                                  Contextual Machine Learning  . . . . . . 796--814
                Yangchun Xu and   
                  Ling Wang and   
             Lanxiang Jiang and   
                     Xuan Zhang   Novel MicroRNA Biomarkers, \em
                                  miR-142-5p, \em miR-550a, \em miR-1826,
                                  and \em miR-1201, Were Identified for
                                  Primary Melanoma . . . . . . . . . . . . 815--824
               Xuedong Wang and   
                Xiaoxi Wang and   
                 Xiaoqin Li and   
                       Yu Chang   Identification of Specific Candidate
                                  Diagnostic Biomarkers for Lung Squamous
                                  Cell Carcinoma Based on Methylation  . . 825--833
                   Xihai Wu and   
                 Yunhui Han and   
                Fangmei Liu and   
                    Lihong Ruan   Downregulations of miR-449a and
                                  miR-145-5p Act as Prognostic Biomarkers
                                  for Endometrial Cancer . . . . . . . . . 834--844

Journal of Computational Biology
Volume 27, Number 6, June, 2020

      Sayanti Guha Majumdar and   
                   Anil Rai and   
              Dwijesh C. Mishra   Integrated Framework for Selection of
                                  Additive and Nonadditive Genetic Markers
                                  for Genomic Selection  . . . . . . . . . 845--855
            Tongchuan Zhang and   
                 Guodong Hu and   
               Yuedong Yang and   
                 Jihua Wang and   
                     Yaoqi Zhou   All-Atom Knowledge-Based Potential for
                                  RNA Structure Discrimination Based on
                                  the Distance-Scaled Finite Ideal-Gas
                                  Reference State  . . . . . . . . . . . . 856--867
              Sultan Alyami and   
                 Chun-Hsi Huang   Nongreedy Unbalanced Huffman Tree
                                  Compressor for Single and Multifasta
                                  Files  . . . . . . . . . . . . . . . . . 868--876
                    Ye Feng and   
                 Chunyu Shi and   
                  Dayu Wang and   
               Xuefeng Wang and   
                       Zhi Chen   Integrated Analysis of DNA Copy Number
                                  Changes and Gene Expression Identifies
                                  Key Genes in Gastric Cancer  . . . . . . 877--887
                     Fan Yu and   
               Zhong-Sen Le and   
                Li-Hua Chen and   
                  Hong Qian and   
                      Bo Yu and   
                   Wen-Hua Chen   Identification of Biomolecular
                                  Information in Rotenone-Induced Cellular
                                  Model of Parkinson's Disease by Public
                                  Microarray Data Analysis . . . . . . . . 888--903
               Sha-Sha Ruan and   
               Yi-Chen Xiao and   
               Pei-Cheng He and   
                    Yi Wang and   
                         Tao Ma   Identification of Potential Gene
                                  Signatures Related to Sleep Deprivation  904--913
                  Lujiao Mo and   
                 Guanhua Xu and   
                  Channi Wu and   
                  Kanda Pan and   
                   Ping Pan and   
                Lingfeng Yu and   
                  Xiaoyuan Shen   Key Regulatory Effect of Activated \em
                                  HIF-1$ \alpha $ /VEGFA Signaling
                                  Pathway in Systemic Capillary Leak
                                  Syndrome Confirmed by Bioinformatics
                                  Analysis . . . . . . . . . . . . . . . . 914--922
                 Xihua Dong and   
                  Xiaoou Yu and   
                     Hua Li and   
                       Hui Kang   Identification of Marker Genes and
                                  Pathways in Patients with Primary
                                  Biliary Cholangitis  . . . . . . . . . . 923--933
                 Chian Chen and   
                  Hsiuying Wang   Logistic Regression Method for Ligand
                                  Discovery  . . . . . . . . . . . . . . . 934--940
               Nermin Jukan and   
           David Zagor\vsek and   
         Julija Lazarevi\vc and   
    Irena Prelo\vznik Zupan and   
          Nata\vsa Debeljak and   
                  Miha Mo\vskon   ViDis: a Platform for Constructing and
                                  Sharing of Medical Algorithms  . . . . . 941--947
                  Teng Zhao and   
                   Kun Qian and   
                       Yi Zhang   High Expression of \em FGF5 Is an
                                  Independent Prognostic Factor for Poor
                                  Overall Survival and Relapse-Free
                                  Survival in Lung Adenocarcinoma  . . . . 948--957
             Fangping Jiang and   
                   Hong Fan and   
                   Lian Luo and   
                         Yun Li   An Integrative Transcriptome Analysis
                                  Reveals Consistently Dysregulated Long
                                  Noncoding RNAs and Their Transcriptional
                                  Regulation Relationships in Heart
                                  Failure  . . . . . . . . . . . . . . . . 958--964
                Lianmei Bai and   
                     Yu Ren and   
                   Tianqing Cui   Overexpression of \em CDCA5, \em KIF4A,
                                  \em TPX2, and \em FOXM1 Coregulated Cell
                                  Cycle and Promoted Hepatocellular
                                  Carcinoma Development  . . . . . . . . . 965--974
           Krishna Kanhaiya and   
           Dwitiya Tyagi-Tiwari   Identification of Drug Targets in Breast
                                  Cancer Metabolic Network . . . . . . . . 975--986
                   Ying Liu and   
             Shenghua Xiong and   
                Shiying Liu and   
                   Jie Chen and   
                   Hao Yang and   
                   Gang Liu and   
                      Gengmi Li   Analysis of Gene Expression in Bladder
                                  Cancer: Possible Involvement of Mitosis
                                  and Complement and Coagulation Cascades
                                  Signaling Pathway  . . . . . . . . . . . 987--998

Journal of Computational Biology
Volume 27, Number 7, July, 2020

          Icaro Alves Pinto and   
Nelson José Freitas Da Silveira   In Silico Identification of Potential
                                  Inhibitors of the Wnt Signaling Pathway
                                  in Human Breast Cancer . . . . . . . . . 999--1010
             Aanchal Mongia and   
           Debarka Sengupta and   
               Angshul Majumdar   deepMc: Deep Matrix Completion for
                                  Imputation of Single-Cell RNA-seq Data   1011--1019
 Sai H. Sankara Subramanian and   
Karpaga Raja Sundari Balachandran and   
 Vijaya Raghavan Rangamaran and   
                  Dharani Gopal   RemeDB: Tool for Rapid Prediction of
                                  Enzymes Involved in Bioremediation from
                                  High-Throughput Metagenome Data Sets . . 1020--1029
                   Yifan Gu and   
               Guoqing Chen and   
                       Yibao Du   Screening of Prognosis-Related Genes in
                                  Primary Breast Carcinoma Using Genomic
                                  Expression Data  . . . . . . . . . . . . 1030--1040
               Weiqing Wang and   
               Shaohua Wang and   
                   Xiao Chu and   
                    Hui Liu and   
                     Ming Xiang   Predicting the Lung Squamous Cell
                                  Carcinoma Diagnosis and Prognosis
                                  Markers by Unique DNA Methylation and
                                  Gene Expression Profiles . . . . . . . . 1041--1054
               Xiaochen Jia and   
                  Yehui Shi and   
                Yuehong Zhu and   
               Wenjing Meng and   
                  Lihong He and   
              Yongsheng Jia and   
                Zhongsheng Tong   Integrated Analysis of
                                  mRNA--miRNA--lncRNA ceRNA Network in
                                  Human HR+/Her-2- Breast Cancer and
                                  Triple Negative Breast Cancer  . . . . . 1055--1066
              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   Distinct Patterns of mRNA and lncRNA
                                  Expression Differences Between Lung
                                  Squamous Cell Carcinoma and
                                  Adenocarcinoma . . . . . . . . . . . . . 1067--1078
                 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   Screening and Identification of Key
                                  Biomarkers in Pancreatic Cancer:
                                  Evidence from Bioinformatic Analysis . . 1079--1091
                  Tian Zeng and   
                   Can Chen and   
                   Pan Yang and   
                 Wenwei Zuo and   
               Xiaoqing Liu and   
                  Yanling Zhang   A Protective Role for RHOJ in NonSmall
                                  Cell Lung Cancer Based on Integrated
                                  Bioinformatics Analysis  . . . . . . . . 1092--1103
                 Ruike Wang and   
                     Xia Du and   
                      Yaqin Zhi   Screening of Critical Genes Involved in
                                  Metastasis and Prognosis of High-Grade
                                  Serous Ovarian Cancer by Gene Expression
                                  Profile Data . . . . . . . . . . . . . . 1104--1114
              Xiaoguang Niu and   
                 Yongtao Xu and   
                     Ni Gao and   
                        Aiwu Li   Weighted Gene Coexpression Network
                                  Analysis Reveals the Critical lncRNAs
                                  and mRNAs in Development of
                                  Hirschsprung's Disease . . . . . . . . . 1115--1129
                  Chao Deng and   
              Timothy Daley and   
            Peter Calabrese and   
                    Jie Ren and   
                Andrew D. Smith   Predicting the Number of Bases to Attain
                                  Sufficient Coverage in High-Throughput
                                  Sequencing Experiments . . . . . . . . . 1130--1143
              Kumar Saurabh and   
            Maxim Solovchuk and   
             Tony Wen Hann Sheu   Solution of Ion Channel Flow Using
                                  Immersed Boundary--Lattice Boltzmann
                                  Methods  . . . . . . . . . . . . . . . . 1144--1156
                Amir Asiaee and   
          Zachary B. Abrams and   
          Samantha Nakayiza and   
              Deepa Sampath and   
               Kevin R. Coombes   Explaining Gene Expression Using
                                  Twenty-One MicroRNAs . . . . . . . . . . 1157--1170
          Vitara Pungpapong and   
                  Min Zhang and   
                    Dabao Zhang   Integrating Biological Knowledge Into
                                  Case--Control Analysis Through Iterated
                                  Conditional Modes/Medians Algorithm  . . 1171--1179

Journal of Computational Biology
Volume 27, Number 8, August, 2020

               Dan Deblasio and   
                 Kwanho Kim and   
                 Carl Kingsford   More Accurate Transcript Assembly via
                                  Parameter Advising . . . . . . . . . . . 1181--1189
            Trung Ngo Trong and   
              Juha Mehtonen and   
    Gerardo González and   
               Roger Kramer and   
       Ville Hautamäki and   
          Merja Heinäniemi   Semisupervised Generative Autoencoder
                                  for Single-Cell Data . . . . . . . . . . 1190--1203
              Zhenghao Chen and   
                Ilya Soifer and   
                Hugo Hilton and   
                Leeat Keren and   
                 Vladimir Jojic   Modeling Multiplexed Images with \em
                                  Spatial--LDA Reveals Novel Tissue
                                  Microenvironments  . . . . . . . . . . . 1204--1218
             Brandon Carter and   
           Maxwell Bileschi and   
                Jamie Smith and   
             Theo Sanderson and   
                Drew Bryant and   
             David Belanger and   
                Lucy J. Colwell   Critiquing Protein Family Classification
                                  Models Using Sufficient Input Subsets    1219--1231
   Katarzyna Górczak and   
        Jürgen Claesen and   
             Tomasz Burzykowski   A Conceptual Framework for Abundance
                                  Estimation of Genomic Targets in the
                                  Presence of Ambiguous Short Sequencing
                                  Reads  . . . . . . . . . . . . . . . . . 1232--1247
       Evaldo Bezerra Costa and   
      Gabriel Pereira Silva and   
      Marcello Goulart Teixeira   An Approach to Parallel Algorithms for
                                  Long DNA Sequences Alignment on Manycore
                                  Architecture . . . . . . . . . . . . . . 1248--1252
                El\.If Pala and   
          Tuba Denkçeken   Evaluation of miRNA Expression Profiles
                                  in Schizophrenia Using
                                  Principal-Component Analysis-Based
                                  Unsupervised Feature Extraction Method   1253--1263
                  Danni Cui and   
               Yingying Liu and   
                   Gang Liu and   
                        Lei Liu   A Multiple-Instance Learning-Based
                                  Convolutional Neural Network Model to
                                  Detect the \em IDH1 Mutation in the
                                  Histopathology Images of Glioma Tissues  1264--1272
               Daniele Pepe and   
                    Jin Hwan Do   Analyzing Apomorphine-Mediated Effects
                                  in a Cell Model for Parkinson's Disease
                                  with Partial Least Squares Structure
                                  Equation Modeling  . . . . . . . . . . . 1273--1282
            Stefano Pirr\`o and   
             Filomena Spada and   
          Emanuela Gadaleta and   
        Federica Ferrentino and   
            Graeme J. Thorn and   
            Gianni Cesareni and   
                 Claude Chelala   HiPPO and PANDA: Two Bioinformatics
                                  Tools to Support Analysis of Mass
                                  Cytometry Data . . . . . . . . . . . . . 1283--1294
                   Xin Duan and   
                 Kejun Wang and   
                     Jia Ke and   
                   Ping Lan and   
                   Feng Gao and   
                    Xiaojian Wu   Multiomics-Based Colorectal Cancer
                                  Molecular Subtyping Using Local Scaling
                                  Network Fusion . . . . . . . . . . . . . 1295--1302
               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   The Potential Role of Protein Tyrosine
                                  Phosphatase, Receptor Type C (CD45) in
                                  the Intestinal Ischemia--Reperfusion
                                  Injury . . . . . . . . . . . . . . . . . 1303--1312
      A. K. M. Firoj Mahmud and   
                   Doo Yang and   
               Per Stenberg and   
             Ilya Ioshikhes and   
               Soumyadeep Nandi   Exploring a \bionameDrosophila
                                  Transcription Factor Interaction Network
                                  to Identify Cis-Regulatory Modules . . . 1313--1328
                Chunling Xu and   
                   Huayi Lu and   
                 Fuqiang Li and   
                    Guanfang Su   Protein Expression Profile on
                                  Differentiation of Bone Marrow
                                  Mesenchymal Stem Cells into Retinal
                                  Ganglion-Like Cells  . . . . . . . . . . 1329--1336

Journal of Computational Biology
Volume 27, Number 9, September, 2020

          Mehmet Eren Ahsen and   
               Robert Vogel and   
         Gustavo A. Stolovitzky   \pkgR/PY-SUMMA: an R/Python Package for
                                  Unsupervised Ensemble Learning for
                                  Binary Classification Problems in
                                  Bioinformatics . . . . . . . . . . . . . 1337--1340
              Zongjiang Fan and   
                Wanqiu Zhao and   
              Shengning Fan and   
                Chunxiao Li and   
                  Jing Qiao and   
                    Yongqing Xu   Identification of Potential Biomarkers
                                  for Intervertebral Disc Degeneration
                                  Using the Genome-Wide Expression
                                  Analysis . . . . . . . . . . . . . . . . 1341--1349
                 Jianye Fan and   
               Shoubin Dong and   
                        Bo Wang   Variant-Kudu: an Efficient Tool kit
                                  Leveraging Distributed Bitmap Index for
                                  Analysis of Massive Genetic Variation
                                  Datasets . . . . . . . . . . . . . . . . 1350--1360
         Amirhossein Karami and   
     Afshin Fayyaz Movaghar and   
             Sabine Mercier and   
                    Louis Ferre   New Approximate Statistical Significance
                                  of Gapped Alignments Based on the Greedy
                                  Extension Model  . . . . . . . . . . . . 1361--1372
                   Yue Wang and   
            Andrey Minarsky and   
              Robert Penner and   
    Christophe Soulé and   
                 Nadya Morozova   Model of Morphogenesis . . . . . . . . . 1373--1383
            Haithem Aouabed and   
  Rodrigo SantamaríA and   
                 Mourad Elloumi   VisBicluster: a Matrix-Based Bicluster
                                  Visualization of Expression Data . . . . 1384--1396
               Xiaoxia Chen and   
                     Hao Li and   
                Lichao Tian and   
                  Qinwei Li and   
               Jinxiang Luo and   
                Yongqiang Zhang   Analysis of the Physicochemical
                                  Properties of Acaricides Based on
                                  Lipinski's Rule of Five  . . . . . . . . 1397--1406
            Fahad Alqahtani and   
               Ion I. M\uandoiu   Statistical Mitogenome Assembly with
                                  RepeaTs  . . . . . . . . . . . . . . . . 1407--1421
               Kohei Yamada and   
             Zhi-zhong Chen and   
                   Lusheng Wang   Improved Practical Algorithms for Rooted
                                  Subtree Prune and Regraft (rSPR)
                                  Distance and Hybridization Number  . . . 1422--1432
                     Yu Shi and   
                   Shan Zhu and   
               Jianxin Yang and   
               Minghai Shao and   
                Wenxiu Ding and   
              Wanrong Jiang and   
                Xinchen Sun and   
                    Ninghua Yao   Investigation of Potential Mechanisms
                                  Associated with Non-small Cell Lung
                                  Cancer . . . . . . . . . . . . . . . . . 1433--1442
                 Feiqi Wang and   
             Tatsuya Akutsu and   
                    Tomoya Mori   Comparison of Pseudoknotted RNA
                                  Secondary Structures by Topological
                                  Centroid Identification and Tree Edit
                                  Distance . . . . . . . . . . . . . . . . 1443--1451
             Shih-Chiang Lo and   
              Chao-Xuan You and   
                    Che-Chi Shu   A Practicable Method of Tuning the Noise
                                  Intensity at Protein Level . . . . . . . 1452--1460
               Lloyd T. Elliott   Kinship Solutions for Partially Observed
                                  Multiphenotype Data  . . . . . . . . . . 1461--1470
              Paulina Urban and   
         Vahid Rezaei Tabar and   
         Micha\l Denkiewicz and   
            Grzegorz Bokota and   
                 Nirmal Das and   
              Subhadip Basu and   
            Dariusz Plewczynski   The Mixture of Autoregressive Hidden
                                  Markov Models of Morphology for
                                  Dentritic Spines During Activation
                                  Process  . . . . . . . . . . . . . . . . 1471--1485
                Weina Zhang and   
                    Yilun Zhang   Integrated Survival Analysis of mRNA and
                                  microRNA Signature of Patients with
                                  Breast Cancer Based on Cox Model . . . . 1486--1494

Journal of Computational Biology
Volume 27, Number 10, October, 2020

               Robert C. Penner   Backbone Free Energy Estimator Applied
                                  to Viral Glycoproteins . . . . . . . . . 1495--1508
                   Yier Qiu and   
                  Guowen Lu and   
                     Yingjie Wu   Coexpression of PBX1 and EMP2 as
                                  Prognostic Biomarkers in Estrogen
                                  Receptor-Negative Breast Cancer via Data
                                  Mining . . . . . . . . . . . . . . . . . 1509--1518
                Yiyang Tang and   
                Lihuang Zha and   
              Xiaofang Zeng and   
                      Zaixin Yu   Identification of Biomarkers Related to
                                  Systemic Sclerosis With or Without
                                  Pulmonary Hypertension Using
                                  Co-expression Analysis . . . . . . . . . 1519--1531
               Shusen Zhang and   
                Yuanyuan Lu and   
               Zhongxin Liu and   
                Xiaopeng Li and   
                Zhihua Wang and   
                    Zhigang Cai   Identification Six Metabolic Genes as
                                  Potential Biomarkers for Lung
                                  Adenocarcinoma . . . . . . . . . . . . . 1532--1543
                    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   Target Specificity of the CRISPR-Cas9
                                  System in \bionameArabidopsis thaliana,
                                  \bionameOryza sativa, and
                                  \bionameGlycine max Genomes  . . . . . . 1544--1552
               Yongqian Shu and   
                Xiaohong Wu and   
                   Jia Shen and   
               Dongdong Luo and   
                   Xiang Li and   
               Hailong Wang and   
               Yuanhua Tom Tang   Tumor Mutation Burden Computation in Two
                                  Pan-Cancer Precision Medicine
                                  Next-Generation Sequencing Panels  . . . 1553--1560

Journal of Computational Biology
Volume 27, Number 11, November, 2020

                Roni Zoller and   
              Meirav Zehavi and   
             Michal Ziv-Ukelson   A New Paradigm for Identifying
                                  Reconciliation-Scenario Altering
                                  Mutations Conferring Environmental
                                  Adaptation . . . . . . . . . . . . . . . 1561--1580
                 Xiyuan Liu and   
                     Di Gao and   
                      Gang Shen   Conditional Random Fields with Least
                                  Absolute Shrinkage and Selection
                                  Operator to Classifying the Barley Genes
                                  Based on Expression Level Affected by
                                  the Fungal Infection . . . . . . . . . . 1581--1594
                  Xin Chang and   
              Mei-Feng Yang and   
                    Wei Fan and   
              Li-Sheng Wang and   
                    Jun Yao and   
               Zhao-Shen Li and   
                     De-Feng Li   Bioinformatic Analysis Suggests That
                                  Three Hub Genes May Be a Vital
                                  Prognostic Biomarker in Pancreatic
                                  Ductal Adenocarcinoma  . . . . . . . . . 1595--1609
            Rutvi Prajapati and   
           Isaac Arnold Emerson   Gene Prioritization in Parkinson's
                                  Disease Using Human Protein--Protein
                                  Interaction Network  . . . . . . . . . . 1610--1621
               Robert C. Penner   Conserved High Free Energy Sites in
                                  Human Coronavirus Spike Glycoprotein
                                  Backbones  . . . . . . . . . . . . . . . 1622--1630

Journal of Computational Biology
Volume 27, Number 12, December, 2020

                  Rong Wang and   
                     Lei Fu and   
                  Jinbin Li and   
                    Di Zhao and   
                 Yulan Zhao and   
                       Ling Yin   Microarray Analysis for Differentially
                                  Expressed Genes Between Stromal and
                                  Epithelial Cells in Development and
                                  Metastasis of Invasive Breast Cancer . . 1631--1643
               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   A Comprehensive Repertoire of Transfer
                                  RNA-Derived Fragments and Their
                                  Regulatory Networks in Colorectal Cancer 1644--1655
                  Maolin Hu and   
              Jiangling Xie and   
                Zhifeng Liu and   
                  Xuan Wang and   
                   Ming Liu and   
                    Jianye Wang   Comprehensive Analysis Identifying Wnt
                                  Ligands Gene Family for Biochemical
                                  Recurrence in Prostate Adenocarcinoma
                                  and Construction of a Nomogram . . . . . 1656--1667
                  Yusong Ye and   
               Zhuoqin Yang and   
                     Jinzhi Lei   DNA Methylation Heterogeneity Induced by
                                  Collaborations Between Enhancers . . . . 1668--1677
                 Baoshan Li and   
                   Yi Jiang and   
                Jingxin Chu and   
                      Qian Zhou   Drug-Target Interaction Network Analysis
                                  of Gene-Phenotype Connectivity
                                  Maintained by Genistein  . . . . . . . . 1678--1687
                    Nan Sun and   
                   Rui Dong and   
                Shaojun Pei and   
             Changchuan Yin and   
              Stephen S.-T. Yau   A New Method Based on Coding Sequence
                                  Density to Cluster Bacteria  . . . . . . 1688--1698


Journal of Computational Biology
Volume 28, Number 1, January, 2021

       Jael Sanyanda Wekesa and   
                 Yushi Luan and   
                       Jun Meng   Predicting Protein Functions Based on
                                  Differential Co-expression and
                                  Neighborhood Analysis  . . . . . . . . . 1--18
   Obiora Cornelius Collins and   
                Kevin Jan Duffy   Mathematical Analyses on the Effects of
                                  Control Measures for a Waterborne
                                  Disease Model with Socioeconomic
                                  Conditions . . . . . . . . . . . . . . . 19--32
                  Buwen Cao and   
              Shuguang Deng and   
                    Hua Qin and   
                 Jiawei Luo and   
                Guanghui Li and   
                    Cheng Liang   Inferring MicroRNA-Disease Associations
                                  Based on the Identification of a
                                  Functional Module  . . . . . . . . . . . 33--42
        Vishnu Kumar Sharma and   
             Prasad V. Bharatam   Identification of Selective Inhibitors
                                  of \em Ld DHFR Enzyme Using
                                  Pharmacoinformatic Methods . . . . . . . 43--59
                   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   Identification of Potential Hub Genes of
                                  Atherosclerosis Through Bioinformatic
                                  Analysis . . . . . . . . . . . . . . . . 60--78
                  Enfa Zhao and   
                   Hang Xie and   
                   Yushun Zhang   Identification of Differentially
                                  Expressed Genes Associated with
                                  Idiopathic Pulmonary Arterial
                                  Hypertension by Integrated
                                  Bioinformatics Approaches  . . . . . . . 79--88
                   Wan Tang and   
                  Degong Mu and   
                   Ling Han and   
                Xianmin Guo and   
                   Bing Han and   
                      Dong Song   Screening of Clinical Factors Related to
                                  Prognosis of Breast Cancer Based on the
                                  Cox Proportional Risk Model  . . . . . . 89--98
                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   Exploration of DNA Methylation-Driven
                                  Genes in Papillary Thyroid Carcinoma
                                  Based on the Cancer Genome Atlas . . . . 99--114

Journal of Computational Biology
Volume 28, Number 2, February, 2021

                Ion Mandoiu and   
               T. M. Murali and   
            Giri Narasimhan and   
    Sanguthevar Rajasekaran and   
                Pavel Skums and   
           Alexander Zelikovsky   Special Issue: 9th International
                                  Computational Advances in Bio and
                                  Medical Sciences (ICCABS 2019) . . . . . 115--116
           Mohammad Mohebbi and   
                 Liang Ding and   
        Russell L. Malmberg and   
                     Liming Cai   Human MicroRNA Target Prediction via
                                  Multi-Hypotheses Learning  . . . . . . . 117--132
              Shuzhen Kuang and   
                Liangjiang Wang   Deep Learning of Sequence Patterns for
                                  CCCTC-Binding Factor-Mediated Chromatin
                                  Loop Formation . . . . . . . . . . . . . 133--145
                  Wutao Yin and   
              Sakib Mostafa and   
                  Fang-xiang Wu   Diagnosis of Autism Spectrum Disorder
                                  Based on Functional Brain Networks with
                                  Deep Learning  . . . . . . . . . . . . . 146--165
        Khajamoinuddin Syed and   
            William Sleeman and   
                 Payal Soni and   
              Michael Hagan and   
             Jatinder Palta and   
             Rishabh Kapoor and   
                  Preetam Ghosh   Machine-Learning Models for Multicenter
                                  Prostate Cancer Treatment Plans  . . . . 166--184
              Matthew Hayes and   
            Derrick Mullins and   
                  Angela Nguyen   Complex Variant Discovery Using
                                  Discordant Cluster Normalization . . . . 185--194
              Hsin-Hao Chen and   
                  Chung-Chin Lu   Optimized Fluorescence-Based Detection
                                  in Single Molecule Synthesis Process . . 195--208
               Ishwor Thapa and   
                     Hesham Ali   A Multiomics Graph Database System for
                                  Biological Data Integration and Cancer
                                  Informatics  . . . . . . . . . . . . . . 209--219
               Chu-Yu Cheng and   
                  Chung-Chin Lu   The Agility of a Neuron: Phase Shift
                                  Between Sinusoidal Current Input and
                                  Firing Rate Curve  . . . . . . . . . . . 220--234

Journal of Computational Biology
Volume 28, Number 3, March, 2021

Alexsandro Oliveira Alexandrino and   
   Andre Rodrigues Oliveira and   
               Ulisses Dias and   
                    Zanoni Dias   Genome Rearrangement Distance with
                                  Reversals, Transpositions, and Indels    235--247
        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   Multiscale Feedback Loops in SARS-CoV-2
                                  Viral Evolution  . . . . . . . . . . . . 248--256
         Gastone Castellani and   
             Leon N. Cooper and   
 Luciana Renata De Oliveira and   
                 Brian S. Blais   Energy Consumption and Entropy
                                  Production in a Stochastic Formulation
                                  of BCM Learning  . . . . . . . . . . . . 257--268
               Jiasong Wang and   
                 Changchuan Yin   A Fast Algorithm for Computing the
                                  Fourier Spectrum of a Fractional Period  269--282
          Concettina Guerra and   
               Sarang Joshi and   
                 Yinquan Lu and   
           Francesco Palini and   
   Umberto Ferraro Petrillo and   
                Jarek Rossignac   Rank-Similarity Measures for Comparing
                                  Gene Prioritizations: a Case Study in
                                  Autism . . . . . . . . . . . . . . . . . 283--295
   Angela M. Taravella Oill and   
        Anagha J. Deshpande and   
             Heini M. Natri and   
              Melissa A. Wilson   PopInf: an Approach for Reproducibly
                                  Visualizing and Assigning Population
                                  Affiliation in Genomic Samples of
                                  Uncertain Origin . . . . . . . . . . . . 296--303
                  Xiao Wang and   
                    Dan Hao and   
            Haja N. Kadarmideen   \pkgGeneDMRs: an R Package for
                                  Gene-Based Differentially Methylated
                                  Regions Analysis . . . . . . . . . . . . 304--316
                  Yijun Xia and   
                   Juan Xie and   
                   Jun Zhao and   
                    Yin Lou and   
                  Dongsheng Cao   Screening and Identification of Key
                                  Biomarkers in Melanoma: Evidence from
                                  Bioinformatic Analyses . . . . . . . . . 317--329
                   Jie Yang and   
               Qing-chun Xu and   
               Zhen-yu Wang and   
                     Xun Lu and   
                Liu-kui Pan and   
                     Jun Wu and   
                      Chen Wang   Integrated Analysis of an
                                  lncRNA-Associated ceRNA Network Reveals
                                  Potential Biomarkers for Hepatocellular
                                  Carcinoma  . . . . . . . . . . . . . . . 330--344

Journal of Computational Biology
Volume 28, Number 4, April, 2021

               Russell Schwartz   RECOMB 2020 Special Issue  . . . . . . . 345
                  Yuzhi Guo and   
                Jiaxiang Wu and   
                  Hehuan Ma and   
                 Sheng Wang and   
                  Junzhou Huang   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 . . . . . . . . . . . 346--361
                  Yuzhi Guo and   
                Jiaxiang Wu and   
                  Hehuan Ma and   
                 Sheng Wang and   
                  Junzhou Huang   EPTool: a New Enhancing PSSM Tool for
                                  Protein Secondary Structure Prediction   362--364
               Gizem Caylak and   
               Oznur Tastan and   
              A. Ercument Cicek   Potpourri: an Epistasis Test
                                  Prioritization Algorithm via Diverse SNP
                                  Selection  . . . . . . . . . . . . . . . 365--377
               Gizem Caylak and   
               Oznur Tastan and   
              A. Ercument Cicek   A Tool for Detecting Complementary
                                  Single Nucleotide Polymorphism Pairs in
                                  Genome-Wide Association Studies for
                                  Epistasis Testing  . . . . . . . . . . . 378--380
              Amatur Rahman and   
                 Paul Medevedev   Representation of $k$-Mer Sets Using
                                  Spectrum-Preserving String Sets  . . . . 381--394
               Hongyu Zheng and   
             Carl Kingsford and   
       Guillaume Marçais   Lower Density Selection Schemes via
                                  Small Universal Hitting Sets with Short
                                  Remaining Path Length  . . . . . . . . . 395--409
  Leonard Bohnenkämper and   
 Marília D. V. Braga and   
               Daniel Doerr and   
                     Jens Stoye   Computing the Rearrangement Distance of
                                  Natural Genomes  . . . . . . . . . . . . 410--431

Journal of Computational Biology
Volume 28, Number 5, May, 2021

               Russell Schwartz   RECOMB 2020 Special Issue  . . . . . . . 433--434
               Brooks Paige and   
                 James Bell and   
     Aurélien Bellet and   
      Adri\`a Gascón and   
                    Daphne Ezer   Reconstructing Genotypes in Private
                                  Genomic Databases from Genetic Risk
                                  Scores . . . . . . . . . . . . . . . . . 435--451
            Brandon Legried and   
             Erin K. Molloy and   
               Tandy Warnow and   
          Sébastien Roch   Polynomial-Time Statistical Estimation
                                  of Species Trees Under Gene Duplication
                                  and Loss . . . . . . . . . . . . . . . . 452--468
           Matthew A. Reyna and   
              Uthsav Chitra and   
            Rebecca Elyanow and   
            Benjamin J. Raphael   NetMix: a Network-Structured Mixture
                                  Model for Reduced-Bias Estimation of
                                  Altered Subnetworks  . . . . . . . . . . 469--484
      Kamran Ghasedi Dizaji and   
                   Wei Chen and   
                     Heng Huang   Deep Large-Scale Multitask Learning
                                  Network for Gene Expression Inference    485--500
                 Songwei Ge and   
                Haohan Wang and   
                 Amir Alavi and   
                  Eric Xing and   
                 Ziv Bar-joseph   Supervised Adversarial Alignment of
                                  Single-Cell RNA-seq Data . . . . . . . . 501--513
                 Emre Sefer and   
                 Carl Kingsford   Metric Labeling and Semimetric Embedding
                                  for Protein Annotation Prediction  . . . 514--525

Journal of Computational Biology
Volume 28, Number 6, June, 2021

             David J. Galas and   
          James Kunert-graf and   
                 Lisa Uechi and   
           Nikita A. Sakhanenko   Toward an Information Theory of
                                  Quantitative Genetics  . . . . . . . . . 527--559
                 Philipp Benner   Computing Leapfrog Regularization Paths
                                  with Applications to Large-Scale $K$-mer
                                  Logistic Regression  . . . . . . . . . . 560--569
         Samaneh Yourdkhani and   
        Elizabeth S. Allman and   
                 John A. Rhodes   Parameter Identifiability for a Profile
                                  Mixture Model of Protein Evolution . . . 570--586
                Shijia Wang and   
                  Shufei Ge and   
            Caroline Colijn and   
            Priscila Biller and   
            Liangliang Wang and   
               Lloyd T. Elliott   Estimating Genetic Similarity Matrices
                                  Using Phylogenies  . . . . . . . . . . . 587--600
                Carlos Soto and   
             Darshan Bryner and   
             Nicola Neretti and   
                Anuj Srivastava   Toward a Three-Dimensional Chromosome
                                  Shape Alphabet . . . . . . . . . . . . . 601--618
                 Jinuk Jung and   
               Hyunwhan Joe and   
                Kyungsik Ha and   
                Jin-muk Lim and   
                   Hong-gee Kim   Biomedical Entity Explorer: a Web Server
                                  for Biomedical Entity Exploration  . . . 619--628
             Sarah E. Innis and   
            Kelsie Reinaltt and   
               Mete Civelek and   
             Warren D. Anderson   GSEAplot: a Package for Customizing Gene
                                  Set Enrichment Analysis in R . . . . . . 629--631

Journal of Computational Biology
Volume 28, Number 7, July, 2021

                      Anonymous   \em JCB Call for Papers for the Special
                                  Issue on ``40 Years of Computational
                                  Biology: In Honor of Professor Michael
                                  Waterman's 80th Birthday'' . . . . . . . 633--635
                Zhipeng Cai and   
                Pavel Skums and   
               Yuri Porozov and   
           Alexander Zelikovsky   Special Issue: 16th International
                                  Symposium on Bioinformatics Research and
                                  Applications (ISBRA 2020)  . . . . . . . 636
                    Wei Dai and   
                Bingxi Chen and   
                   Wei Peng and   
                     Xia Li and   
            Jiancheng Zhong and   
                   Jianxin Wang   A Novel Multi-Ensemble Method for
                                  Identifying Essential Proteins . . . . . 637--649
                Lingzhi Zhu and   
                  Cheng Yan and   
                    Guihua Duan   Prediction of Virus--Receptor
                                  Interactions Based on Improving
                                  Similarities . . . . . . . . . . . . . . 650--659
                  Gaoyan Wu and   
               Mengyun Yang and   
                 Yaohang Li and   
                   Jianxin Wang   De Novo Prediction of Drug--Target
                                  Interactions Using Laplacian Regularized
                                  Schatten $p$-Norm Minimization . . . . . 660--673
             Chun-cheng Liu and   
             Tao-chuan Shih and   
                Tun-wen Pai and   
                Chin-hwa Hu and   
                Wen-shyong Tzou   Enhanced Over-Representation Analysis
                                  for the Differential Regulation of
                                  Birc5a and HIF2 $ \alpha $-Knockdown
                                  Approaches . . . . . . . . . . . . . . . 674--686
                  Nian Wang and   
                   Min Zeng and   
                  Yiming Li and   
              Fang-xiang Wu and   
                         Min Li   Essential Protein Prediction Based on
                                  node2vec and XGBoost . . . . . . . . . . 687--700
    Nikolai Nòjgaard and   
             Walter Fontana and   
              Marc Hellmuth and   
                  Daniel Merkle   Cayley Graphs of Semigroups Applied to
                                  Atom Tracking in Chemistry . . . . . . . 701--715
        Kseniia Cheloshkina and   
          Islam Bzhikhatlov and   
                 Maria Poptsova   Randomness in Cancer Breakpoint
                                  Prediction . . . . . . . . . . . . . . . 716--731
               Zhineng Chen and   
                   Sai Wang and   
                 Caiyan Jia and   
                     Kai Hu and   
                Xiongjun Ye and   
                  Xuanya Li and   
                    Xieping Gao   CRDet: Improving Signet Ring Cell
                                  Detection by Reinforcing the
                                  Classification Branch  . . . . . . . . . 732--743
                      Anonymous   \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)  744

Journal of Computational Biology
Volume 28, Number 8, August, 2021

                Zhipeng Cai and   
                Pavel Skums and   
               Yuri Porozov and   
           Alexander Zelikovsky   Special Issue: 16th International
                                  Symposium on Bioinformatics Research and
                                  Applications (ISBRA 2020)  . . . . . . . 745--746
    Ekaterina M. Myasnikova and   
           Marat A. Sabirov and   
            Alexander V. Spirov   Quantitative Analysis of the Dynamics of
                                  Maternal Gradients in the Early
                                  \bionameDrosophila Embryo  . . . . . . . 747--757
           Jaros\law Paszek and   
              Alexey Markin and   
      Pawe\l Górecki and   
              Oliver Eulenstein   Taming the Duplication-Loss-Coalescence
                                  Model with Integer Linear Programming    758--773
                  Wenyan Gu and   
               Aizhong Zhou and   
               Lusheng Wang and   
                 Shiwei Sun and   
                Xuefeng Cui and   
                     Daming Zhu   SVLR: Genome Structural Variant
                                  Detection Using Long-Read Sequencing
                                  Data . . . . . . . . . . . . . . . . . . 774--788
                   Wen Yang and   
                   Lusheng Wang   Fast and Accurate Algorithms for Mapping
                                  and Aligning Long Reads  . . . . . . . . 789--803
               Qiuyue Huang and   
                   Jun Wang and   
           Xiangliang Zhang and   
                  Maozu Guo and   
                     Guoxian Yu   IsoDA: Isoform--Disease Association
                                  Prediction by Multiomics Data Fusion . . 804--819
              Marmar Moussa and   
               Ion I. M\uandoiu   SC1: a Tool for Interactive Web-Based
                                  Single-Cell RNA-Seq Data Analysis  . . . 820--841
       Filipp Martin Rondel and   
              Roya Hosseini and   
               Bikram Sahoo and   
             Sergey Knyazev and   
               Igor Mandric and   
              Frank Stewart and   
           Ion I. M\uandoiu and   
            Bogdan Pasaniuc and   
               Yuri Porozov and   
           Alexander Zelikovsky   Pipeline for Analyzing Activity of
                                  Metabolic Pathways in Planktonic
                                  Communities Using Metatranscriptomic
                                  Data . . . . . . . . . . . . . . . . . . 842--855