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Table of Contents: July 2008

COVER

Image Credit: Monica Frazier and Matthew Redinbo
Issue Image
Long-range correlated motions are essential for nuclear receptor activity.

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.

Message from ISCB

ISCB Honors David Haussler and Aviv Regev

Clare Sansom, B. J. Morrison McKay

Perspectives

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

Wannipha Tongsima, Sissades Tongsima, Prasit Palittapongarnpim

Computational Biology Resources Lack Persistence and Usability

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

Review

Research Articles

Predicting and Validating Protein Interactions Using Network Structure

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

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

Optimal Compensation for Temporal Uncertainty in Movement Planning

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

Dynamics of Immune Escape during HIV/SIV Infection

Christian L. Althaus, Rob J. De Boer

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

Similarity Queries for Temporal Toxicogenomic Expression Profiles

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

Intrinsic Gain Modulation and Adaptive Neural Coding

Sungho Hong, Brian Nils Lundstrom, Adrienne L. Fairhall

Memory Switches in Chemical Reaction Space

Naren Ramakrishnan, Upinder S. Bhalla

Emergent Synchronous Bursting of Oxytocin Neuronal Network

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

Unraveling Protein Networks with Power Graph Analysis

Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder

The Generation of Promoter-Mediated Transcriptional Noise in Bacteria

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

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

Probing the Extent of Randomness in Protein Interaction Networks

Joseph Ivanic, Anders Wallqvist, Jaques Reifman

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

Circadian Phase Resetting via Single and Multiple Control Targets

Neda Bagheri, Jörg Stelling, Francis J. Doyle III

Local Function Conservation in Sequence and Structure Space

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

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