PLOS Computational Biology

2005 - 2022

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Volume 2, issue 12, 2006

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

Rutger Hermsen, Sander Tans and Pieter Rein ten Wolde

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

Detecting Statistically Significant Common Insertion Sites in Retroviral Insertional Mutagenesis Screens pp. 1-13

Jeroen de Ridder, Anthony Uren, Jaap Kool, Marcel Reinders and Lodewyk Wessels

DARPP-32 Is a Robust Integrator of Dopamine and Glutamate Signals pp. 1-15

Éric Fernandez, Renaud Schiappa, Jean-Antoine Girault and Nicolas Le Novère

On Side-Chain Conformational Entropy of Proteins pp. 1-6

Jinfeng Zhang and Jun S Liu

Volume 2, issue 11, 2006

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

Robustness and Fragility in Immunosenescence pp. 1-7

Sean P Stromberg and Jean Carlson

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

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

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

Philip E Bourne and Iddo Friedberg

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

Simulating Properties of In Vitro Epithelial Cell Morphogenesis pp. 1-17

Mark R Grant, Keith E Mostov, Thea D Tlsty and C Anthony Hunt

Volume 2, issue 9, 2006

Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation pp. 1-14

Manuel Barrio, Kevin Burrage, André Leier and Tianhai Tian

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

Raul Rodriguez-Esteban, Ivan Iossifov and Andrey Rzhetsky

Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability pp. 1-13

Stefan Legewie, Nils Blüthgen and Hanspeter Herzel

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

Thomas Hamelryck, John T Kent and Anders Krogh

Transient Calcium and Dopamine Increase PKA Activity and DARPP-32 Phosphorylation pp. 1-16

Maria Lindskog, MyungSook Kim, Martin A Wikström, Kim T Blackwell and Jeanette Hellgren Kotaleski

Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors pp. 1-12

Xiaolin Cheng, Hailong Wang, Barry Grant, Steven M Sine and J Andrew McCammon

Ten Simple Rules for Reviewers pp. 1-2

Philip E Bourne and Alon Korngreen

Scientific Software Development Is Not an Oxymoron pp. 1-4

Susan M Baxter, Steven W Day, Jacquelyn S Fetrow and Stephanie J Reisinger

Volume 2, issue 8, 2006

One Year of PLoS Computational Biology pp. 1-2

Philip E Bourne

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

Transient Resetting: A Novel Mechanism for Synchrony and Its Biological Examples pp. 1-7

Chunguang Li, Luonan Chen and Kazuyuki Aihara

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

Robert C Cannon and Giampaolo D'Alessandro

High Epitope Expression Levels Increase Competition between T Cells pp. 1-11

Almut Scherer, Marcel Salathé and Sebastian Bonhoeffer

Volume 2, issue 7, 2006

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

Jenny Gu, Michael Gribskov and Philip E Bourne

Key Role of Local Regulation in Chemosensing Revealed by a New Molecular Interaction-Based Modeling Method pp. 1-15

Martin Meier-Schellersheim, Xuehua Xu, Bastian Angermann, Eric J Kunkel, Tian Jin and Ronald N Germain

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

Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition pp. 1-11

Jin Wang, Qiang Lu and H Peter Lu

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

On the Estimation of Intron Evolution pp. 1-1

Miklós Csűrös

Toward a Census of Bacteria in Soil pp. 1-8

Patrick D Schloss and Jo Handelsman

Authors' Reply pp. 1-2

Hung D Nguyen, Maki Yoshihama and Naoya Kenmochi

Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome pp. 1-18

Adrian H Elcock

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

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

On Modeling HIV and T Cells In Vivo: Assessing Causal Estimators in Vaccine Trials pp. 1-10

W David Wick, Peter B Gilbert and Steven G Self

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

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

Noise-Induced Min Phenotypes in E. coli pp. 1-12

David Fange and Johan Elf

Parametric Alignment of Drosophila Genomes pp. 1-9

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

Volume 2, issue 5, 2006

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

Rhonald C Lua and Alexander Y Grosberg

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

Transcription Factor Map Alignment of Promoter Regions pp. 1-14

Enrique Blanco, Xavier Messeguer, Temple F Smith and Roderic Guigó

Volume 2, issue 4, 2006

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

Kenzie D MacIsaac and Ernest Fraenkel

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

The Signal in the Genomes pp. 1-2

David Sankoff

Volume 2, issue 3, 2006

Authors' Reply pp. 1-2

Eliot C Bush and Bruce T Lahn

Role of Mechanical Factors in the Morphology of the Primate Cerebral Cortex pp. 1-14

Claus C Hilgetag and Helen Barbas

The Emergence of Up and Down States in Cortical Networks pp. 1-8

David Holcman and Misha Tsodyks

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

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

Kai Puolamäki, Mikael Fortelius and Heikki Mannila

The Fragile Breakage versus Random Breakage Models of Chromosome Evolution pp. 1-12

Qian Peng, Pavel A Pevzner and Glenn Tesler

Ten Simple Rules for Getting Grants pp. 1-2

Philip E Bourne and Leo M Chalupa

ISMB 2006 pp. 1-1

Goran Neshich, Philip E Bourne and Søren Brunak