PLOS Computational Biology

2005 - 2025

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Volume 2, issue 12, 2006

Cooperation is Fleeting in the World of Transposable Elements pp. 1-8

Andreas Wagner

Gene Expression of Caenorhabditis elegans Neurons Carries Information on Their Synaptic Connectivity pp. 1-7

Alon Kaufman, Gideon Dror, Isaac Meilijson and Eytan Ruppin

Transcriptional Regulation by Competing Transcription Factor Modules pp. 1-9

Rutger Hermsen, Sander Tans and Pieter Rein ten Wolde

Volume 2, issue 11, 2006

Robustness and Fragility in Immunosenescence pp. 1-7

Sean P Stromberg and Jean Carlson

Optimal Noise Filtering in the Chemotactic Response of Escherichia coli pp. 1-12

Burton W Andrews, Tau-Mu Yi and Pablo A Iglesias

Meta-Analysis of Differentiating Mouse Embryonic Stem Cell Gene Expression Kinetics Reveals Early Change of a Small Gene Set pp. 1-12

Clive H Glover, Michael Marin, Connie J Eaves, Cheryl D Helgason, James M Piret and Jennifer Bryan

Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle pp. 1-10

Jin Wang, Bo Huang, Xuefeng Xia and Zhirong Sun

Humans Can Adopt Optimal Discounting Strategy under Real-Time Constraints pp. 1-8

N Schweighofer, K Shishida, C E Han, Y Okamoto, S C Tanaka, S Yamawaki and K Doya

Ten Simple Rules for Selecting a Postdoctoral Position pp. 1-2

Philip E Bourne and Iddo Friedberg

Computational Inference of Neural Information Flow Networks pp. 1-14

V Anne Smith, Jing Yu, Tom V Smulders, Alexander J Hartemink and Erich D Jarvis

Volume 2, issue 10, 2006

Cooperation Prevails When Individuals Adjust Their Social Ties pp. 1-8

Francisco C Santos, Jorge M Pacheco and Tom Lenaerts

Volume 2, issue 9, 2006

Ten Simple Rules for Reviewers pp. 1-2

Philip E Bourne and Alon Korngreen

Imitating Manual Curation of Text-Mined Facts in Biomedicine pp. 1-14

Raul Rodriguez-Esteban, Ivan Iossifov and Andrey Rzhetsky

Sampling Realistic Protein Conformations Using Local Structural Bias pp. 1-13

Thomas Hamelryck, John T Kent and Anders Krogh

Volume 2, issue 8, 2006

Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families pp. 1-7

Guohui Ding, Jiuhong Kang, Qi Liu, Tieliu Shi, Gang Pei and Yixue Li

The Ion Channel Inverse Problem: Neuroinformatics Meets Biophysics pp. 1-8

Robert C Cannon and Giampaolo D'Alessandro

Volume 2, issue 7, 2006

Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles pp. 1-11

Markus J Herrgård, Stephen S Fong and Bernhard Ø Palsson

Complex Parameter Landscape for a Complex Neuron Model pp. 1-11

Pablo Achard and Erik De Schutter

Nonoptimal Component Placement, but Short Processing Paths, due to Long-Distance Projections in Neural Systems pp. 1-11

Marcus Kaiser and Claus C Hilgetag

Authors' Reply pp. 1-2

Hung D Nguyen, Maki Yoshihama and Naoya Kenmochi

On the Estimation of Intron Evolution pp. 1-1

Miklós Csűrös

Wiggle—Predicting Functionally Flexible Regions from Primary Sequence pp. 1-17

Jenny Gu, Michael Gribskov and Philip E Bourne

Volume 2, issue 6, 2006

A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules pp. 1-11

Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, Derek Basch, Kasper Lamberth, Mikkel Harndahl, Ward Fleri, Stephen S Wilson, John Sidney, Ole Lund, Soren Buus and Alessandro Sette

Assessing the Accuracy of Ancestral Protein Reconstruction Methods pp. 1-8

Paul D Williams, David D Pollock, Benjamin P Blackburne and Richard A Goldstein

Parametric Alignment of Drosophila Genomes pp. 1-9

Colin N Dewey, Peter M Huggins, Kevin Woods, Bernd Sturmfels and Lior Pachter

How Does Cross-Reactive Stimulation Affect the Longevity of CD8+ T Cell Memory? pp. 1-10

Vitaly V Ganusov, Sergei S Pilyugin, Rafi Ahmed and Rustom Antia

Volume 2, issue 5, 2006

Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays pp. 1-10

Rameen Beroukhim, Ming Lin, Yuhyun Park, Ke Hao, Xiaojun Zhao, Levi A Garraway, Edward A Fox, Ephraim P Hochberg, Ingo K Mellinghoff, Matthias D Hofer, Aurelien Descazeaud, Mark A Rubin, Matthew Meyerson, Wing Hung Wong, William R Sellers and Cheng Li

Iterative Reconstruction of Transcriptional Regulatory Networks: An Algorithmic Approach pp. 1-10

Christian L Barrett and Bernhard O Palsson

Reverse Engineering the Gap Gene Network of Drosophila melanogaster pp. 1-12

Theodore J Perkins, Johannes Jaeger, John Reinitz and Leon Glass

Statistics of Knots, Geometry of Conformations, and Evolution of Proteins pp. 1-8

Rhonald C Lua and Alexander Y Grosberg

Volume 2, issue 4, 2006

The Signal in the Genomes pp. 1-2

David Sankoff

Conformational Changes in Protein Loops and Helices Induced by Post-Translational Phosphorylation pp. 1-13

Eli S Groban, Arjun Narayanan and Matthew P Jacobson

Codon Usage Domains over Bacterial Chromosomes pp. 1-13

Marc Bailly-Bechet, Antoine Danchin, Mudassar Iqbal, Matteo Marsili and Massimo Vergassola

Practical Strategies for Discovering Regulatory DNA Sequence Motifs pp. 1-10

Kenzie D MacIsaac and Ernest Fraenkel

Volume 2, issue 3, 2006

Circadian Clocks Are Resounding in Peripheral Tissues pp. 1-10

Andrey A Ptitsyn, Sanjin Zvonic, Steven A Conrad, L Keith Scott, Randall L Mynatt and Jeffrey M Gimble

Volume 2, issue 2, 2006

Ten Simple Rules for Getting Grants pp. 1-2

Philip E Bourne and Leo M Chalupa

Seriation in Paleontological Data Using Markov Chain Monte Carlo Methods pp. 1-9

Kai Puolamäki, Mikael Fortelius and Heikki Mannila

Volume 1, issue 7, 2005

New Maximum Likelihood Estimators for Eukaryotic Intron Evolution pp. 1-8

Hung D Nguyen, Maki Yoshihama and Naoya Kenmochi

PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny pp. 1-23

Rahul Siddharthan, Eric D Siggia and Erik van Nimwegen

Volume 1, issue 6, 2005

Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection pp. 1-13

Rajeev K Azad and Jeffrey G Lawrence

A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes pp. 1-10

Daniel H Haft, Jeremy Selengut, Emmanuel F Mongodin and Karen E Nelson

Quantitative Analysis of Genetic and Neuronal Multi-Perturbation Experiments pp. 1-7

Alon Kaufman, Alon Keinan, Isaac Meilijson, Martin Kupiec and Eytan Ruppin

Bioinformatics Education—Perspectives and Challenges pp. 1-2

Shoba Ranganathan

Volume 1, issue 5, 2005

Protein Molecular Function Prediction by Bayesian Phylogenomics pp. 1-

Barbara E Engelhardt, Michael I Jordan, Kathryn E Muratore and Steven E Brenner

Ten Simple Rules for Getting Published pp. 1-2

Philip E Bourne

The ISCB: Growing and Evolving in Step with Science pp. 1-6

Michael Gribskov

Genomic Variability within an Organism Exposes Its Cell Lineage Tree pp. 1-13

Dan Frumkin, Adam Wasserstrom, Shai Kaplan, Uriel Feige and Ehud Shapiro

Volume 1, issue 4, 2005

Inferring Hypotheses on Functional Relationships of Genes: Analysis of the Arabidopsis thaliana Subtilase Gene Family pp. 1-

Carsten Rautengarten, Dirk Steinhauser, Dirk Büssis, Annick Stintzi, Andreas Schaller, Joachim Kopka and Thomas Altmann

Volume 1, issue 2, 2005

Recognition of Unknown Conserved Alternatively Spliced Exons pp. 1-

Uwe Ohler, Noam Shomron and Christopher B Burge

Volume 1, issue 1, 2005

Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a β -Hairpin pp. 1-

Laxmi Parida and Ruhong Zhou