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Table of Contents

February 2007

Cover

100-ns simulation of a three-component lipid bilayer
Issue Image

Snapshot from the end of a 100-ns simulation of a three-component lipid bilayer: POPC molecules are shown in gray, PSM in orange, CHOL in yellow, and water in cyan. The ratio of different lipids here is POPC:PSM:CHOL = 1:1:1 (see Niemelä et al).

Image Credit: Cover design by Perttu Niemelä. Created with the VMD and Raster3D software packages.

Perspective

From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research

Jomol P Mathew, Barry S Taylor, Gary D Bader, Saiju Pyarajan, Marco Antoniotti, Arul M Chinnaiyan, Chris Sander, Steven J Burakoff, Bud Mishra

PLOS Computational Biology: published February 23, 2007 | https://doi.org/10.1371/journal.pcbi.0030012

Research Articles

Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology

Stefano Ciliberti, Olivier C Martin, Andreas Wagner

PLOS Computational Biology: published February 2, 2007 | https://doi.org/10.1371/journal.pcbi.0030015

Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association

Lawrence C Lee, Florence Horn, Fred E Cohen

PLOS Computational Biology: published February 2, 2007 | https://doi.org/10.1371/journal.pcbi.0030016

Efficiency and Cost of Economical Brain Functional Networks

Sophie Achard, Ed Bullmore

PLOS Computational Biology: published February 2, 2007 | https://doi.org/10.1371/journal.pcbi.0030017

Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning

Gunnar Rätsch, Sören Sonnenburg, Jagan Srinivasan, Hanh Witte, Klaus-R Müller, Ralf-J Sommer, Bernhard Schölkopf

PLOS Computational Biology: published February 23, 2007 | https://doi.org/10.1371/journal.pcbi.0030020

Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations

Haibo Yu, Liang Ma, Yang Yang, Qiang Cui

PLOS Computational Biology: published February 9, 2007 | https://doi.org/10.1371/journal.pcbi.0030021

Related Articles

  1. Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues

Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel

David L Bostick, Charles L. Brooks III

PLOS Computational Biology: published February 9, 2007 | https://doi.org/10.1371/journal.pcbi.0030022

Mechanochemical Coupling in the Myosin Motor Domain. II. Analysis of Critical Residues

Haibo Yu, Liang Ma, Yang Yang, Qiang Cui

PLOS Computational Biology: published February 16, 2007 | https://doi.org/10.1371/journal.pcbi.0030023

Related Articles

  1. Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations

Specificity and Evolvability in Eukaryotic Protein Interaction Networks

Pedro Beltrao, Luis Serrano

PLOS Computational Biology: published February 16, 2007 | https://doi.org/10.1371/journal.pcbi.0030025

Related Articles

  1. Correction: Specificity and Evolvability in Eukaryotic Protein Interaction Networks

Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning

Rachel Karchin, Alvaro N. A Monteiro, Sean V Tavtigian, Marcelo A Carvalho, Andrej Sali

PLOS Computational Biology: published February 16, 2007 | https://doi.org/10.1371/journal.pcbi.0030026

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

Philippe Lemey, Sergei L Kosakovsky Pond, Alexei J Drummond, Oliver G Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut

PLOS Computational Biology: published February 16, 2007 | https://doi.org/10.1371/journal.pcbi.0030029

Unsupervised Learning of Visual Features through Spike Timing Dependent Plasticity

Timothée Masquelier, Simon J Thorpe

PLOS Computational Biology: published February 16, 2007 | https://doi.org/10.1371/journal.pcbi.0030031

Repressor Dimerization in the Zebrafish Somitogenesis Clock

Olivier Cinquin

PLOS Computational Biology: published February 16, 2007 | https://doi.org/10.1371/journal.pcbi.0030032

Assessing the Nature of Lipid Raft Membranes

Perttu S Niemelä, Samuli Ollila, Marja T Hyvönen, Mikko Karttunen, Ilpo Vattulainen

PLOS Computational Biology: published February 23, 2007 | https://doi.org/10.1371/journal.pcbi.0030034

Persistent Activity in Neural Networks with Dynamic Synapses

Omri Barak, Misha Tsodyks

PLOS Computational Biology: published February 23, 2007 | https://doi.org/10.1371/journal.pcbi.0030035

Related Articles

  1. Correction: Persistent Activity in Neural Networks with Dynamic Synapses

Corrections

Correction: Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays

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, Cheng Li

PLOS Computational Biology: published February 23, 2007 | https://doi.org/10.1371/journal.pcbi.0030040

Related Articles

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

Correction: The Role of Compensatory Mutations in the Emergence of Drug Resistance

Andreas Handel, Roland R Regoes, Rustom Antia

PLOS Computational Biology: published February 23, 2007 | https://doi.org/10.1371/journal.pcbi.0030046

Related Articles

  1. The Role of Compensatory Mutations in the Emergence of Drug Resistance

Correction: The Genome: An Outsider's View

Carl Zimmer

PLOS Computational Biology: published February 23, 2007 | https://doi.org/10.1371/journal.pcbi.0030047

Related Articles

  1. The Genome: An Outsider's View