Table of Contents

March 2012

This image illustrates a B4 neuron from the mollusk Lymnaea stagnalis on a background of mathematical expressions, simulation data, and binary digits, which represent the implicit assumption that nervous systems can be modeled and simulated in a digital computer. In this issue, Vavoulis et al. (10.1371/journal.pcbi.1002401) present a method for estimating dynamic states and parameters in data-driven models of neurons and neural networks based on principles of Bayesian statistics and Sequential Monte Carlo simulation.

Image Credit: Dimitrios V. Vavoulis and Volko A. Straub, the Universities of Warwick and Leicester, United Kingdom, 2012.


Ten Simple Rules for Starting a Company

Anthony C. Fletcher, Philip E. Bourne

Topic Pages: PLoS Computational Biology Meets Wikipedia

Shoshana J. Wodak, Daniel Mietchen, Andrew M. Collings, Robert B. Russell, Philip E. Bourne

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Marc S. Sherman, Barak A. Cohen

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Neural Network Mechanisms Underlying Stimulus Driven Variability Reduction

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Collective Dynamics Differentiates Functional Divergence in Protein Evolution

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Comprehensive Modelling of the Neurospora Circadian Clock and Its Temperature Compensation

Yu-Yao Tseng, Suzanne M. Hunt, Christian Heintzen, Susan K. Crosthwaite, Jean-Marc Schwartz

The Rate of Beneficial Mutations Surfing on the Wave of a Range Expansion

Rémi Lehe, Oskar Hallatschek, Luca Peliti

Dynamical Modeling of Collective Behavior from Pigeon Flight Data: Flock Cohesion and Dispersion

Graciano Dieck Kattas, Xiao-Ke Xu, Michael Small

Impact of Network Structure and Cellular Response on Spike Time Correlations

James Trousdale, Yu Hu, Eric Shea-Brown, Krešimir Josić

Implications of Behavioral Architecture for the Evolution of Self-Organized Division of Labor

A. Duarte, E. Scholtens, F. J. Weissing

Feedforward Inhibition and Synaptic Scaling – Two Sides of the Same Coin?

Christian Keck, Cristina Savin, Jörg Lücke

Corresponding Functional Dynamics across the Hsp90 Chaperone Family: Insights from a Multiscale Analysis of MD Simulations

Giulia Morra, Raffaello Potestio, Cristian Micheletti, Giorgio Colombo

Hemodynamic Traveling Waves in Human Visual Cortex

Kevin M. Aquino, Mark M. Schira, P. A. Robinson, Peter M. Drysdale, Michael Breakspear

Dynamic Effective Connectivity of Inter-Areal Brain Circuits

Demian Battaglia, Annette Witt, Fred Wolf, Theo Geisel

Traffic Instabilities in Self-Organized Pedestrian Crowds

Mehdi Moussaïd, Elsa G. Guillot, Mathieu Moreau, Jérôme Fehrenbach, Olivier Chabiron, Samuel Lemercier, Julien Pettré, Cécile Appert-Rolland, Pierre Degond, Guy Theraulaz

Cell Shape Dynamics: From Waves to Migration

Meghan K. Driscoll, Colin McCann, Rael Kopace, Tess Homan, John T. Fourkas, Carole Parent, Wolfgang Losert

AutoClickChem: Click Chemistry in Silico

Jacob D. Durrant, J. Andrew McCammon

Neurogenesis Drives Stimulus Decorrelation in a Model of the Olfactory Bulb

Siu-Fai Chow, Stuart D. Wick, Hermann Riecke

Network Evolution: Rewiring and Signatures of Conservation in Signaling

Mark G. F. Sun, Martin Sikora, Michael Costanzo, Charles Boone, Philip M. Kim

Highly Sensitive and Specific Detection of Rare Variants in Mixed Viral Populations from Massively Parallel Sequence Data

Alexander R. Macalalad, Michael C. Zody, Patrick Charlebois, Niall J. Lennon, Ruchi M. Newman, Christine M. Malboeuf, Elizabeth M. Ryan, Christian L. Boutwell, Karen A. Power, Doug E. Brackney, Kendra N. Pesko, Joshua Z. Levin, Gregory D. Ebel, Todd M. Allen, Bruce W. Birren, Matthew R. Henn

The Impact of Oxygen on Metabolic Evolution: A Chemoinformatic Investigation

Ying-Ying Jiang, De-Xin Kong, Tao Qin, Xiao Li, Gustavo Caetano-Anollés, Hong-Yu Zhang

Entropic Tension in Crowded Membranes

Martin Lindén, Pierre Sens, Rob Phillips

State-Space Analysis of Time-Varying Higher-Order Spike Correlation for Multiple Neural Spike Train Data

Hideaki Shimazaki, Shun-ichi Amari, Emery N. Brown, Sonja Grün

Epitope Flexibility and Dynamic Footprint Revealed by Molecular Dynamics of a pMHC-TCR Complex

Cyril F. Reboul, Grischa R. Meyer, Benjamin T. Porebski, Natalie A. Borg, Ashley M. Buckle

Bonsai Trees in Your Head: How the Pavlovian System Sculpts Goal-Directed Choices by Pruning Decision Trees

Quentin J. M. Huys, Neir Eshel, Elizabeth O'Nions, Luke Sheridan, Peter Dayan, Jonathan P. Roiser

Inferring Epidemic Contact Structure from Phylogenetic Trees

Gabriel E. Leventhal, Roger Kouyos, Tanja Stadler, Viktor von Wyl, Sabine Yerly, Jürg Böni, Cristina Cellerai, Thomas Klimkait, Huldrych F. Günthard, Sebastian Bonhoeffer

Does Sex Speed Up Evolutionary Rate and Increase Biodiversity?

Carlos J. Melián, David Alonso, Stefano Allesina, Richard S. Condit, Rampal S. Etienne

Mitochondrial Variability as a Source of Extrinsic Cellular Noise

Iain G. Johnston, Bernadett Gaal, Ricardo Pires das Neves, Tariq Enver, Francisco J. Iborra, Nick S. Jones

Cytoskeletal Signaling: Is Memory Encoded in Microtubule Lattices by CaMKII Phosphorylation?

Travis J. A. Craddock, Jack A. Tuszynski, Stuart Hameroff

Ensemble Models of Neutrophil Trafficking in Severe Sepsis

Sang O. K. Song, Justin Hogg, Zhi-Yong Peng, Robert Parker, John A. Kellum, Gilles Clermont

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Efficient Sparse Coding in Early Sensory Processing: Lessons from Signal Recovery

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A Self-Organizing State-Space-Model Approach for Parameter Estimation in Hodgkin-Huxley-Type Models of Single Neurons

Dimitrios V. Vavoulis, Volko A. Straub, John A. D. Aston, Jianfeng Feng

How Cells Integrate Complex Stimuli: The Effect of Feedback from Phosphoinositides and Cell Shape on Cell Polarization and Motility

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Exploring the Evolution of Novel Enzyme Functions within Structurally Defined Protein Superfamilies

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Changes in Lysozyme Flexibility upon Mutation Are Frequent, Large and Long-Ranged

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System-Level Insights into Yeast Metabolism by Thermodynamic Analysis of Elementary Flux Modes

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