Table of Contents: February 2012

This three-dimensional rendering illustrates light hitting a neuron bearing light-sensitive channels. When light impinges upon the neuron, the channels open, electrically exciting the neuron (depicted as white highlights). (See Börgers et al., doi:10.1371/journal.pcbi.1002362)

Image Credit: Courtesy of Ed Boyden, McGovern Institute for Brain Research at MIT, and Sputnik Animation.


Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

Purvesh Khatri, Marina Sirota, Atul J. Butte

The Efficiency of the Human CD8+ T Cell Response: How Should We Quantify It, What Determines It, and Does It Matter?

Marjet Elemans, Nafisa-Katrin Seich al Basatena, Becca Asquith

Research Articles

A Cell-based Computational Modeling Approach for Developing Site-Directed Molecular Probes

Jing-yu Yu, Nan Zheng, Gerta Mane, Kyoung Ah Min, Juan P. Hinestroza, Huaning Zhu, Kathleen A. Stringer, Gus R. Rosania

Structural Consensus among Antibodies Defines the Antigen Binding Site

Vered Kunik, Bjoern Peters, Yanay Ofran

Effects of Electrical and Structural Remodeling on Atrial Fibrillation Maintenance: A Simulation Study

Trine Krogh-Madsen, Geoffrey W. Abbott, David J. Christini

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data

Santiago Treviño III, Yudong Sun, Tim F. Cooper, Kevin E. Bassler

Comparison of Insertional RNA Editing in Myxomycetes

Cai Chen, David Frankhouser, Ralf Bundschuh

Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke

Yukikazu Hidaka, Cheol E. Han, Steven L. Wolf, Carolee J. Winstein, Nicolas Schweighofer

On the Effect of Thermodynamic Equilibrium on the Assembly Efficiency of Complex Multi-Layered Virus-Like Particles (VLP): the Case of Rotavirus VLP

António Roldão, Maria Candida M. Mellado, J. C. Lima, Manuel J. T. Carrondo, Paula M. Alves, R. Oliveira

Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function

Giulio Quarta, Ken Sin, Tamar Schlick

A Race between Tumor Immunoescape and Genome Maintenance Selects for Optimum Levels of (epi)genetic Instability

Shingo Iwami, Hiroshi Haeno, Franziska Michor

Joint Analysis of Multiple Metagenomic Samples

Yael Baran, Eran Halperin

Branch Mode Selection during Early Lung Development

Denis Menshykau, Conradin Kraemer, Dagmar Iber

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

Markus Hartenfeller, Heiko Zettl, Miriam Walter, Matthias Rupp, Felix Reisen, Ewgenij Proschak, Sascha Weggen, Holger Stark, Gisbert Schneider

Paradoxical Evidence Integration in Rapid Decision Processes

Johannes Rüter, Nicolas Marcille, Henning Sprekeler, Wulfram Gerstner, Michael H. Herzog

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

Paul D. Thomas, Valerie Wood, Christopher J. Mungall, Suzanna E. Lewis, Judith A. Blake, on behalf of the Gene Ontology Consortium

Noise and Robustness in Phyllotaxis

Vincent Mirabet, Fabrice Besnard, Teva Vernoux, Arezki Boudaoud

The Role of Conserved Waters in Conformational Transitions of Q61H K-ras

Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A. Gorfe

Using Functional Signatures to Identify Repositioned Drugs for Breast, Myelogenous Leukemia and Prostate Cancer

Daichi Shigemizu, Zhenjun Hu, Jui-Hung Hung, Chia-Ling Huang, Yajie Wang, Charles DeLisi

Minimal Size of Cell Assemblies Coordinated by Gamma Oscillations

Christoph Börgers, Giovanni Talei Franzesi, Fiona E. N. LeBeau, Edward S. Boyden, Nancy J. Kopell

Control of Whole Heart Geometry by Intramyocardial Mechano-Feedback: A Model Study

Theo Arts, Joost Lumens, Wilco Kroon, Tammo Delhaas

Multi-Scale Modeling of HIV Infection in vitro and APOBEC3G-Based Anti-Retroviral Therapy

Iraj Hosseini, Feilim Mac Gabhann

Subcellular Location of PKA Controls Striatal Plasticity: Stochastic Simulations in Spiny Dendrites

Rodrigo F. Oliveira, MyungSook Kim, Kim T. Blackwell

Human Visual Search Does Not Maximize the Post-Saccadic Probability of Identifying Targets

Camille Morvan, Laurence T. Maloney

In silico Experimentation of Glioma Microenvironment Development and Anti-tumor Therapy

Yu Wu, Yao Lu, Weiqiang Chen, Jianping Fu, Rong Fan

Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina

Pranidhi Sood, Robert J. Johnston Jr., Edo Kussell

Early Warning Signals for Critical Transitions: A Generalized Modeling Approach

Steven J. Lade, Thilo Gross

Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures

Nadav Rappoport, Michal Linial

Novel Approach to Meta-Analysis of Microarray Datasets Reveals Muscle Remodeling-related Drug Targets and Biomarkers in Duchenne Muscular Dystrophy

Ekaterina Kotelnikova, Maria A. Shkrob, Mikhail A. Pyatnitskiy, Alessandra Ferlini, Nikolai Daraselia