Speeding Up Ecological and Evolutionary Computations in R; Essentials of High Performance Computing for Biologists

Marco D. Visser, Sean M. McMahon, Cory Merow, Philip M. Dixon, Sydne Record, Eelke Jongejans

PLOS Computational Biology: published March 26, 2015 | https://doi.org/10.1371/journal.pcbi.1004140

Integrating Interactive Computational Modeling in Biology Curricula

Tomáš Helikar, Christine E. Cutucache, Lauren M. Dahlquist, Tyler A. Herek, Joshua J. Larson, Jim A. Rogers

PLOS Computational Biology: published March 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004131

Improved Estimation and Interpretation of Correlations in Neural Circuits

Dimitri Yatsenko, Krešimir Josić, Alexander S. Ecker, Emmanouil Froudarakis, R. James Cotton, Andreas S. Tolias

PLOS Computational Biology: published March 31, 2015 | https://doi.org/10.1371/journal.pcbi.1004083

The Neuroglial Potassium Cycle during Neurotransmission: Role of Kir4.1 Channels

Jérémie Sibille, Khanh Dao Duc, David Holcman, Nathalie Rouach

PLOS Computational Biology: published March 31, 2015 | https://doi.org/10.1371/journal.pcbi.1004137

Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens

Yu-Chen Lo, Silvia Senese, Chien-Ming Li, Qiyang Hu, Yong Huang, Robert Damoiseaux, Jorge Z. Torres

PLOS Computational Biology: published March 31, 2015 | https://doi.org/10.1371/journal.pcbi.1004153

Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association

Davide Provasi, Mustafa Burak Boz, Jennifer M. Johnston, Marta Filizola

PLOS Computational Biology: published March 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004148

Identifying and Tracking Simulated Synaptic Inputs from Neuronal Firing: Insights from In Vitro Experiments

Maxim Volgushev, Vladimir Ilin, Ian H. Stevenson

PLOS Computational Biology: published March 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004167

Hedging Your Bets: Intermediate Movements as Optimal Behavior in the Context of an Incomplete Decision

Adrian M. Haith, David M. Huberdeau, John W. Krakauer

PLOS Computational Biology: published March 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004171

3-way Networks: Application of Hypergraphs for Modelling Increased Complexity in Comparative Genomics

Deborah A Weighill, Daniel A Jacobson

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004079

Evolving Nutritional Strategies in the Presence of Competition: A Geometric Agent-Based Model

Alistair M. Senior, Michael A. Charleston, Mathieu Lihoreau, Jerome Buhl, David Raubenheimer, Stephen J. Simpson

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004111

Behavioral Modeling of Human Choices Reveals Dissociable Effects of Physical Effort and Temporal Delay on Reward Devaluation

Miriam C. Klein-Flügge, Steven W. Kennerley, Ana C. Saraiva, Will D. Penny, Sven Bestmann

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004116

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Kinetically-Defined Component Actions in Gene Repression

Carson C. Chow, Kelsey K. Finn, Geoffery B. Storchan, Xinping Lu, Xiaoyan Sheng, S. Stoney Simons Jr.

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004122

An Integrative Approach for Modeling and Simulation of Heterocyst Pattern Formation in Cyanobacteria Filaments

Alejandro Torres-Sánchez, Jesús Gómez-Gardeñes, Fernando Falo

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004129

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Ligand-Target Prediction by Structural Network Biology Using nAnnoLyze

Francisco Martínez-Jiménez, Marc A. Marti-Renom

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004157

Theory of Choice in Bandit, Information Sampling and Foraging Tasks

Bruno B. Averbeck

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004164

Mapping Shape to Visuomotor Mapping: Learning and Generalisation of Sensorimotor Behaviour Based on Contextual Information

Loes C. J. van Dam, Marc O. Ernst

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004172

Explaining Diversity in Metagenomic Datasets by Phylogenetic-Based Feature Weighting

Davide Albanese, Carlotta De Filippo, Duccio Cavalieri, Claudio Donati

PLOS Computational Biology: published March 27, 2015 | https://doi.org/10.1371/journal.pcbi.1004186

Delayed Response and Biosonar Perception Explain Movement Coordination in Trawling Bats

Luca Giuggioli, Thomas J. McKetterick, Marc Holderied

PLOS Computational Biology: published March 26, 2015 | https://doi.org/10.1371/journal.pcbi.1004089

Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species

Amanda Miguel, Jen Hsin, Tianyun Liu, Grace Tang, Russ B. Altman, Kerwyn Casey Huang

PLOS Computational Biology: published March 26, 2015 | https://doi.org/10.1371/journal.pcbi.1004117

A Biologically Plausible Computational Theory for Value Integration and Action Selection in Decisions with Competing Alternatives

Vassilios Christopoulos, James Bonaiuto, Richard A. Andersen

PLOS Computational Biology: published March 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004104

Evolution of Bow-Tie Architectures in Biology

Tamar Friedlander, Avraham E. Mayo, Tsvi Tlusty, Uri Alon

PLOS Computational Biology: published March 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004055

Anticipation and Choice Heuristics in the Dynamic Consumption of Pain Relief

Giles W. Story, Ivo Vlaev, Peter Dayan, Ben Seymour, Ara Darzi, Raymond J. Dolan

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004030

On the Number of Neurons and Time Scale of Integration Underlying the Formation of Percepts in the Brain

Adrien Wohrer, Christian K. Machens

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004082

Improved Statistical Methods Enable Greater Sensitivity in Rhythm Detection for Genome-Wide Data

Alan L. Hutchison, Mark Maienschein-Cline, Andrew H. Chiang, S. M. Ali Tabei, Herman Gudjonson, Neil Bahroos, Ravi Allada, Aaron R. Dinner

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004094

Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells

Fiete Haack, Heiko Lemcke, Roland Ewald, Tareck Rharass, Adelinde M. Uhrmacher

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004106

Intra-Tumour Signalling Entropy Determines Clinical Outcome in Breast and Lung Cancer

Christopher R. S. Banerji, Simone Severini, Carlos Caldas, Andrew E. Teschendorff

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004115

When Can Species Abundance Data Reveal Non-neutrality?

Omar Al Hammal, David Alonso, Rampal S. Etienne, Stephen J. Cornell

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004134

Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

James A. Geraets, Eric C. Dykeman, Peter G. Stockley, Neil A. Ranson, Reidun Twarock

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004146

Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations

Fan Yang, Evangelia Petsalaki, Thomas Rolland, David E. Hill, Marc Vidal, Frederick P. Roth

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004147

Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process

Cheng Lv, Xiaoguang Li, Fangting Li, Tiejun Li

PLOS Computational Biology: published March 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004156

Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy

Feng Fu, Martin A. Nowak, Sebastian Bonhoeffer

PLOS Computational Biology: published March 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004142

Detailed Contact Data and the Dissemination of Staphylococcus aureus in Hospitals

Thomas Obadia, Romain Silhol, Lulla Opatowski, Laura Temime, Judith Legrand, Anne C. M. Thiébaut, Jean-Louis Herrmann, Éric Fleury, Didier Guillemot, Pierre-Yves Boëlle, on behalf of the I-Bird Study Group

PLOS Computational Biology: published March 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004170

Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data

Kristen Fortney, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming Sound-Tsao, Igor Jurisica

PLOS Computational Biology: published March 18, 2015 | https://doi.org/10.1371/journal.pcbi.1004068

Within-Host Stochastic Emergence Dynamics of Immune-Escape Mutants

Matthew Hartfield, Samuel Alizon

PLOS Computational Biology: published March 18, 2015 | https://doi.org/10.1371/journal.pcbi.1004149

Proportionality: A Valid Alternative to Correlation for Relative Data

David Lovell, Vera Pawlowsky-Glahn, Juan José Egozcue, Samuel Marguerat, Jürg Bähler

PLOS Computational Biology: published March 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004075

On the Firing Rate Dependency of the Phase Response Curve of Rat Purkinje Neurons In Vitro

João Couto, Daniele Linaro, E De Schutter, Michele Giugliano

PLOS Computational Biology: published March 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004112

Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles

Minseung Kim, Violeta Zorraquino, Ilias Tagkopoulos

PLOS Computational Biology: published March 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004127

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Angiogenic Activity of Breast Cancer Patients’ Monocytes Reverted by Combined Use of Systems Modeling and Experimental Approaches

Nicolas Guex, Isaac Crespo, Sylvian Bron, Assia Ifticene-Treboux, Eveline Faes-van’t Hull, Solange Kharoubi, Robin Liechti, Patricia Werffeli, Mark Ibberson, Francois Majo, Michäel Nicolas, Julien Laurent, Abhishek Garg, Khalil Zaman, Hans-Anton Lehr, Brian J. Stevenson, Curzio Rüegg, George Coukos, Jean-François Delaloye, Ioannis Xenarios, Marie-Agnès Doucey

PLOS Computational Biology: published March 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004050

Physiology of Layer 5 Pyramidal Neurons in Mouse Primary Visual Cortex: Coincidence Detection through Bursting

Adam S. Shai, Costas A. Anastassiou, Matthew E. Larkum, Christof Koch

PLOS Computational Biology: published March 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004090

Transcriptome Sequencing Reveals Potential Mechanism of Cryptic 3’ Splice Site Selection in SF3B1-mutated Cancers

Christopher DeBoever, Emanuela M. Ghia, Peter J. Shepard, Laura Rassenti, Christian L. Barrett, Kristen Jepsen, Catriona H. M. Jamieson, Dennis Carson, Thomas J. Kipps, Kelly A. Frazer

PLOS Computational Biology: published March 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004105

HPV Clearance and the Neglected Role of Stochasticity

Marc D. Ryser, Evan R. Myers, Rick Durrett

PLOS Computational Biology: published March 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004113

A Neural Mechanism for Background Information-Gated Learning Based on Axonal-Dendritic Overlaps

Matteo Mainetti, Giorgio A. Ascoli

PLOS Computational Biology: published March 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004155

Predicting Epidemic Risk from Past Temporal Contact Data

Eugenio Valdano, Chiara Poletto, Armando Giovannini, Diana Palma, Lara Savini, Vittoria Colizza

PLOS Computational Biology: published March 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004152

Model-based Traction Force Microscopy Reveals Differential Tension in Cellular Actin Bundles

Jérôme R. D. Soiné, Christoph A. Brand, Jonathan Stricker, Patrick W. Oakes, Margaret L. Gardel, Ulrich S. Schwarz

PLOS Computational Biology: published March 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004076

Evolution and Phenotypic Selection of Cancer Stem Cells

Jan Poleszczuk, Philip Hahnfeldt, Heiko Enderling

PLOS Computational Biology: published March 5, 2015 | https://doi.org/10.1371/journal.pcbi.1004025

Protein Topology Determines Cysteine Oxidation Fate: The Case of Sulfenyl Amide Formation among Protein Families

Lucas A. Defelipe, Esteban Lanzarotti, Diego Gauto, Marcelo A. Marti, Adrián G. Turjanski

PLOS Computational Biology: published March 5, 2015 | https://doi.org/10.1371/journal.pcbi.1004051

How Attention Can Create Synaptic Tags for the Learning of Working Memories in Sequential Tasks

Jaldert O. Rombouts, Sander M. Bohte, Pieter R. Roelfsema

PLOS Computational Biology: published March 5, 2015 | https://doi.org/10.1371/journal.pcbi.1004060

Mining Host-Pathogen Protein Interactions to Characterize Burkholderia mallei Infectivity Mechanisms

Vesna Memišević, Nela Zavaljevski, Seesandra V. Rajagopala, Keehwan Kwon, Rembert Pieper, David DeShazer, Jaques Reifman, Anders Wallqvist

PLOS Computational Biology: published March 4, 2015 | https://doi.org/10.1371/journal.pcbi.1004088

Highly Loaded Behavior of Kinesins Increases the Robustness of Transport Under High Resisting Loads

Woochul Nam, Bogdan I. Epureanu

PLOS Computational Biology: published March 3, 2015 | https://doi.org/10.1371/journal.pcbi.1003981

PRIMAL: Fast and Accurate Pedigree-based Imputation from Sequence Data in a Founder Population

Oren E. Livne, Lide Han, Gorka Alkorta-Aranburu, William Wentworth-Sheilds, Mark Abney, Carole Ober, Dan L. Nicolae

PLOS Computational Biology: published March 3, 2015 | https://doi.org/10.1371/journal.pcbi.1004139

Molecular Dynamics Simulations of the Bacterial UraA H⁺-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin

Antreas C. Kalli, Mark S. P. Sansom, Reinhart A. F. Reithmeier

PLOS Computational Biology: published March 2, 2015 | https://doi.org/10.1371/journal.pcbi.1004123