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

Deciding Not to Decide: Computational and Neural Evidence for Hidden Behavior in Sequential Choice

Sebastian Gluth, Jörg Rieskamp, Christian Büchel

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

Related Articles

  1. New Methods Section in PLOS Computational Biology

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

Related Articles

  1. Correction: Integrative Modelling of the Influence of MAPK Network on Cancer Cell Fate Decision

The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters

Chunfeng Zhao, Sergei Yu. Noskov

An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis

Pralay Mitra, David Shultis, Jeffrey R. Brender, Jeff Czajka, David Marsh, Felicia Gray, Tomasz Cierpicki, Yang Zhang

Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells

Giovanna De Palo, Robert G. Endres

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins

Mu Gao, Jeffrey Skolnick

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

Dongjun Chung, Dan Park, Kevin Myers, Jeffrey Grass, Patricia Kiley, Robert Landick, Sündüz Keleş

Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks

Sushmita Roy, Stephen Lagree, Zhonggang Hou, James A. Thomson, Ron Stewart, Audrey P. Gasch

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

Donald R. Olson, Kevin J. Konty, Marc Paladini, Cecile Viboud, Lone Simonsen

Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery

Andreas Spitzmüller, Jordi Mestres

Analysis of Initial Cell Spreading Using Mechanistic Contact Formulations for a Deformable Cell Model

Tim Odenthal, Bart Smeets, Paul Van Liedekerke, Engelbert Tijskens, Hans Van Oosterwyck, Herman Ramon

Dynamic Change of Global and Local Information Processing in Propofol-Induced Loss and Recovery of Consciousness

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

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

Rogan Carr, Shai S. Shen-Orr, Elhanan Borenstein

Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments

Francesca Falcetta, Monica Lupi, Valentina Colombo, Paolo Ubezio

GINI: From ISH Images to Gene Interaction Networks

Kriti Puniyani, Eric P. Xing

Human Genome Replication Proceeds through Four Chromatin States

Hanna Julienne, Azedine Zoufir, Benjamin Audit, Alain Arneodo

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data

Julien Racle, Flora Picard, Laurence Girbal, Muriel Cocaign-Bousquet, Vassily Hatzimanikatis

Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data

Joshua G. Schraiber, Yulia Mostovoy, Tiffany Y. Hsu, Rachel B. Brem

Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire

Paola Carrillo-Bustamante, Can Keşmir, Rob J. de Boer

A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes

Daniel B. Larremore, Aaron Clauset, Caroline O. Buckee

Thermal Adaptation of Conformational Dynamics in Ribonuclease H

Kate A. Stafford, Paul Robustelli, Arthur G. Palmer III

Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae

Rene Rex, Nelli Bill, Kerstin Schmidt-Hohagen, Dietmar Schomburg

Sensitive Detection of Viral Transcripts in Human Tumor Transcriptomes

Sven-Eric Schelhorn, Matthias Fischer, Laura Tolosi, Janine Altmüller, Peter Nürnberg, Herbert Pfister, Thomas Lengauer, Frank Berthold

ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data

André Yoshiaki Kashiwabara, Ígor Bonadio, Vitor Onuchic, Felipe Amado, Rafael Mathias, Alan Mitchell Durham

The Lazy Visual Word Form Area: Computational Insights into Location-Sensitivity

Thomas Hannagan, Jonathan Grainger

Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways

Farzad Farkhooi, Anja Froese, Eilif Muller, Randolf Menzel, Martin P. Nawrot

Target Prediction for an Open Access Set of Compounds Active against Mycobacterium tuberculosis

Francisco Martínez-Jiménez, George Papadatos, Lun Yang, Iain M. Wallace, Vinod Kumar, Ursula Pieper, Andrej Sali, James R. Brown, John P. Overington, Marc A. Marti-Renom

Lipid Receptor S1P1 Activation Scheme Concluded from Microsecond All-Atom Molecular Dynamics Simulations

Shuguang Yuan, Rongliang Wu, Dorota Latek, Bartosz Trzaskowski, Slawomir Filipek

Balanced Excitatory and Inhibitory Synaptic Currents Promote Efficient Coding and Metabolic Efficiency

Biswa Sengupta, Simon B. Laughlin, Jeremy E. Niven