Table of Contents: October 2013

The ligand (purple dots) binds to intrinsically disordered protein (c-Myc) at different sites along the chain and behaves like "ligand clouds" (purple clouds). See Jin et al.

Image Credit: Fan Jin, Luhua Lai, and Zhirong Liu (College of Chemistry and Molecular Engineering, Peking University, China).


Ten Simple Rules for Reproducible Computational Research

Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig

Messages from ISCB

Explain Bioinformatics to Your Grandmother!

Virginie Bernard, Magali Michaut

APBioNet—Transforming Bioinformatics in the Asia-Pacific Region

Asif M. Khan, Tin Wee Tan, Christian Schönbach, Shoba Ranganathan

Research Articles

A Dendritic Mechanism for Decoding Traveling Waves: Principles and Applications to Motor Cortex

Stewart Heitmann, Tjeerd Boonstra, Michael Breakspear

Reverse-Engineering Post-Transcriptional Regulation of Gap Genes in Drosophila melanogaster

Kolja Becker, Eva Balsa-Canto, Damjan Cicin-Sain, Astrid Hoermann, Hilde Janssens, Julio R. Banga, Johannes Jaeger

A Brain-Machine Interface for Control of Medically-Induced Coma

Maryam M. Shanechi, Jessica J. Chemali, Max Liberman, Ken Solt, Emery N. Brown

A Complex-Valued Firing-Rate Model That Approximates the Dynamics of Spiking Networks

Evan S. Schaffer, Srdjan Ostojic, L. F. Abbott

Synaptic Scaling Enables Dynamically Distinct Short- and Long-Term Memory Formation

Christian Tetzlaff, Christoph Kolodziejski, Marc Timme, Misha Tsodyks, Florentin Wörgötter

The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics

Ramakrishnan Iyer, Vilas Menon, Michael Buice, Christof Koch, Stefan Mihalas

Attention-Dependent Modulation of Cortical Taste Circuits Revealed by Granger Causality with Signal-Dependent Noise

Qiang Luo, Tian Ge, Fabian Grabenhorst, Jianfeng Feng, Edmund T. Rolls

Properties of MHC Class I Presented Peptides That Enhance Immunogenicity

Jorg J. A. Calis, Matt Maybeno, Jason A. Greenbaum, Daniela Weiskopf, Aruna D. De Silva, Alessandro Sette, Can Keşmir, Bjoern Peters

CAPE: An R Package for Combined Analysis of Pleiotropy and Epistasis

Anna L. Tyler, Wei Lu, Justin J. Hendrick, Vivek M. Philip, Gregory W. Carter

The Convallis Rule for Unsupervised Learning in Cortical Networks

Pierre Yger, Kenneth D. Harris

Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin

Lennart Hilbert, Genevieve Bates, Horia N. Roman, Jenna L. Blumenthal, Nedjma B. Zitouni, Apolinary Sobieszek, Michael C. Mackey, Anne-Marie Lauzon

Keeping up with the Joneses: Interpersonal Prediction Errors and the Correlation of Behavior in a Tandem Sequential Choice Task

Terry Lohrenz, Meghana Bhatt, Nathan Apple, P. Read Montague

Novel Methods for Analysing Bacterial Tracks Reveal Persistence in Rhodobacter sphaeroides

Gabriel Rosser, Alexander G. Fletcher, David A. Wilkinson, Jennifer A. de Beyer, Christian A. Yates, Judith P. Armitage, Philip K. Maini, Ruth E. Baker

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Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening

Arnab Bhattacherjee, Stefan Wallin

Comprehensive Repertoire of Foldable Regions within Whole Genomes

Guilhem Faure, Isabelle Callebaut

Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision

Luca Grieco, Laurence Calzone, Isabelle Bernard-Pierrot, François Radvanyi, Brigitte Kahn-Perlès, Denis Thieffry

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dPeak: High Resolution Identification of Transcription Factor Binding Sites from PET and SET ChIP-Seq Data

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Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales

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Martin M. Monti, Evan S. Lutkenhoff, Mikail Rubinov, Pierre Boveroux, Audrey Vanhaudenhuyse, Olivia Gosseries, Marie-Aurélie Bruno, Quentin Noirhomme, Mélanie Boly, Steven Laureys

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