Last update:
Fri Jun 3 08:25:39 MDT 2022
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
Salem Maliki\'c and
Farid Rashidi Mehrabadi and
Erfan Sadeqi Azer and
Mohammad Haghir Ebrahimabadi and
Suleyman Cenk Sahinalp Studying the History of Tumor Evolution
from Single-Cell Sequencing Data by
Exploring the Space of Binary Matrices 857--879
Caesar Z. Li and
Eric S. Kawaguchi and
Gang Li A New $ \ell_0$-Regularized Log-Linear
Poisson Graphical Model with
Applications to RNA Sequencing Data . . 880--891
Vo Hong Thanh and
Dani Korpela and
Pekka Orponen Cotranscriptional Kinetic Folding of RNA
Secondary Structures Including
Pseudoknots . . . . . . . . . . . . . . 892--908
Sunil Thomas Mapping the Nonstructural Transmembrane
Proteins of Severe Acute Respiratory
Syndrome Coronavirus 2 . . . . . . . . . 909--921
Shisheng Wang and
Yi Zhong and
Jingqiu Cheng and
Hao Yang EnrichVisBox: a Versatile and Powerful
Web Toolbox for Visualizing Complex
Functional Enrichment Results of Omics
Data . . . . . . . . . . . . . . . . . . 922--930
Bruno César Feltes and
Joice De Faria Poloni and
Márcio Dorn Benchmarking and Testing Machine
Learning Approaches with BARRA:CuRDa, a
\em Curated RNA-Seq Database for Cancer
Research . . . . . . . . . . . . . . . . 931--944
Yury Orlovich and
Kirill Kukharenko and
Volker Kaibel and
Pavel Skums Scale-Free Spanning Trees and Their
Application in Genomic Epidemiology . . 945--960
Junfeng Liu and
Yi Wang and
Hongyu Zhao Calculating Orthologous Protein-Coding
Sequence Set Probability Using the
Poisson Process . . . . . . . . . . . . 961--974
Jeyakodi Gopal and
Vigneshwar Suriya Prakash Sinnarasan and
Amouda Venkatesan Identification of Repurpose Drugs by
Computational Analysis of
Disease--Gene--Drug Associations . . . . 975--984
J. B. Nation and
Justin Cabot-Miller and
Oren Segal and
Robert Lucito and
Kira Adaricheva Combining Algorithms to Find Signatures
That Predict Risk in Early-Stage Stomach
Cancer . . . . . . . . . . . . . . . . . 985--1006
Wei Zhang and
Shu-lin Wang and
Yue Liu Identification of Cancer Driver Modules
Based on Graph Clustering from
Multiomics Data . . . . . . . . . . . . 1007--1020
Rudolfs Petrovs and
Egils Stalidzans and
Agris Pentjuss IMFLer: a Web Application for
Interactive Metabolic Flux Analysis and
Visualization . . . . . . . . . . . . . 1021--1032
Sumit Kumar Jha and
Ion M\uandoiu and
Sanguthevar Rajasekaran and
Pavel Skums and
Alexander Zelikovsky Special Issue: 10th International
Computational Advances in Bio and
Medical Sciences (ICCABS 2020) . . . . . 1033--1034
Xuecong Fu and
Haoyun Lei and
Yifeng Tao and
Kerstin Heselmeyer-haddad and
Irianna Torres and
Michael Dean and
Thomas Ried and
Russell Schwartz Joint Clustering of Single-Cell
Sequencing and Fluorescence In Situ
Hybridization Data for Reconstructing
Clonal Heterogeneity in Cancers . . . . 1035--1051
Francesco Andreace and
Cinzia Pizzi and
Matteo Comin MetaProb 2: Metagenomic Reads Binning
Based on Assembly Using Minimizers and
$K$-Mers Statistics . . . . . . . . . . 1052--1062
Gustavo A. Arango-argoty and
Lenwood S. Heath and
Amy Pruden and
Peter J. Vikesland and
Liqing Zhang MetaMLP: a Fast Word Embedding Based
Classifier to Profile Target Gene
Databases in Metagenomic Samples . . . . 1063--1074
Abdur Rahman M. A. Basher and
Ryan J. Mclaughlin and
Steven J. Hallam Metabolic Pathway Prediction Using
Non-Negative Matrix Factorization with
Improved Precision . . . . . . . . . . . 1075--1103
Subrata Saha and
Ahmed Soliman and
Sanguthevar Rajasekaran A Novel Pathway Network Analytics Method
Based on Graph Theory . . . . . . . . . 1104--1112
Andrew Melnyk and
Fatemeh Mohebbi and
Sergey Knyazev and
Bikram Sahoo and
Roya Hosseini and
Pavel Skums and
Alex Zelikovsky and
Murray Patterson From Alpha to Zeta: Identifying Variants
and Subtypes of SARS-CoV-2 Via
Clustering . . . . . . . . . . . . . . . 1113--1129
Daniel Novikov and
Sergey Knyazev and
Mark Grinshpon and
Pelin Icer and
Pavel Skums and
Alex Zelikovsky Scalable Reconstruction of SARS-CoV-2
Phylogeny with Recurrent Mutations . . . 1130--1141
Sarwan Ali and
Simone Ciccolella and
Lorenzo Lucarella and
Gianluca Della Vedova and
Murray Patterson Simpler and Faster Development of Tumor
Phylogeny Pipelines . . . . . . . . . . 1142--1155
Qiaoji Xu and
Lingling Jin and
Yue Zhang and
Xiaomeng Zhang and
Chunfang Zheng and
James H. Leebens-mack and
David Sankoff Ancestral Flowering Plant Chromosomes
and Gene Orders Based on Generalized
Adjacencies and Chromosomal Gene
Co-Occurrences . . . . . . . . . . . . . 1156--1179
Merc\`e Llabrés and
Francesc Rosselló and
Gabriel Valiente The Generalized Robinson--Foulds
Distance for Phylogenetic Trees . . . . 1181--1195
Esmaeil Nourani GoVec: Gene Ontology Representation
Learning Using Weighted Heterogeneous
Graph and Meta-Path . . . . . . . . . . 1196--1207
Shaoxun Liu and
Yi Kou and
Lin Chen Novel Few-Shot Learning Neural Network
for Predicting Carbohydrate-Active
Enzyme Affinity Toward
Fructo-Oligosaccharides . . . . . . . . 1208--1218
Xuejun Chen and
Zhenran Jiang ISFMDA: Learning Interactions of
Selected Features-Based Method for
Predicting Potential MicroRNA-Disease
Associations . . . . . . . . . . . . . . 1219--1227
Poonam Dhankhar and
Vikram Dalal and
Viney Kumar Screening of Severe Acute Respiratory
Syndrome Coronavirus 2 RNA-Dependent RNA
Polymerase Inhibitors Using
Computational Approach . . . . . . . . . 1228--1247
Dikscha Sapra and
Harpreet Kaur and
Anjali Dhall and
Gajendra P. S. Raghava ProCanBio: a Database of Manually
Curated Biomarkers for Prostate Cancer 1248--1257
Anonymous Acknowledgment of Reviewers 2021 . . . . 1
Jian Peng RECOMB 2021 Special Issue . . . . . . . 2
Pinar Demetci and
Rebecca Santorella and
Björn Sandstede and
William Stafford Noble and
Ritambhara Singh SCOT: Single-Cell Multi-Omics Alignment
with Optimal Transport . . . . . . . . . 3--18
Pinar Demetci and
Rebecca Santorella and
Björn Sandstede and
William Stafford Noble and
Ritambhara Singh Single-Cell Multiomics Integration by
SCOT . . . . . . . . . . . . . . . . . . 19--22
Tianyi Sun and
Dongyuan Song and
Wei Vivian Li and
Jingyi Jessica Li Simulating Single-Cell Gene Expression
Count Data with Preserved Gene
Correlations by scDesign2 . . . . . . . 23--26
Harsh Shrivastava and
Xiuwei Zhang and
Le Song and
Srinivas Aluru GRNUlar: a Deep Learning Framework for
Recovering Single-Cell Gene Regulatory
Networks . . . . . . . . . . . . . . . . 27--44
Rami Nasser and
Yonina C. Eldar and
Roded Sharan Deep Unfolding for Non-Negative Matrix
Factorization with Application to
Mutational Signature Analysis . . . . . 45--55
Nicholas Franzese and
Jason Fan and
Roded Sharan and
Mark D. M. Leiserson ScalpelSig Designs Targeted Genomic
Panels from Data to Detect Activity of
Mutational Signatures . . . . . . . . . 56--73
Paul Zaharias and
Martin Grosshauser and
Tandy Warnow Re-evaluating Deep Neural Networks for
Phylogeny Estimation: The Issue of Taxon
Sampling . . . . . . . . . . . . . . . . 74--89
Jian Peng RECOMB 2021 Special Issue . . . . . . . 91
Lupeng Kong and
Fusong Ju and
Wei-mou Zheng and
Jianwei Zhu and
Shiwei Sun and
Jinbo Xu and
Dongbo Bu ProALIGN: Directly Learning Alignments
for Protein Structure Prediction via
Exploiting Context-Specific Alignment
Motifs . . . . . . . . . . . . . . . . . 92--105
Yuxuan Du and
Sarah M. Laperriere and
Jed Fuhrman and
Fengzhu Sun Normalizing Metagenomic Hi-C Data and
Detecting Spurious Contacts Using
Zero-Inflated Negative Binomial
Regression . . . . . . . . . . . . . . . 106--120
Hongyu Zheng and
Cong Ma and
Carl Kingsford Deriving Ranges of Optimal Estimated
Transcript Expression due to
Nonidentifiability . . . . . . . . . . . 121--139
Yoshihiro Shibuya and
Djamal Belazzougui and
Gregory Kucherov Set-Min Sketch: a Probabilistic Map for
Power-Law Distributions with Application
to $k$-Mer Annotation . . . . . . . . . 140--154
Antonio Blanca and
Robert S. Harris and
David Koslicki and
Paul Medvedev The Statistics of $k$-mers from a
Sequence Undergoing a Simple Mutation
Process Without Spurious Matches . . . . 155--168
Massimiliano Rossi and
Marco Oliva and
Ben Langmead and
Travis Gagie and
Christina Boucher MONI: a Pangenomic Index for Finding
Maximal Exact Matches . . . . . . . . . 169--187
Massimiliano Rossi and
Marco Oliva and
Paola Bonizzoni and
Ben Langmead and
Travis Gagie and
Christina Boucher Finding Maximal Exact Matches Using the
$r$-Index . . . . . . . . . . . . . . . 188--194
Jim Shaw and
Yun William Yu \pkgflopp: Extremely Fast Long-Read
Polyploid Haplotype Phasing by Uniform
Tree Partitioning . . . . . . . . . . . 195--211
Veronica Tozzo and
Chloé-agathe Azencott and
Samuele Fiorini and
Emanuele Fava and
Andrea Trucco and
Annalisa Barla Where Do We Stand in Regularization for
Life Science Studies? . . . . . . . . . 213--232
Haohan Wang and
Bryon Aragam and
Eric P. Xing Trade-offs of Linear Mixed Models in
Genome-Wide Association Studies . . . . 233--242
Alexsandro Oliveira Alexandrino and
Andre Rodrigues Oliveira and
Ulisses Dias and
Zanoni Dias Labeled Cycle Graph for Transposition
and Indel Distance . . . . . . . . . . . 243--256
Heewon Park and
Rui Yamaguchi and
Seiya Imoto and
Satoru Miyano Uncovering Molecular Mechanisms of Drug
Resistance via Network-Constrained
Common Structure Identification . . . . 257--275
Hossein Hassani and
Zakieh Avazzadeh and
J. A. Tenreiro Machado and
Praveen Agarwal and
Maryam Bakhtiar Optimal Solution of a Fractional
HIV/AIDS Epidemic Mathematical Model . . 276--291
Muhsen Hammoud and
Charles Morphy D. Santos and
João Paulo Gois Comparing Phylogenetic Trees Side by
Side Through iPhyloC, a New Interactive
Web-Based Framework . . . . . . . . . . 292--303
Yuval Emek and
Saket Navlakha Special Issue: Biological Distributed
Algorithms 2021 . . . . . . . . . . . . 305
Arjun Chandrasekhar and
Magdalena M. Julkowska A Mathematical Framework for Analyzing
Wild Tomato Root Architecture . . . . . 306--316
Michael Feldmann and
Andreas Padalkin and
Christian Scheideler and
Shlomi Dolev Coordinating Amoebots via Reconfigurable
Circuits . . . . . . . . . . . . . . . . 317--343
Emily Zhang and
Jiajia Zhao and
Nancy Lynch An Upper and Lower Bound for the
Convergence Time of House-Hunting in
\bionameTemnothorax Ant Colonies . . . . 344--357
Martin Kunev and
Petr Kuznetsov and
Denis Sheynikhovich Agreement in Spiking Neural Networks . . 358--369
Keith T. Murray and
Mien Brabeeba Wang and
Nancy Lynch Emergence of Direction-Selective Retinal
Cell Types in Task-Optimized Deep
Learning Models . . . . . . . . . . . . 370--381
Jiajia Zhao and
Nancy Lynch and
Stephen C. Pratt The Power of Population Effect in
\bionameTemnothorax Ant House-Hunting: a
Computational Modeling Approach . . . . 382--408
Jeremy Bigness and
Xavier Loinaz and
Shalin Patel and
Erica Larschan and
Ritambhara Singh Integrating Long-Range Regulatory
Interactions to Predict Gene Expression
Using Graph Convolutional Networks . . . 409--424
Qianghui Guo and
Yinglie Jin and
Mengqin Li and
Lisa Hui Sun and
Yanyan Xu On the Number of Saturated and Optimal
Extended 2-Regular Simple Stacks in the
Nussinov--Jacobson Energy Model . . . . 425--440
Aanchal Mongia and
Stuti Jain and
Emilie Chouzenoux and
Angshul Majumdar DeepVir: Graphical Deep Matrix
Factorization for In Silico Antiviral
Repositioning --- Application to
COVID-19 . . . . . . . . . . . . . . . . 441--452
Micah Thornton and
Monnie Mcgee Use of DFT Distance Metrics for
Classification of SARS-CoV-2 Genomes . . 453--464
Luqin Gan and
Giuseppe Vinci and
Genevera I. Allen Correlation Imputation for Single-Cell
RNA-seq . . . . . . . . . . . . . . . . 465--482
Cristian C. Espitia and
Miguel A. Botina and
Marco A. Solarte and
Ivan Hernandez and
Ricardo A. Riascos and
João F. Meyer Mathematical Model of HIV/AIDS
Considering Sexual Preferences Under
Antiretroviral Therapy, a Case Study in
San Juan de Pasto, Colombia . . . . . . 483--493