Ten Simple Rules for Reproducible Computational Research

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PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003285

How Can PLOS Computational Biology Help the Biological Sciences?

Ruth Nussinov

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003262

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PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003305

APBioNet—Transforming Bioinformatics in the Asia-Pacific Region

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

PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003317

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

Stewart Heitmann, Tjeerd Boonstra, Michael Breakspear

PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003260

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

PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003281

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

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

PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003284

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

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

PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003301

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

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

PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003307

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

Sebastian Gluth, Jörg Rieskamp, Christian Büchel

PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003309

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Conformational Changes in Talin on Binding to Anionic Phospholipid Membranes Facilitate Signaling by Integrin Transmembrane Helices

Antreas C. Kalli, Iain D. Campbell, Mark S. P. Sansom

PLOS Computational Biology: published October 31, 2013 | https://doi.org/10.1371/journal.pcbi.1003316

The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003248

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003265

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003266

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003270

The Convallis Rule for Unsupervised Learning in Cortical Networks

Pierre Yger, Kenneth D. Harris

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003272

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003273

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003275

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003276

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Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening

Arnab Bhattacherjee, Stefan Wallin

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003277

Comprehensive Repertoire of Foldable Regions within Whole Genomes

Guilhem Faure, Isabelle Callebaut

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003280

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003286

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The Molecular Mechanism of Ion-Dependent Gating in Secondary Transporters

Chunfeng Zhao, Sergei Yu. Noskov

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003296

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

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003298

Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells

Giovanna De Palo, Robert G. Endres

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003300

A Comprehensive Survey of Small-Molecule Binding Pockets in Proteins

Mu Gao, Jeffrey Skolnick

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003302

Emergence of Metastable State Dynamics in Interconnected Cortical Networks with Propagation Delays

Katrina M. Kutchko, Flavio Fröhlich

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003304

Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue

José Lourenço, Mario Recker

PLOS Computational Biology: published October 24, 2013 | https://doi.org/10.1371/journal.pcbi.1003308

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

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003246

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

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003252

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

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003256

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

Andreas Spitzmüller, Jordi Mestres

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003257

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

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003267

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

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003271

Model of Fission Yeast Cell Shape Driven by Membrane-Bound Growth Factors and the Cytoskeleton

Tyler Drake, Dimitrios Vavylonis

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003287

On the Role of Aggregation Prone Regions in Protein Evolution, Stability, and Enzymatic Catalysis: Insights from Diverse Analyses

Patrick M. Buck, Sandeep Kumar, Satish K. Singh

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003291

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution

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

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003292

Dynamic Rendering of the Heterogeneous Cell Response to Anticancer Treatments

Francesca Falcetta, Monica Lupi, Valentina Colombo, Paolo Ubezio

PLOS Computational Biology: published October 17, 2013 | https://doi.org/10.1371/journal.pcbi.1003293

GINI: From ISH Images to Gene Interaction Networks

Kriti Puniyani, Eric P. Xing

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003227

Human Genome Replication Proceeds through Four Chromatin States

Hanna Julienne, Azedine Zoufir, Benjamin Audit, Alain Arneodo

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003233

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

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

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003240

Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks

Yuri Pritykin, Mona Singh

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003243

A Horizontal Alignment Tool for Numerical Trend Discovery in Sequence Data: Application to Protein Hydropathy

Omar Hadzipasic, James O. Wrabl, Vincent J. Hilser

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003247

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Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses

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PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003254

Inferring Evolutionary Histories of Pathway Regulation from Transcriptional Profiling Data

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

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003255

A Simple Rule for Dendritic Spine and Axonal Bouton Formation Can Account for Cortical Reorganization after Focal Retinal Lesions

Markus Butz, Arjen van Ooyen

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003259

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Virus Encoded MHC-Like Decoys Diversify the Inhibitory KIR Repertoire

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

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003264

A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes

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

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003268

Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes

Ryan Suderman, Eric J. Deeds

PLOS Computational Biology: published October 10, 2013 | https://doi.org/10.1371/journal.pcbi.1003278

Thermal Adaptation of Conformational Dynamics in Ribonuclease H

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

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003218

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

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

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003224

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

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003228

ToPS: A Framework to Manipulate Probabilistic Models of Sequence Data

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

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003234

Ligand Clouds around Protein Clouds: A Scenario of Ligand Binding with Intrinsically Disordered Proteins

Fan Jin, Chen Yu, Luhua Lai, Zhirong Liu

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003249

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

Thomas Hannagan, Jonathan Grainger

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003250

Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways

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

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003251

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

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003253

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

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

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

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

PLOS Computational Biology: published October 3, 2013 | https://doi.org/10.1371/journal.pcbi.1003263