Table of Contents

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.


Teaching Bioinformatics at the Secondary School Level

Fran Lewitter, Philip E. Bourne

Ten Simple Rules for Teaching Bioinformatics at the High School Level

David Form, Fran Lewitter

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


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


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

Research Articles

Receptive Field Inference with Localized Priors

Mijung Park, Jonathan W. Pillow

Conformation Regulation of the X Chromosome Inactivation Center: A Model

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

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

Matthieu Gilson, Timothée Masquelier, Etienne Hugues

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

Nicholas J. Gustafson, Nathaniel D. Daw

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

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

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

Second Order Dimensionality Reduction Using Minimum and Maximum Mutual Information Models

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

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

Accelerated Profile HMM Searches

Sean R. Eddy

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

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

A Neurodynamic Account of Spontaneous Behaviour

Jun Namikawa, Ryunosuke Nishimoto, Jun Tani

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

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

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

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes

Yinyin Yuan, Richard S. Savage, Florian Markowetz

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

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

Integrated Information Increases with Fitness in the Evolution of Animats

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

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

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

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

Representation of Dynamical Stimuli in Populations of Threshold Neurons

Tatjana Tchumatchenko, Fred Wolf

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

David Venet, Jacques E. Dumont, Vincent Detours

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

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

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

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

Armin Biess, Eduard Korkotian, David Holcman

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

Bastien Berret, Enrico Chiovetto, Francesco Nori, Thierry Pozzo

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

George Shirreff, Lorenzo Pellis, Oliver Laeyendecker, Christophe Fraser

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

Identification of Potent EGFR Inhibitors from TCM Database@Taiwan

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

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

The Dynamics of Supply and Demand in mRNA Translation

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

Brain Rhythms Reveal a Hierarchical Network Organization

G. Karl Steinke, Roberto F. Galán

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

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

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

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

Chemical Basis of Metabolic Network Organization

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

Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing

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

Thousands of Rab GTPases for the Cell Biologist

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

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

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

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

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

Robert B. Levy, Alex D. Reyes

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

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