“Broadband” Bioinformatics Skills Transfer with the Knowledge Transfer Programme (KTP): Educational Model for Upliftment and Sustainable Development

Emile R. Chimusa, Mamana Mbiyavanga, Velaphi Masilela, Judit Kumuthini

PLOS Computational Biology: published November 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004512

Regulation of Spatiotemporal Patterns by Biological Variability: General Principles and Applications to Dictyostelium discoideum

Miriam Grace, Marc-Thorsten Hütt

PLOS Computational Biology: published November 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004367

Integrated Modeling of Gene Regulatory and Metabolic Networks in Mycobacterium tuberculosis

Shuyi Ma, Kyle J. Minch, Tige R. Rustad, Samuel Hobbs, Suk-Lin Zhou, David R. Sherman, Nathan D. Price

PLOS Computational Biology: published November 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004543

Multiscale Embedded Gene Co-expression Network Analysis

Won-Min Song, Bin Zhang

PLOS Computational Biology: published November 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004574

Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics

Jonathan W. Armond, Edward F. Harry, Andrew D. McAinsh, Nigel J. Burroughs

PLOS Computational Biology: published November 30, 2015 | https://doi.org/10.1371/journal.pcbi.1004607

VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires

Mikhail Shugay, Dmitriy V. Bagaev, Maria A. Turchaninova, Dmitriy A. Bolotin, Olga V. Britanova, Ekaterina V. Putintseva, Mikhail V. Pogorelyy, Vadim I. Nazarov, Ivan V. Zvyagin, Vitalina I. Kirgizova, Kirill I. Kirgizov, Elena V. Skorobogatova, Dmitriy M. Chudakov

PLOS Computational Biology: published November 25, 2015 | https://doi.org/10.1371/journal.pcbi.1004503

Reputation Effects in Public and Private Interactions

Hisashi Ohtsuki, Yoh Iwasa, Martin A. Nowak

PLOS Computational Biology: published November 25, 2015 | https://doi.org/10.1371/journal.pcbi.1004527

Towards a Molecular Understanding of the Link between Imatinib Resistance and Kinase Conformational Dynamics

Silvia Lovera, Maria Morando, Encarna Pucheta-Martinez, Jorge L. Martinez-Torrecuadrada, Giorgio Saladino, Francesco L. Gervasio

PLOS Computational Biology: published November 25, 2015 | https://doi.org/10.1371/journal.pcbi.1004578

SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis

Minzhe Guo, Hui Wang, S. Steven Potter, Jeffrey A. Whitsett, Yan Xu

PLOS Computational Biology: published November 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004575

A Model of Drosophila Larva Chemotaxis

Alex Davies, Matthieu Louis, Barbara Webb

PLOS Computational Biology: published November 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004606

A Jump-from-Cavity Pyrophosphate Ion Release Assisted by a Key Lysine Residue in T7 RNA Polymerase Transcription Elongation

Lin-Tai Da, Chao E, Baogen Duan, Chuanbiao Zhang, Xin Zhou, Jin Yu

PLOS Computational Biology: published November 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004624

Red Queen Processes Drive Positive Selection on Major Histocompatibility Complex (MHC) Genes

Maciej Jan Ejsmond, Jacek Radwan

PLOS Computational Biology: published November 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004627

Remodeling and Tenacity of Inhibitory Synapses: Relationships with Network Activity and Neighboring Excitatory Synapses

Anna Rubinski, Noam E. Ziv

PLOS Computational Biology: published November 24, 2015 | https://doi.org/10.1371/journal.pcbi.1004632

Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns

Andrea Maesani, Pavan Ramdya, Steeve Cruchet, Kyle Gustafson, Richard Benton, Dario Floreano

PLOS Computational Biology: published November 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004577

Computational Modelling of Metastasis Development in Renal Cell Carcinoma

Etienne Baratchart, Sébastien Benzekry, Andreas Bikfalvi, Thierry Colin, Lindsay S. Cooley, Raphäel Pineau, Emeline J Ribot, Olivier Saut, Wilfried Souleyreau

PLOS Computational Biology: published November 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004626

A Systematic Bayesian Integration of Epidemiological and Genetic Data

Max S. Y. Lau, Glenn Marion, George Streftaris, Gavin Gibson

PLOS Computational Biology: published November 23, 2015 | https://doi.org/10.1371/journal.pcbi.1004633

Quantifying Stochastic Noise in Cultured Circadian Reporter Cells

Peter C. St. John, Francis J. Doyle III

PLOS Computational Biology: published November 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004451

Stochastic Regulation of her1/7 Gene Expression Is the Source of Noise in the Zebrafish Somite Clock Counteracted by Notch Signalling

Robert P. Jenkins, Anja Hanisch, Cristian Soza-Ried, Erik Sahai, Julian Lewis

PLOS Computational Biology: published November 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004459

Finding New Order in Biological Functions from the Network Structure of Gene Annotations

Kimberly Glass, Michelle Girvan

PLOS Computational Biology: published November 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004565

A Dual Model for Prioritizing Cancer Mutations in the Non-coding Genome Based on Germline and Somatic Events

Jia Li, Marie-Anne Poursat, Damien Drubay, Arnaud Motz, Zohra Saci, Antonin Morillon, Stefan Michiels, Daniel Gautheret

PLOS Computational Biology: published November 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004583

Computational Model of MicroRNA Control of HIF-VEGF Pathway: Insights into the Pathophysiology of Ischemic Vascular Disease and Cancer

Chen Zhao, Aleksander S. Popel

PLOS Computational Biology: published November 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004612

Parsimony, Exhaustivity and Balanced Detection in Neocortex

Alberto Romagnoni, Jérôme Ribot, Daniel Bennequin, Jonathan Touboul

PLOS Computational Biology: published November 20, 2015 | https://doi.org/10.1371/journal.pcbi.1004623

A Bio-inspired Collision Avoidance Model Based on Spatial Information Derived from Motion Detectors Leads to Common Routes

Olivier J. N. Bertrand, Jens P. Lindemann, Martin Egelhaaf

PLOS Computational Biology: published November 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004339

Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding

Satohiro Tajima, Toru Yanagawa, Naotaka Fujii, Taro Toyoizumi

PLOS Computational Biology: published November 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004537

Regulation of Early Steps of GPVI Signal Transduction by Phosphatases: A Systems Biology Approach

Joanne L. Dunster, Francoise Mazet, Michael J. Fry, Jonathan M. Gibbins, Marcus J. Tindall

PLOS Computational Biology: published November 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004589

Learning of Chunking Sequences in Cognition and Behavior

Jordi Fonollosa, Emre Neftci, Mikhail Rabinovich

PLOS Computational Biology: published November 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004592

Differences in Visual-Spatial Input May Underlie Different Compression Properties of Firing Fields for Grid Cell Modules in Medial Entorhinal Cortex

Florian Raudies, Michael E. Hasselmo

PLOS Computational Biology: published November 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004596

SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data

Zhongyang Zhang, Ke Hao

PLOS Computational Biology: published November 19, 2015 | https://doi.org/10.1371/journal.pcbi.1004618

Beyond the E-Value: Stratified Statistics for Protein Domain Prediction

Alejandro Ochoa, John D. Storey, Manuel Llinás, Mona Singh

PLOS Computational Biology: published November 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004509

Random Wiring, Ganglion Cell Mosaics, and the Functional Architecture of the Visual Cortex

Manuel Schottdorf, Wolfgang Keil, David Coppola, Leonard E. White, Fred Wolf

PLOS Computational Biology: published November 17, 2015 | https://doi.org/10.1371/journal.pcbi.1004602

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Inferring the Clonal Structure of Viral Populations from Time Series Sequencing

Donatien F. Chedom, Pablo R. Murcia, Chris D. Greenman

PLOS Computational Biology: published November 16, 2015 | https://doi.org/10.1371/journal.pcbi.1004344

Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis

Pablo Cordero, Rhiju Das

PLOS Computational Biology: published November 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004473

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Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

Benjamin D. Heavner, Nathan D. Price

PLOS Computational Biology: published November 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004530

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy J. Laurent, Alex Williams, Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton

PLOS Computational Biology: published November 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004573

Improving Collective Estimations Using Resistance to Social Influence

Gabriel Madirolas, Gonzalo G. de Polavieja

PLOS Computational Biology: published November 13, 2015 | https://doi.org/10.1371/journal.pcbi.1004594

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Neuromechanistic Model of Auditory Bistability

James Rankin, Elyse Sussman, John Rinzel

PLOS Computational Biology: published November 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004555

Dynamic Redox Regulation of IL-4 Signaling

Gaurav Dwivedi, Margaret A. Gran, Pritha Bagchi, Melissa L. Kemp

PLOS Computational Biology: published November 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004582

Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

Dmitry Svetlichnyy, Hana Imrichova, Mark Fiers, Zeynep Kalender Atak, Stein Aerts

PLOS Computational Biology: published November 12, 2015 | https://doi.org/10.1371/journal.pcbi.1004590

Network Events on Multiple Space and Time Scales in Cultured Neural Networks and in a Stochastic Rate Model

Guido Gigante, Gustavo Deco, Shimon Marom, Paolo Del Giudice

PLOS Computational Biology: published November 11, 2015 | https://doi.org/10.1371/journal.pcbi.1004547

The Elementary Operations of Human Vision Are Not Reducible to Template-Matching

Peter Neri

PLOS Computational Biology: published November 10, 2015 | https://doi.org/10.1371/journal.pcbi.1004499

The Encoding of Decision Difficulty and Movement Time in the Primate Premotor Cortex

Marina Martinez-Garcia, Andrea Insabato, Mario Pannunzi, Jose L. Pardo-Vazquez, Carlos Acuña, Gustavo Deco

PLOS Computational Biology: published November 10, 2015 | https://doi.org/10.1371/journal.pcbi.1004502

Non-canonical Activation of Akt in Serum-Stimulated Fibroblasts, Revealed by Comparative Modeling of Pathway Dynamics

Tri Hieu Nim, Le Luo, Jacob K. White, Marie-Véronique Clément, Lisa Tucker-Kellogg

PLOS Computational Biology: published November 10, 2015 | https://doi.org/10.1371/journal.pcbi.1004505

An Ovol2-Zeb1 Mutual Inhibitory Circuit Governs Bidirectional and Multi-step Transition between Epithelial and Mesenchymal States

Tian Hong, Kazuhide Watanabe, Catherine Ha Ta, Alvaro Villarreal-Ponce, Qing Nie, Xing Dai

PLOS Computational Biology: published November 10, 2015 | https://doi.org/10.1371/journal.pcbi.1004569

From Sensory Signals to Modality-Independent Conceptual Representations: A Probabilistic Language of Thought Approach

Goker Erdogan, Ilker Yildirim, Robert A. Jacobs

PLOS Computational Biology: published November 10, 2015 | https://doi.org/10.1371/journal.pcbi.1004610

Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules

Sandeep Choubey, Jane Kondev, Alvaro Sanchez

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004345

Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics

Laura Hindersin, Arne Traulsen

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004437

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Network Plasticity as Bayesian Inference

David Kappel, Stefan Habenschuss, Robert Legenstein, Wolfgang Maass

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004485

On the Adjacency Matrix of RyR2 Cluster Structures

Mark A. Walker, Tobias Kohl, Stephan E. Lehnart, Joseph L. Greenstein, W. J. Lederer, Raimond L. Winslow

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004521

A Kinetic Platform to Determine the Fate of Hydrogen Peroxide in Escherichia coli

Kristin J. Adolfsen, Mark P. Brynildsen

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004562

A Voltage-Based STDP Rule Combined with Fast BCM-Like Metaplasticity Accounts for LTP and Concurrent “Heterosynaptic” LTD in the Dentate Gyrus In Vivo

Peter Jedlicka, Lubica Benuskova, Wickliffe C. Abraham

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004588

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Mechanism of Focal Adhesion Kinase Mechanosensing

Jing Zhou, Camilo Aponte-Santamaría, Sebastian Sturm, Jakob Tómas Bullerjahn, Agnieszka Bronowska, Frauke Gräter

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004593

A Quantitative Model of the GIRK1/2 Channel Reveals That Its Basal and Evoked Activities Are Controlled by Unequal Stoichiometry of Gα and Gβγ

Daniel Yakubovich, Shai Berlin, Uri Kahanovitch, Moran Rubinstein, Isabella Farhy-Tselnicker, Boaz Styr, Tal Keren-Raifman, Carmen W. Dessauer, Nathan Dascal

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004598

Lévy Walks Suboptimal under Predation Risk

Masato S. Abe, Masakazu Shimada

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004601

Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution

M. Senthil Kumar, Joshua B. Plotkin, Sridhar Hannenhalli

PLOS Computational Biology: published November 6, 2015 | https://doi.org/10.1371/journal.pcbi.1004603

Bayesian Estimation of Conditional Independence Graphs Improves Functional Connectivity Estimates

Max Hinne, Ronald J. Janssen, Tom Heskes, Marcel A.J. van Gerven

PLOS Computational Biology: published November 5, 2015 | https://doi.org/10.1371/journal.pcbi.1004534

Learning to Estimate Dynamical State with Probabilistic Population Codes

Joseph G. Makin, Benjamin K. Dichter, Philip N. Sabes

PLOS Computational Biology: published November 5, 2015 | https://doi.org/10.1371/journal.pcbi.1004554

A Unifying Probabilistic View of Associative Learning

Samuel J. Gershman

PLOS Computational Biology: published November 4, 2015 | https://doi.org/10.1371/journal.pcbi.1004567

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Neural Sequence Generation Using Spatiotemporal Patterns of Inhibition

Jonathan Cannon, Nancy Kopell, Timothy Gardner, Jeffrey Markowitz

PLOS Computational Biology: published November 4, 2015 | https://doi.org/10.1371/journal.pcbi.1004581

Direct Measurements of Local Coupling between Myosin Molecules Are Consistent with a Model of Muscle Activation

Sam Walcott, Neil M. Kad

PLOS Computational Biology: published November 4, 2015 | https://doi.org/10.1371/journal.pcbi.1004599

Parallel Representation of Value-Based and Finite State-Based Strategies in the Ventral and Dorsal Striatum

Makoto Ito, Kenji Doya

PLOS Computational Biology: published November 3, 2015 | https://doi.org/10.1371/journal.pcbi.1004540

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants

David Bednar, Koen Beerens, Eva Sebestova, Jaroslav Bendl, Sagar Khare, Radka Chaloupkova, Zbynek Prokop, Jan Brezovsky, David Baker, Jiri Damborsky

PLOS Computational Biology: published November 3, 2015 | https://doi.org/10.1371/journal.pcbi.1004556

Mathematical Modelling of Molecular Pathways Enabling Tumour Cell Invasion and Migration

David P. A. Cohen, Loredana Martignetti, Sylvie Robine, Emmanuel Barillot, Andrei Zinovyev, Laurence Calzone

PLOS Computational Biology: published November 3, 2015 | https://doi.org/10.1371/journal.pcbi.1004571