October 2011

This image artistically depicts a snapshot taken when each neuron in a cortical population is subject to the same periodic stimulus. The darker lines running from left to right represent the response amplitude and phase of each individual neuron. In this study (see Tchumatchenko and Wolf, 10.1371/journal.pcbi.1002239) the authors used a threshold model framework that accounts for the collective encoding of dynamical stimuli by a population of cortical neurons. The paper presents an analytical approach to understanding the key parameters determining the spike dynamics in response to time changing stimuli that are presented in the mean or the variance of the input current.

Image Credit: Tatjana Tchumatchenko, Max Planck Institute for Dynamics and Self-Organization, Göttingen, Germany.

Editorials

Ten Simple Rules for Getting Involved in Your Scientific Community

Magali Michaut

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002232

Teaching Bioinformatics at the Secondary School Level

Fran Lewitter, Philip E. Bourne

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002242

Ten Simple Rules for Teaching Bioinformatics at the High School Level

David Form, Fran Lewitter

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002243

Ten Simple Rules for Developing a Short Bioinformatics Training Course

Allegra Via, Javier De Las Rivas, Teresa K. Attwood, David Landsman, Michelle D. Brazas, Jack A. M. Leunissen, Anna Tramontano, Maria Victoria Schneider

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002245

Education

A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms

Suzanne Renick Gallagher, William Coon, Kristin Donley, Abby Scott, Debra S. Goldberg

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002244

Perspective

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

Laurence D. Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Marco Dall'Olio, Daniel C. Swan, Lars Juhl Jensen, Simon J. Cockell, Brent S. Pedersen, Mary E. Mangan, Christopher A. Miller, Istvan Albert

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002216

Research Articles

Receptive Field Inference with Localized Priors

Mijung Park, Jonathan W. Pillow

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002219

Conformation Regulation of the X Chromosome Inactivation Center: A Model

Antonio Scialdone, Ilaria Cataudella, Mariano Barbieri, Antonella Prisco, Mario Nicodemi

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002229

STDP Allows Fast Rate-Modulated Coding with Poisson-Like Spike Trains

Matthieu Gilson, Timothée Masquelier, Etienne Hugues

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002231

Grid Cells, Place Cells, and Geodesic Generalization for Spatial Reinforcement Learning

Nicholas J. Gustafson, Nathaniel D. Daw

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002235

Unbiased Simulations Reveal the Inward-Facing Conformation of the Human Serotonin Transporter and Na⁺ Ion Release

Heidi Koldsø, Pernille Noer, Julie Grouleff, Henriette Elisabeth Autzen, Steffen Sinning, Birgit Schiøtt

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002246

LTS and FS Inhibitory Interneurons, Short-Term Synaptic Plasticity, and Cortical Circuit Dynamics

Itai Hayut, Erika E. Fanselow, Barry W. Connors, David Golomb

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002248

Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models

Jeffrey D. Fitzgerald, Ryan J. Rowekamp, Lawrence C. Sincich, Tatyana O. Sharpee

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002249

A Sparse Coding Model with Synaptically Local Plasticity and Spiking Neurons Can Account for the Diverse Shapes of V1 Simple Cell Receptive Fields

Joel Zylberberg, Jason Timothy Murphy, Michael Robert DeWeese

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002250

Metabolic Regulation in Progression to Autoimmune Diabetes

Marko Sysi-Aho, Andrey Ermolov, Peddinti V. Gopalacharyulu, Abhishek Tripathi, Tuulikki Seppänen-Laakso, Johanna Maukonen, Ismo Mattila, Suvi T. Ruohonen, Laura Vähätalo, Laxman Yetukuri, Taina Härkönen, Erno Lindfors, Janne Nikkilä, Jorma Ilonen, Olli Simell, Maria Saarela, Mikael Knip, Samuel Kaski, Eriika Savontaus, Matej Orešič

PLOS Computational Biology: published October 27, 2011 | https://doi.org/10.1371/journal.pcbi.1002257

Accelerated Profile HMM Searches

Sean R. Eddy

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002195

Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling

Benjamin A. Hall, Judith P. Armitage, Mark S. P. Sansom

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002204

A Neurodynamic Account of Spontaneous Behaviour

Jun Namikawa, Ryunosuke Nishimoto, Jun Tani

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002221

Decoding Complex Chemical Mixtures with a Physical Model of a Sensor Array

Julia Tsitron, Addison D. Ault, James R. Broach, Alexandre V. Morozov

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002224

Replication Timing: A Fingerprint for Cell Identity and Pluripotency

Tyrone Ryba, Ichiro Hiratani, Takayo Sasaki, Dana Battaglia, Michael Kulik, Jinfeng Zhang, Stephen Dalton, David M. Gilbert

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002225

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes

Yinyin Yuan, Richard S. Savage, Florian Markowetz

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002227

A Semi-Quantitative, Synteny-Based Method to Improve Functional Predictions for Hypothetical and Poorly Annotated Bacterial and Archaeal Genes

Alexis P. Yelton, Brian C. Thomas, Sheri L. Simmons, Paul Wilmes, Adam Zemla, Michael P. Thelen, Nicholas Justice, Jillian F. Banfield

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002230

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Hyun Joo, Archana G. Chavan, Ryan Day, Kristin P. Lennox, Paul Sukhanov, David B. Dahl, Marina Vannucci, Jerry Tsai

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002234

Integrated Information Increases with Fitness in the Evolution of Animats

Jeffrey A. Edlund, Nicolas Chaumont, Arend Hintze, Christof Koch, Giulio Tononi, Christoph Adami

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002236

Explaining Observed Infection and Antibody Age-Profiles in Populations with Urogenital Schistosomiasis

Kate M. Mitchell, Francisca Mutapi, Nicholas J. Savill, Mark E. J. Woolhouse

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002237

Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants

Özlem Demir, Roberta Baronio, Faezeh Salehi, Christopher D. Wassman, Linda Hall, G. Wesley Hatfield, Richard Chamberlin, Peter Kaiser, Richard H. Lathrop, Rommie E. Amaro

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002238

Representation of Dynamical Stimuli in Populations of Threshold Neurons

Tatjana Tchumatchenko, Fred Wolf

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002239

Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome

David Venet, Jacques E. Dumont, Vincent Detours

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002240

NHE Inhibition Does Not Improve Na⁺ or Ca²⁺ Overload During Reperfusion: Using Modeling to Illuminate the Mechanisms Underlying a Therapeutic Failure

Byron N. Roberts, David J. Christini

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002241

The Effects of Dominance on Leadership and Energetic Gain: A Dynamic Game between Pairs of Social Foragers

Sean A. Rands

PLOS Computational Biology: published October 20, 2011 | https://doi.org/10.1371/journal.pcbi.1002252

A Peptide Filtering Relation Quantifies MHC Class I Peptide Optimization

Neil Dalchau, Andrew Phillips, Leonard D. Goldstein, Mark Howarth, Luca Cardelli, Stephen Emmott, Tim Elliott, Joern M. Werner

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002144

Inversion of the Balance between Hydrophobic and Hydrogen Bonding Interactions in Protein Folding and Aggregation

Anthony W. Fitzpatrick, Tuomas P. J. Knowles, Christopher A. Waudby, Michele Vendruscolo, Christopher M. Dobson

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002169

Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation

César Augusto F. de Oliveira, Barry J. Grant, Michelle Zhou, J. Andrew McCammon

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002178

Barriers to Diffusion in Dendrites and Estimation of Calcium Spread Following Synaptic Inputs

Armin Biess, Eduard Korkotian, David Holcman

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002182

Evidence for Composite Cost Functions in Arm Movement Planning: An Inverse Optimal Control Approach

Bastien Berret, Enrico Chiovetto, Francesco Nori, Thierry Pozzo

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002183

Transmission Selects for HIV-1 Strains of Intermediate Virulence: A Modelling Approach

George Shirreff, Lorenzo Pellis, Oliver Laeyendecker, Christophe Fraser

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002185

Heat Shock Partially Dissociates the Overlapping Modules of the Yeast Protein-Protein Interaction Network: A Systems Level Model of Adaptation

Ágoston Mihalik, Peter Csermely

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002187

Neural Computation via Neural Geometry: A Place Code for Inter-whisker Timing in the Barrel Cortex?

Stuart P. Wilson, James A. Bednar, Tony J. Prescott, Ben Mitchinson

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002188

Identification of Potent EGFR Inhibitors from TCM Database@Taiwan

Shun-Chieh Yang, Su-Sen Chang, Hsin-Yi Chen, Calvin Yu-Chian Chen

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002189

Quantifying Intramolecular Binding in Multivalent Interactions: A Structure-Based Synergistic Study on Grb2-Sos1 Complex

Anurag Sethi, Byron Goldstein, S. Gnanakaran

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002192

Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques

Davide Provasi, Marta Camacho Artacho, Ana Negri, Juan Carlos Mobarec, Marta Filizola

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002193

Assessing Vaccination Sentiments with Online Social Media: Implications for Infectious Disease Dynamics and Control

Marcel Salathé, Shashank Khandelwal

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002199

The Dynamics of Supply and Demand in mRNA Translation

Chris A. Brackley, M. Carmen Romano, Marco Thiel

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002203

Brain Rhythms Reveal a Hierarchical Network Organization

G. Karl Steinke, Roberto F. Galán

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002207

Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks

Mark Hallen, Bochong Li, Yu Tanouchi, Cheemeng Tan, Mike West, Lingchong You

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002209

Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer

Anup Dewanji, Jihyoun Jeon, Rafael Meza, E. Georg Luebeck

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002213

Chemical Basis of Metabolic Network Organization

Qiang Zhu, Tao Qin, Ying-Ying Jiang, Cong Ji, De-Xin Kong, Bin-Guang Ma, Hong-Yu Zhang

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002214

Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing

Stuart Aitken, Ross D. Alexander, Jean D. Beggs

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002215

Thousands of Rab GTPases for the Cell Biologist

Yoan Diekmann, Elsa Seixas, Marc Gouw, Filipe Tavares-Cadete, Miguel C. Seabra, José B. Pereira-Leal

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002217

Bacteria Modulate the CD8+ T Cell Epitope Repertoire of Host Cytosol-Exposed Proteins to Manipulate the Host Immune Response

Yaakov Maman, Ran Nir-Paz, Yoram Louzoun

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002220

Coupled Information Diffusion–Pest Dynamics Models Predict Delayed Benefits of Farmer Cooperation in Pest Management Programs

François Rebaudo, Olivier Dangles

PLOS Computational Biology: published October 13, 2011 | https://doi.org/10.1371/journal.pcbi.1002222

Conflicting Biomedical Assumptions for Mathematical Modeling: The Case of Cancer Metastasis

Anna Divoli, Eneida A. Mendonça, James A. Evans, Andrey Rzhetsky

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002132

Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning

Z. Nevin Gerek, S. Banu Ozkan

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002154

A Multi-cell, Multi-scale Model of Vertebrate Segmentation and Somite Formation

Susan D. Hester, Julio M. Belmonte, J. Scott Gens, Sherry G. Clendenon, James A. Glazier

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002155

Coexistence of Lateral and Co-Tuned Inhibitory Configurations in Cortical Networks

Robert B. Levy, Alex D. Reyes

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002161

Model Cortical Association Fields Account for the Time Course and Dependence on Target Complexity of Human Contour Perception

Vadas Gintautas, Michael I. Ham, Benjamin Kunsberg, Shawn Barr, Steven P. Brumby, Craig Rasmussen, John S. George, Ilya Nemenman, Luís M. A. Bettencourt, Garret T. Kenyon

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002162

High-Precision, In Vitro Validation of the Sequestration Mechanism for Generating Ultrasensitive Dose-Response Curves in Regulatory Networks

Francesco Ricci, Alexis Vallée-Bélisle, Kevin W. Plaxco

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002171

Using Structure to Explore the Sequence Alignment Space of Remote Homologs

Andrew Kuziemko, Barry Honig, Donald Petrey

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002175

Synchronous Chaos and Broad Band Gamma Rhythm in a Minimal Multi-Layer Model of Primary Visual Cortex

Demian Battaglia, David Hansel

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002176

Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases

Anshuman Dixit, Gennady M. Verkhivker

PLOS Computational Biology: published October 6, 2011 | https://doi.org/10.1371/journal.pcbi.1002179

Cover

Individual neurons may not always hit the global rhythm, but they are strong as a group.

Editorials

Education

Perspective

Research Articles

Related Articles