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Table of Contents | January 2012

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About This Image

An Australian desert ant deciding which way is home.

When displaced from their regular routes, workers of the Australian desert ant Melophorus bagoti rotate on the spot, producing visual scans of the world, before setting off in a seemingly purposeful manner. In this image a worker with her prized cookie crumb is photographed on a goniometer that is used to record her directional choice. (See Baddeley et al., doi:10.1371/journal.pcbi.1002336)

Image Credit: Antoine Wystrach (University of Sussex, Brighton, UK)

Editorial

A Review of 2011 for PLoS Computational Biology

Rosemary Dickin, Chris James Hall, Laura K. Taylor, Andrew M. Collings, Ruth Nussinov, Philip E. Bourne

Perspective

Beyond Statistical Significance: Implications of Network Structure on Neuronal Activity

Ioannis Vlachos, Ad Aertsen, Arvind Kumar

Review

Computational and Statistical Analysis of Protein Mass Spectrometry Data

William Stafford Noble, Michael J. MacCoss

Research Articles

A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser

Justin Hsia, William J. Holtz, Daniel C. Huang, Murat Arcak, Michel M. Maharbiz

Balancing Feed-Forward Excitation and Inhibition via Hebbian Inhibitory Synaptic Plasticity

Yotam Luz, Maoz Shamir

Macro-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress

Patrick D. McMullen, Erin Z. Aprison, Peter B. Winter, Luis A. N. Amaral, Richard I. Morimoto, Ilya Ruvinsky

Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer

Xinan Yang, Kelly Regan, Yong Huang, Qingbei Zhang, Jianrong Li, Tanguy Y. Seiwert, Ezra E. W. Cohen, H. Rosie Xing, Yves A. Lussier

Senescent Cells in Growing Tumors: Population Dynamics and Cancer Stem Cells

Caterina A. M. La Porta, Stefano Zapperi, James P. Sethna

Learning and Generalization under Ambiguity: An fMRI Study

J. R. Chumbley, G. Flandin, D. R. Bach, J. Daunizeau, E. Fehr, R. J. Dolan, K. J. Friston

A Theory of Rate Coding Control by Intrinsic Plasticity Effects

J. Naudé, J. T. Paz, H. Berry, B. Delord

Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism

Fiona Achcar, Eduard J. Kerkhoven, Barbara M. Bakker, Michael P. Barrett, Rainer Breitling, The SilicoTryp Consortium

Membrane Properties and the Balance between Excitation and Inhibition Control Gamma-Frequency Oscillations Arising from Feedback Inhibition

Michael N. Economo, John A. White

HIV-1 Polymerase Inhibition by Nucleoside Analogs: Cellular- and Kinetic Parameters of Efficacy, Susceptibility and Resistance Selection

Max von Kleist, Philipp Metzner, Roland Marquet, Christof Schütte

Prediction by Promoter Logic in Bacterial Quorum Sensing

Navneet Rai, Rajat Anand, Krishna Ramkumar, Varun Sreenivasan, Sugat Dabholkar, K. V. Venkatesh, Mukund Thattai

Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana

Michael Seifert, André Gohr, Marc Strickert, Ivo Grosse

Lipid Exchange Mechanism of the Cholesteryl Ester Transfer Protein Clarified by Atomistic and Coarse-grained Simulations

Artturi Koivuniemi, Timo Vuorela, Petri T. Kovanen, Ilpo Vattulainen, Marja T. Hyvönen

Global Analysis of Small Molecule Binding to Related Protein Targets

Felix A. Kruger, John P. Overington

Protein Design Using Continuous Rotamers

Pablo Gainza, Kyle E. Roberts, Bruce R. Donald

A Dynamic View of Domain-Motif Interactions

Eyal Akiva, Gilgi Friedlander, Zohar Itzhaki, Hanah Margalit

Adjusting Phenotypes by Noise Control

Kyung H. Kim, Herbert M. Sauro

Network Model of Immune Responses Reveals Key Effectors to Single and Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth

Juilee Thakar, Ashutosh K. Pathak, Lisa Murphy, Réka Albert, Isabella M. Cattadori

Maximization of Learning Speed in the Motor Cortex Due to Neuronal Redundancy

Ken Takiyama, Masato Okada

Kinetic Rate Constant Prediction Supports the Conformational Selection Mechanism of Protein Binding

Iain H. Moal, Paul A. Bates

Residual Structures, Conformational Fluctuations, and Electrostatic Interactions in the Synergistic Folding of Two Intrinsically Disordered Proteins

Weihong Zhang, Debabani Ganguly, Jianhan Chen

Short Conduction Delays Cause Inhibition Rather than Excitation to Favor Synchrony in Hybrid Neuronal Networks of the Entorhinal Cortex

Shuoguo Wang, Lakshmi Chandrasekaran, Fernando R. Fernandez, John A. White, Carmen C. Canavier

Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection

Richard P. Mann, Andrea Perna, Daniel Strömbom, Roman Garnett, James E. Herbert-Read, David J. T. Sumpter, Ashley J. W. Ward

Failure of Adaptive Self-Organized Criticality during Epileptic Seizure Attacks

Christian Meisel, Alexander Storch, Susanne Hallmeyer-Elgner, Ed Bullmore, Thilo Gross

Dopamine, Affordance and Active Inference

Karl J. Friston, Tamara Shiner, Thomas FitzGerald, Joseph M. Galea, Rick Adams, Harriet Brown, Raymond J. Dolan, Rosalyn Moran, Klaas Enno Stephan, Sven Bestmann

Landscape Epidemiology and Control of Pathogens with Cryptic and Long-Distance Dispersal: Sudden Oak Death in Northern Californian Forests

João A. N. Filipe, Richard C. Cobb, Ross K. Meentemeyer, Christopher A. Lee, Yana S. Valachovic, Alex R. Cook, David M. Rizzo, Christopher A. Gilligan

A Dynamical Model of Oocyte Maturation Unveils Precisely Orchestrated Meiotic Decisions

Benjamin Pfeuty, Jean-Francois Bodart, Ralf Blossey, Marc Lefranc

Joint Modelling of Confounding Factors and Prominent Genetic Regulators Provides Increased Accuracy in Genetical Genomics Studies

Nicoló Fusi, Oliver Stegle, Neil D. Lawrence

A Model of Ant Route Navigation Driven by Scene Familiarity

Bart Baddeley, Paul Graham, Philip Husbands, Andrew Philippides

A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis

Yu-Kang Cheng, Rameen Beroukhim, Ross L. Levine, Ingo K. Mellinghoff, Eric C. Holland, Franziska Michor

A Viral Dynamic Model for Treatment Regimens with Direct-acting Antivirals for Chronic Hepatitis C Infection

Bambang S. Adiwijaya, Tara L. Kieffer, Joshua Henshaw, Karen Eisenhauer, Holly Kimko, John J. Alam, Robert S. Kauffman, Varun Garg

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