Moving Education Forward, Again!

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PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003390

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PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003391

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The Spirit of Competition: To Win or Not To Win

Teresa Szczepinska, Wataru Iwasaki, Thomas Abeel

PLOS Computational Biology: published December 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003413

Flow Cytometry Bioinformatics

Kieran O'Neill, Nima Aghaeepour, Josef Špidlen, Ryan Brinkman

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003365

Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges

Sara El-Metwally, Taher Hamza, Magdi Zakaria, Mohamed Helmy

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003345

Sharpness of Spike Initiation in Neurons Explained by Compartmentalization

Romain Brette

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003338

Use of Long Term Molecular Dynamics Simulation in Predicting Cancer Associated SNPs

Ambuj Kumar, Rituraj Purohit

PLOS Computational Biology: published April 10, 2014 | https://doi.org/10.1371/journal.pcbi.1003318

Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations

Nevena Todorova, Adam J. Makarucha, Nicholas D. M. Hine, Arash A. Mostofi, Irene Yarovsky

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003360

A Network Inference Method for Large-Scale Unsupervised Identification of Novel Drug-Drug Interactions

Roger Guimerà, Marta Sales-Pardo

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003374

Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks

Sriram Chandrasekaran, Nathan D. Price

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003370

A Sequential Vesicle Pool Model with a Single Release Sensor and a Ca²⁺-Dependent Priming Catalyst Effectively Explains Ca²⁺-Dependent Properties of Neurosecretion

Alexander M. Walter, Paulo S. Pinheiro, Matthijs Verhage, Jakob B. Sørensen

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003362

Actions, Action Sequences and Habits: Evidence That Goal-Directed and Habitual Action Control Are Hierarchically Organized

Amir Dezfouli, Bernard W. Balleine

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003364

Membrane Binding of MinE Allows for a Comprehensive Description of Min-Protein Pattern Formation

Mike Bonny, Elisabeth Fischer-Friedrich, Martin Loose, Petra Schwille, Karsten Kruse

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003347

Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information

Anne Lopes, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty, Alessandra Carbone

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003369

Transformation of Stimulus Correlations by the Retina

Kristina D. Simmons, Jason S. Prentice, Gašper Tkačik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson, Vijay Balasubramanian

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003344

Determinants of Cell-to-Cell Variability in Protein Kinase Signaling

Matthias Jeschke, Stephan Baumgärtner, Stefan Legewie

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003357

Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei

Eduard J. Kerkhoven, Fiona Achcar, Vincent P. Alibu, Richard J. Burchmore, Ian H. Gilbert, Maciej Trybiło, Nicole N. Driessen, David Gilbert, Rainer Breitling, Barbara M. Bakker, Michael P. Barrett

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003371

Extrapolating Weak Selection in Evolutionary Games

Bin Wu, Julián García, Christoph Hauert, Arne Traulsen

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003381

Understanding Variation in Transcription Factor Binding by Modeling Transcription Factor Genome-Epigenome Interactions

Chieh-Chun Chen, Shu Xiao, Dan Xie, Xiaoyi Cao, Chun-Xiao Song, Ting Wang, Chuan He, Sheng Zhong

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003367

Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin

Ayse Ozlem Aykut, Ali Rana Atilgan, Canan Atilgan

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003366

Cortical and Hippocampal Correlates of Deliberation during Model-Based Decisions for Rewards in Humans

Aaron M. Bornstein, Nathaniel D. Daw

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003387

Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset

Tjaart A. P. de Beer, Roman A. Laskowski, Sarah L. Parks, Botond Sipos, Nick Goldman, Janet M. Thornton

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003382

Epidemic Spread on Weighted Networks

Christel Kamp, Mathieu Moslonka-Lefebvre, Samuel Alizon

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003352

Systems Modeling of Anti-apoptotic Pathways in Prostate Cancer: Psychological Stress Triggers a Synergism Pattern Switch in Drug Combination Therapy

Xiaoqiang Sun, Jiguang Bao, Kyle C. Nelson, King Chuen Li, George Kulik, Xiaobo Zhou

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003358

Detecting Genetic Association of Common Human Facial Morphological Variation Using High Density 3D Image Registration

Shouneng Peng, Jingze Tan, Sile Hu, Hang Zhou, Jing Guo, Li Jin, Kun Tang

PLOS Computational Biology: published December 5, 2013 | https://doi.org/10.1371/journal.pcbi.1003375

Time Scales in Epigenetic Dynamics and Phenotypic Heterogeneity of Embryonic Stem Cells

Masaki Sasai, Yudai Kawabata, Koh Makishi, Kazuhito Itoh, Tomoki P. Terada

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003380

Forward and Backward Inference in Spatial Cognition

Will D. Penny, Peter Zeidman, Neil Burgess

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003383

Inferring Developmental Stage Composition from Gene Expression in Human Malaria

Regina Joice, Vagheesh Narasimhan, Jacqui Montgomery, Amar Bir Sidhu, Keunyoung Oh, Evan Meyer, Willythssa Pierre-Louis, Karl Seydel, Danny Milner, Kim Williamson, Roger Wiegand, Daouda Ndiaye, Johanna Daily, Dyann Wirth, Terrie Taylor, Curtis Huttenhower, Matthias Marti

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003392

Decipher the Mechanisms of Protein Conformational Changes Induced by Nucleotide Binding through Free-Energy Landscape Analysis: ATP Binding to Hsp70

Adrien Nicolaï, Patrice Delarue, Patrick Senet

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003379

Utilizing a Dynamical Description of IspH to Aid in the Development of Novel Antimicrobial Drugs

Patrick G. Blachly, César A. F. de Oliveira, Sarah L. Williams, J. Andrew McCammon

PLOS Computational Biology: published December 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003395

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

Richard R. Stein, Vanni Bucci, Nora C. Toussaint, Charlie G. Buffie, Gunnar Rätsch, Eric G. Pamer, Chris Sander, João B. Xavier

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003388

Modeling the Afferent Dynamics of the Baroreflex Control System

Adam Mahdi, Jacob Sturdy, Johnny T. Ottesen, Mette S. Olufsen

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003384

Structural Control of Metabolic Flux

Max Sajitz-Hermstein, Zoran Nikoloski

PLOS Computational Biology: published December 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003368

GDI-Mediated Cell Polarization in Yeast Provides Precise Spatial and Temporal Control of Cdc42 Signaling

Ben Klünder, Tina Freisinger, Roland Wedlich-Söldner, Erwin Frey

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003396

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale

Michela Candotti, Alberto Pérez, Carles Ferrer-Costa, Manuel Rueda, Tim Meyer, Josep Lluís Gelpí, Modesto Orozco

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003393

A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα

Srinivasan Sivanandan, Athi N. Naganathan

PLOS Computational Biology: published December 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003403

Heterogeneity, Mixing, and the Spatial Scales of Mosquito-Borne Pathogen Transmission

T. Alex Perkins, Thomas W. Scott, Arnaud Le Menach, David L. Smith

PLOS Computational Biology: published December 12, 2013 | https://doi.org/10.1371/journal.pcbi.1003327

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Artemis Koukounari, Christl A. Donnelly, Irini Moustaki, Edridah M. Tukahebwa, Narcis B. Kabatereine, Shona Wilson, Joanne P. Webster, André M. Deelder, Birgitte J. Vennervald, Govert J. van Dam

PLOS Computational Biology: published December 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003402

Electrodiffusive Model for Astrocytic and Neuronal Ion Concentration Dynamics

Geir Halnes, Ivar Østby, Klas H. Pettersen, Stig W. Omholt, Gaute T. Einevoll

PLOS Computational Biology: published December 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003386

Inferring the Source of Transmission with Phylogenetic Data

Erik M. Volz, Simon D. W. Frost

PLOS Computational Biology: published December 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003397

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Phenome-Wide Association Studies on a Quantitative Trait: Application to TPMT Enzyme Activity and Thiopurine Therapy in Pharmacogenomics

Antoine Neuraz, Laurent Chouchana, Georgia Malamut, Christine Le Beller, Denis Roche, Philippe Beaune, Patrice Degoulet, Anita Burgun, Marie-Anne Loriot, Paul Avillach

PLOS Computational Biology: published December 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003405

Metabolic and Demographic Feedbacks Shape the Emergent Spatial Structure and Function of Microbial Communities

Sylvie Estrela, Sam P. Brown

PLOS Computational Biology: published December 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003398

Cortically-Controlled Population Stochastic Facilitation as a Plausible Substrate for Guiding Sensory Transfer across the Thalamic Gateway

Sébastien Béhuret, Charlotte Deleuze, Leonel Gomez, Yves Frégnac, Thierry Bal

PLOS Computational Biology: published December 26, 2013 | https://doi.org/10.1371/journal.pcbi.1003401

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

Evan J. Molinelli, Anil Korkut, Weiqing Wang, Martin L. Miller, Nicholas P. Gauthier, Xiaohong Jing, Poorvi Kaushik, Qin He, Gordon Mills, David B. Solit, Christine A. Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, Chris Sander

PLOS Computational Biology: published December 19, 2013 | https://doi.org/10.1371/journal.pcbi.1003290