Table of Contents

January 2011

Antibiotics have been the mainstay of treatment for a variety of infectious diseases such as pneumonia. Due to the increasing incidence of antimicrobial resistance, we are at risk of returning to the pre-antibiotic era, and the need to develop new drugs rapidly is becoming more urgent. A new computational method could provide quantitative insights to the interaction between an antimicrobial agent and a pathogen, which would facilitate new agent development by rationally guiding selection of dosing regimens. (See Tam and Nikolau, doi:10.1371/journal.pcbi.1001043.)

Image Credit: Thomas Shea, University of Houston Cullen College of Engineering


A Review of 2010 for PLoS Computational Biology

Rosemary Dickin, Cecy Marden, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne

Research Articles

Detecting Remote Evolutionary Relationships among Proteins by Large-Scale Semantic Embedding

Iain Melvin, Jason Weston, William Stafford Noble, Christina Leslie

Estimation of Parent Specific DNA Copy Number in Tumors using High-Density Genotyping Arrays

Hao Chen, Haipeng Xing, Nancy R. Zhang

Erratic Flu Vaccination Emerges from Short-Sighted Behavior in Contact Networks

Daniel M. Cornforth, Timothy C. Reluga, Eunha Shim, Chris T. Bauch, Alison P. Galvani, Lauren Ancel Meyers

The Role of Additive Neurogenesis and Synaptic Plasticity in a Hippocampal Memory Model with Grid-Cell Like Input

Peter A. Appleby, Gerd Kempermann, Laurenz Wiskott

Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map

Nozomu Yachie, Rintaro Saito, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama

Risk, Unexpected Uncertainty, and Estimation Uncertainty: Bayesian Learning in Unstable Settings

Elise Payzan-LeNestour, Peter Bossaerts

Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA

Dina Zhabinskaya, Craig J. Benham

Practical Measures of Integrated Information for Time-Series Data

Adam B. Barrett, Anil K. Seth

From Spiking Neuron Models to Linear-Nonlinear Models

Srdjan Ostojic, Nicolas Brunel

Is My Network Module Preserved and Reproducible?

Peter Langfelder, Rui Luo, Michael C. Oldham, Steve Horvath

A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System

Bing Liu, Jing Zhang, Pei Yi Tan, David Hsu, Anna M. Blom, Benjamin Leong, Sunil Sethi, Bow Ho, Jeak Ling Ding, P. S. Thiagarajan

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

Thomas J. Sharpton, Samantha J. Riesenfeld, Steven W. Kembel, Joshua Ladau, James P. O'Dwyer, Jessica L. Green, Jonathan A. Eisen, Katherine S. Pollard

Benchmarking Ontologies: Bigger or Better?

Lixia Yao, Anna Divoli, Ilya Mayzus, James A. Evans, Andrey Rzhetsky

Thermodynamic Stability of Histone H3 Is a Necessary but not Sufficient Driving Force for its Evolutionary Conservation

Srinivas Ramachandran, Lisa Vogel, Brian D. Strahl, Nikolay V. Dokholyan

A Comprehensive Model of the Spatio-Temporal Stem Cell and Tissue Organisation in the Intestinal Crypt

Peter Buske, Jörg Galle, Nick Barker, Gabriela Aust, Hans Clevers, Markus Loeffler

Relationships between Gene Expression and Brain Wiring in the Adult Rodent Brain

Leon French, Paul Pavlidis

Measuring the Evolutionary Rewiring of Biological Networks

Chong Shou, Nitin Bhardwaj, Hugo Y. K. Lam, Koon-Kiu Yan, Philip M. Kim, Michael Snyder, Mark B. Gerstein

Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations

Stefano Vanni, Marilisa Neri, Ivano Tavernelli, Ursula Rothlisberger

Using Transcription Modules to Identify Expression Clusters Perturbed in Williams-Beuren Syndrome

Charlotte N. Henrichsen, Gábor Csárdi, Marie-Thérèse Zabot, Carmela Fusco, Sven Bergmann, Giuseppe Merla, Alexandre Reymond