Table of Contents: January 2011


Looming danger of returning to the pre-antibiotic era.

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


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

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

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

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

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

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

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

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