International Society for Computational Biology Honors David Eisenberg with 2013 Accomplishment by a Senior Scientist Award

Christiana N. Fogg, Diane E. Kovats

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003116

Bioinformatics Goes to School—New Avenues for Teaching Contemporary Biology

Louisa Wood, Philipp Gebhardt

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003089

Cooperative Binding

Melanie I. Stefan, Nicolas Le Novère

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003106

Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data

Yan Zhang, Hye Kyong Kweon, Christian Shively, Anuj Kumar, Philip C. Andrews

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003077

Flux Balance Analysis of Cyanobacterial Metabolism: The Metabolic Network of Synechocystis sp. PCC 6803

Henning Knoop, Marianne Gründel, Yvonne Zilliges, Robert Lehmann, Sabrina Hoffmann, Wolfgang Lockau, Ralf Steuer

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003081

Dynamic Excitatory and Inhibitory Gain Modulation Can Produce Flexible, Robust and Optimal Decision-making

Ritwik K. Niyogi, KongFatt Wong-Lin

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003099

A Design Principle of Group-level Decision Making in Cell Populations

Koichi Fujimoto, Satoshi Sawai

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003110

Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module

Diane M. Longo, Jangir Selimkhanov, Jeffrey D. Kearns, Jeff Hasty, Alexander Hoffmann, Lev S. Tsimring

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003112

Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1

Lyudmyla Dorosh, Olesya A. Kharenko, Nandhakishore Rajagopalan, Michele C. Loewen, Maria Stepanova

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003114

Understanding the Molecular Determinants Driving the Immunological Specificity of the Protective Pilus 2a Backbone Protein of Group B Streptococcus

Annalisa Nuccitelli, C. Daniela Rinaudo, Barbara Brogioni, Roberta Cozzi, Mario Ferrer-Navarro, Daniel Yero, John L. Telford, Guido Grandi, Xavier Daura, Martin Zacharias, Domenico Maione

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003115

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

William R. Harcombe, Nigel F. Delaney, Nicholas Leiby, Niels Klitgord, Christopher J. Marx

PLOS Computational Biology: published June 20, 2013 | https://doi.org/10.1371/journal.pcbi.1003091

Integrative Analysis of Deep Sequencing Data Identifies Estrogen Receptor Early Response Genes and Links ATAD3B to Poor Survival in Breast Cancer

Kristian Ovaska, Filomena Matarese, Korbinian Grote, Iryna Charapitsa, Alejandra Cervera, Chengyu Liu, George Reid, Martin Seifert, Hendrik G. Stunnenberg, Sampsa Hautaniemi

PLOS Computational Biology: published June 20, 2013 | https://doi.org/10.1371/journal.pcbi.1003100

How the Dynamics and Structure of Sexual Contact Networks Shape Pathogen Phylogenies

Katy Robinson, Nick Fyson, Ted Cohen, Christophe Fraser, Caroline Colijn

PLOS Computational Biology: published June 20, 2013 | https://doi.org/10.1371/journal.pcbi.1003105

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples

David R. Riley, Karsten B. Sieber, Kelly M. Robinson, James Robert White, Ashwinkumar Ganesan, Syrus Nourbakhsh, Julie C. Dunning Hotopp

PLOS Computational Biology: published June 20, 2013 | https://doi.org/10.1371/journal.pcbi.1003107

Patterns of Proliferative Activity in the Colonic Crypt Determine Crypt Stability and Rates of Somatic Evolution

Rui Zhao, Franziska Michor

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003082

Unsupervised Clustering of Subcellular Protein Expression Patterns in High-Throughput Microscopy Images Reveals Protein Complexes and Functional Relationships between Proteins

Louis-François Handfield, Yolanda T. Chong, Jibril Simmons, Brenda J. Andrews, Alan M. Moses

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003085

Exploring Volatile General Anesthetic Binding to a Closed Membrane-Bound Bacterial Voltage-Gated Sodium Channel via Computation

S. G. Raju, Annika F. Barber, David N. LeBard, Michael L. Klein, Vincenzo Carnevale

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003090

Mate Choice and the Origin of Menopause

Richard A. Morton, Jonathan R. Stone, Rama S. Singh

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003092

Emotional Valence and the Free-Energy Principle

Mateus Joffily, Giorgio Coricelli

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003094

Fibrin Networks Regulate Protein Transport during Thrombus Development

Oleg V. Kim, Zhiliang Xu, Elliot D. Rosen, Mark S. Alber

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003095

Modelling Co-Infection with Malaria and Lymphatic Filariasis

Hannah C. Slater, Manoj Gambhir, Paul E. Parham, Edwin Michael

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003096

A Forced Damped Oscillation Framework for Undulatory Swimming Provides New Insights into How Propulsion Arises in Active and Passive Swimming

Amneet Pal Singh Bhalla, Boyce E. Griffith, Neelesh A. Patankar

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003097

Neuronal Functional Connection Graphs among Multiple Areas of the Rat Somatosensory System during Spontaneous and Evoked Activities

Antonio G. Zippo, Riccardo Storchi, Sara Nencini, Gian Carlo Caramenti, Maurizio Valente, Gabriele Eliseo M. Biella

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003104

Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach

Meagan C. Small, Pedro Lopes, Rodrigo B. Andrade, Alexander D. MacKerell Jr

PLOS Computational Biology: published June 13, 2013 | https://doi.org/10.1371/journal.pcbi.1003113

Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study

Jörg Bornschein, Marc Henniges, Jörg Lücke

PLOS Computational Biology: published June 6, 2013 | https://doi.org/10.1371/journal.pcbi.1003062

Theta Coordinated Error-Driven Learning in the Hippocampus

Nicholas Ketz, Srinimisha G. Morkonda, Randall C. O'Reilly

PLOS Computational Biology: published June 6, 2013 | https://doi.org/10.1371/journal.pcbi.1003067

Constraint and Contingency in Multifunctional Gene Regulatory Circuits

Joshua L. Payne, Andreas Wagner

PLOS Computational Biology: published June 6, 2013 | https://doi.org/10.1371/journal.pcbi.1003071

Quantitative Analysis of Glycerol Accumulation, Glycolysis and Growth under Hyper Osmotic Stress

Elzbieta Petelenz-Kurdziel, Clemens Kuehn, Bodil Nordlander, Dagmara Klein, Kuk-Ki Hong, Therese Jacobson, Peter Dahl, Jörg Schaber, Jens Nielsen, Stefan Hohmann, Edda Klipp

PLOS Computational Biology: published June 6, 2013 | https://doi.org/10.1371/journal.pcbi.1003084

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Combinatorial Clustering of Residue Position Subsets Predicts Inhibitor Affinity across the Human Kinome

Drew H. Bryant, Mark Moll, Paul W. Finn, Lydia E. Kavraki

PLOS Computational Biology: published June 6, 2013 | https://doi.org/10.1371/journal.pcbi.1003087

Scrutinizing MHC-I Binding Peptides and Their Limits of Variation

Christian P. Koch, Anna M. Perna, Max Pillong, Nickolay K. Todoroff, Paul Wrede, Gerd Folkers, Jan A. Hiss, Gisbert Schneider

PLOS Computational Biology: published June 6, 2013 | https://doi.org/10.1371/journal.pcbi.1003088

Leveraging Prior Information to Detect Causal Variants via Multi-Variant Regression

Nanye Long, Samuel P. Dickson, Jessica M. Maia, Hee Shin Kim, Qianqian Zhu, Andrew S. Allen

PLOS Computational Biology: published June 6, 2013 | https://doi.org/10.1371/journal.pcbi.1003093

Gag-Pol Processing during HIV-1 Virion Maturation: A Systems Biology Approach

Balázs Könnyű, S. Kashif Sadiq, Tamás Turányi, Rita Hírmondó, Barbara Müller, Hans-Georg Kräusslich, Peter V. Coveney, Viktor Müller

PLOS Computational Biology: published June 6, 2013 | https://doi.org/10.1371/journal.pcbi.1003103

PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data

Gabriel E. Hoffman, Benjamin A. Logsdon, Jason G. Mezey

PLOS Computational Biology: published June 27, 2013 | https://doi.org/10.1371/journal.pcbi.1003101