July 2008

AF-2 domains of nuclear receptors mediate crucial protein–protein interactions with transcriptional coactivators. The AF-2 domains (magenta) of the human nuclear xenobiotic receptor PXR (cyan) were demonstrated using molecular dynamics to move together in an "active-ready" conformation, poised to bind to their cognate protein partners (see Teotico et al. pcbi.1000111). Other nuclear receptors were also shown to follow suit.

Image Credit: Monica Frazier and Matthew Redinbo

Message from ISCB

ISCB Honors David Haussler and Aviv Regev

Clare Sansom, B. J. Morrison McKay

PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000101

Perspectives

Computational Biology Resources Lack Persistence and Usability

Stella Veretnik, J. Lynn Fink, Philip E. Bourne

PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000136

Outlook on Thailand's Genomics and Computational Biology Research and Development

Wannipha Tongsima, Sissades Tongsima, Prasit Palittapongarnpim

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000115

Review

Nonnegative Matrix Factorization: An Analytical and Interpretive Tool in Computational Biology

Karthik Devarajan

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000029

Research Articles

Kinetic Modeling of the Assembly, Dynamic Steady State, and Contraction of the FtsZ Ring in Prokaryotic Cytokinesis

Ivan V. Surovtsev, Jeffrey J. Morgan, Paul A. Lindahl

PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000102

Dynamics of Immune Escape during HIV/SIV Infection

Christian L. Althaus, Rob J. De Boer

PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000103

Circadian Phase Resetting via Single and Multiple Control Targets

Neda Bagheri, Jörg Stelling, Francis J. Doyle III

PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000104

Local Function Conservation in Sequence and Structure Space

Nils Weinhold, Oliver Sander, Francisco S. Domingues, Thomas Lengauer, Ingolf Sommer

PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000105

Increased Brain Signal Variability Accompanies Lower Behavioral Variability in Development

Anthony Randal McIntosh, Natasa Kovacevic, Roxane J. Itier

PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000106

Quantitative Predictions of Peptide Binding to Any HLA-DR Molecule of Known Sequence: NetMHCIIpan

Morten Nielsen, Claus Lundegaard, Thomas Blicher, Bjoern Peters, Alessandro Sette, Sune Justesen, Søren Buus, Ole Lund

PLOS Computational Biology: published July 4, 2008 | https://doi.org/10.1371/journal.pcbi.1000107

Unraveling Protein Networks with Power Graph Analysis

Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder

PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000108

The Generation of Promoter-Mediated Transcriptional Noise in Bacteria

Namiko Mitarai, Ian B. Dodd, Michael T. Crooks, Kim Sneppen

PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000109

The Ascent of the Abundant: How Mutational Networks Constrain Evolution

Matthew C. Cowperthwaite, Evan P. Economo, William R. Harcombe, Eric L. Miller, Lauren Ancel Meyers

PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000110

Active Nuclear Receptors Exhibit Highly Correlated AF-2 Domain Motions

Denise G. Teotico, Monica L. Frazier, Feng Ding, Nikolay V. Dokholyan, Brenda R. S. Temple, Matthew R. Redinbo

PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000111

Evolution of Evolvability in Gene Regulatory Networks

Anton Crombach, Paulien Hogeweg

PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000112

Probing the Extent of Randomness in Protein Interaction Networks

Joseph Ivanic, Anders Wallqvist, Jaques Reifman

PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000114

Similarity Queries for Temporal Toxicogenomic Expression Profiles

Adam A. Smith, Aaron Vollrath, Christopher A. Bradfield, Mark Craven

PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000116

Intrinsic Gain Modulation and Adaptive Neural Coding

Sungho Hong, Brian Nils Lundstrom, Adrienne L. Fairhall

PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000119

Using Expression Profiles of Caenorhabditis elegans Neurons To Identify Genes That Mediate Synaptic Connectivity

Leehod Baruch, Shalev Itzkovitz, Michal Golan-Mashiach, Ehud Shapiro, Eran Segal

PLOS Computational Biology: published July 11, 2008 | https://doi.org/10.1371/journal.pcbi.1000120

Memory Switches in Chemical Reaction Space

Naren Ramakrishnan, Upinder S. Bhalla

PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000122

Emergent Synchronous Bursting of Oxytocin Neuronal Network

Enrico Rossoni, Jianfeng Feng, Brunello Tirozzi, David Brown, Gareth Leng, Françoise Moos

PLOS Computational Biology: published July 18, 2008 | https://doi.org/10.1371/journal.pcbi.1000123

Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels

Dmitry A. Dmitriev, Roman A. Rakitov

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000113

Predicting and Validating Protein Interactions Using Network Structure

Pao-Yang Chen, Charlotte M. Deane, Gesine Reinert

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000118

Protein Complex Evolution Does Not Involve Extensive Network Rewiring

Teunis J. P. van Dam, Berend Snel

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000132

Prediction by Graph Theoretic Measures of Structural Effects in Proteins Arising from Non-Synonymous Single Nucleotide Polymorphisms

Tammy M. K. Cheng, Yu-En Lu, Michele Vendruscolo, Pietro Lio', Tom L. Blundell

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000135

Isolation-by-Distance and Outbreeding Depression Are Sufficient to Drive Parapatric Speciation in the Absence of Environmental Influences

Guy A. Hoelzer, Rich Drewes, Jeffrey Meier, René Doursat

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000126

The Spatiotemporal Pattern of Src Activation at Lipid Rafts Revealed by Diffusion-Corrected FRET Imaging

Shaoying Lu, Mingxing Ouyang, Jihye Seong, Jin Zhang, Shu Chien, Yingxiao Wang

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000127

Optimal Compensation for Temporal Uncertainty in Movement Planning

Todd E. Hudson, Laurence T. Maloney, Michael S. Landy

PLOS Computational Biology: published July 25, 2008 | https://doi.org/10.1371/journal.pcbi.1000130

Cover

Long-range correlated motions are essential for nuclear receptor activity.