November 2011

This image shows a simple mathematical rule describing collective decision-making. In this study (see Pérez-Escudero and de Polavieja, 10.1371/journal.pcbi.1002282) the authors used as their starting point that brains estimate the likely structure of the world from uncertain sensory data. Applying this to the case in which sensory data contains nonsocial and social components, the authors derive simple expressions for individual decisions that give rise to collective behaviors. The authors also show that these expressions correspond to existing data on fish collective decisions.

Image Credit: Sara Arganda, Alfonso Pérez-Esdudero & Gonzalo G. de Polavieja, Instituto Cajal, CSIC, Madrid, España.

Perspective

PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011

Pedro Madrigal, Noa Sela, Simon M. Lin

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002259

Review

The What and Where of Adding Channel Noise to the Hodgkin-Huxley Equations

Joshua H. Goldwyn, Eric Shea-Brown

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002247

Research Articles

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

Chao Cheng, Koon-Kiu Yan, Woochang Hwang, Jiang Qian, Nitin Bhardwaj, Joel Rozowsky, Zhi John Lu, Wei Niu, Pedro Alves, Masaomi Kato, Michael Snyder, Mark Gerstein

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002190

Robust Signal Processing in Living Cells

Ralf Steuer, Steffen Waldherr, Victor Sourjik, Markus Kollmann

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002218

Significance of Input Correlations in Striatal Function

Man Yi Yim, Ad Aertsen, Arvind Kumar

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002254

Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits

Rutger Hermsen, David W. Erickson, Terence Hwa

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002265

Virus Replication Strategies and the Critical CTL Numbers Required for the Control of Infection

Andrew J. Yates, Minus Van Baalen, Rustom Antia

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002274

Gene Expression Divergence is Coupled to Evolution of DNA Structure in Coding Regions

Zhiming Dai, Xianhua Dai

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002275

Optimizing Experimental Design for Comparing Models of Brain Function

Jean Daunizeau, Kerstin Preuschoff, Karl Friston, Klaas Stephan

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002280

Sparse Gamma Rhythms Arising through Clustering in Adapting Neuronal Networks

Zachary P. Kilpatrick, Bard Ermentrout

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002281

Collective Animal Behavior from Bayesian Estimation and Probability Matching

Alfonso Pérez-Escudero, Gonzalo G. de Polavieja

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002282

Genome Majority Vote Improves Gene Predictions

Michael E. Wall, Sindhu Raghavan, Judith D. Cohn, John Dunbar

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002284

Replication Pauses of the Wild-Type and Mutant Mitochondrial DNA Polymerase Gamma: A Simulation Study

Zhuo Song, Yang Cao, David C. Samuels

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002287

Deciphering the Arginine-Binding Preferences at the Substrate-Binding Groove of Ser/Thr Kinases by Computational Surface Mapping

Avraham Ben-Shimon, Masha Y. Niv

PLOS Computational Biology: published November 17, 2011 | https://doi.org/10.1371/journal.pcbi.1002288

Phosphorylation of the Arp2 Subunit Relieves Auto-inhibitory Interactions for Arp2/3 Complex Activation

Arjun Narayanan, Lawrence L. LeClaire III, Diane L. Barber, Matthew P. Jacobson

PLOS Computational Biology: published November 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002226

Identification of Biochemical Network Modules Based on Shortest Retroactive Distances

Gautham Vivek Sridharan, Soha Hassoun, Kyongbum Lee

PLOS Computational Biology: published November 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002262

Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation

Joshua Lequieu, Anirikh Chakrabarti, Satyaprakash Nayak, Jeffrey D. Varner

PLOS Computational Biology: published November 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002263

Stochastic Delay Accelerates Signaling in Gene Networks

Krešimir Josić, José Manuel López, William Ott, LieJune Shiau, Matthew R. Bennett

PLOS Computational Biology: published November 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002264

Representational Switching by Dynamical Reorganization of Attractor Structure in a Network Model of the Prefrontal Cortex

Yuichi Katori, Kazuhiro Sakamoto, Naohiro Saito, Jun Tanji, Hajime Mushiake, Kazuyuki Aihara

PLOS Computational Biology: published November 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002266

Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia

Assieh Saadatpour, Rui-Sheng Wang, Aijun Liao, Xin Liu, Thomas P. Loughran, István Albert, Réka Albert

PLOS Computational Biology: published November 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002267

A Density-Dependent Switch Drives Stochastic Clustering and Polarization of Signaling Molecules

Alexandra Jilkine, Sigurd B. Angenent, Lani F. Wu, Steven J. Altschuler

PLOS Computational Biology: published November 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002271

Reversible and Noisy Progression towards a Commitment Point Enables Adaptable and Reliable Cellular Decision-Making

Anna Kuchina, Lorena Espinar, Jordi Garcia-Ojalvo, Gürol M. Süel

PLOS Computational Biology: published November 10, 2011 | https://doi.org/10.1371/journal.pcbi.1002273

Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons

Lars Buesing, Johannes Bill, Bernhard Nessler, Wolfgang Maass

PLOS Computational Biology: published November 3, 2011 | https://doi.org/10.1371/journal.pcbi.1002211

Transcriptomic Coordination in the Human Metabolic Network Reveals Links between n-3 Fat Intake, Adipose Tissue Gene Expression and Metabolic Health

Melissa J. Morine, Audrey C. Tierney, Ben van Ommen, Hannelore Daniel, Sinead Toomey, Ingrid M. F. Gjelstad, Isobel C. Gormley, Pablo Pérez-Martinez, Christian A. Drevon, Jose López-Miranda, Helen M. Roche

PLOS Computational Biology: published November 3, 2011 | https://doi.org/10.1371/journal.pcbi.1002223

Cover

Deriving the rules of collective behavior from basic properties of perception.