Modeling Planarian Regeneration: A Primer for Reverse-Engineering the Worm

Daniel Lobo, Wendy S. Beane, Michael Levin

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002481

Rise and Demise of Bioinformatics? Promise and Progress

Christos A. Ouzounis

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002487

Storage of Correlated Patterns in Standard and Bistable Purkinje Cell Models

Claudia Clopath, Jean-Pierre Nadal, Nicolas Brunel

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002448

Deconvolution of the Cellular Force-Generating Subsystems that Govern Cytokinesis Furrow Ingression

Christopher C. Poirier, Win Pin Ng, Douglas N. Robinson, Pablo A. Iglesias

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002467

Determinants of Sexual Network Structure and Their Impact on Cumulative Network Measures

Boris V. Schmid, Mirjam Kretzschmar

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002470

Exploring the Contextual Sensitivity of Factors that Determine Cell-to-Cell Variability in Receptor-Mediated Apoptosis

Suzanne Gaudet, Sabrina L. Spencer, William W. Chen, Peter K. Sorger

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002482

Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics

Karen van Eunen, José A. L. Kiewiet, Hans V. Westerhoff, Barbara M. Bakker

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002483

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

Dina Zhabinskaya, Craig J. Benham

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002484

Microarray Analysis of LTR Retrotransposon Silencing Identifies Hdac1 as a Regulator of Retrotransposon Expression in Mouse Embryonic Stem Cells

Judith Reichmann, James H. Crichton, Monika J. Madej, Mary Taggart, Philippe Gautier, Jose Luis Garcia-Perez, Richard R. Meehan, Ian R. Adams

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002486

Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons

Kyriaki Sidiropoulou, Panayiota Poirazi

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002489

Tension and Robustness in Multitasking Cellular Networks

Jeffrey V. Wong, Bochong Li, Lingchong You

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002491

Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota

Vanni Bucci, Serena Bradde, Giulio Biroli, Joao B. Xavier

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002497

Are Long-Range Structural Correlations Behind the Aggregration Phenomena of Polyglutamine Diseases?

Mahmoud Moradi, Volodymyr Babin, Christopher Roland, Celeste Sagui

PLOS Computational Biology: published April 26, 2012 | https://doi.org/10.1371/journal.pcbi.1002501

Non-Additive Coupling Enables Propagation of Synchronous Spiking Activity in Purely Random Networks

Raoul-Martin Memmesheimer, Marc Timme

PLOS Computational Biology: published April 19, 2012 | https://doi.org/10.1371/journal.pcbi.1002384

The Emergence and Early Evolution of Biological Carbon-Fixation

Rogier Braakman, Eric Smith

PLOS Computational Biology: published April 19, 2012 | https://doi.org/10.1371/journal.pcbi.1002455

Exploration of Multi-State Conformational Dynamics and Underlying Global Functional Landscape of Maltose Binding Protein

Yong Wang, Chun Tang, Erkang Wang, Jin Wang

PLOS Computational Biology: published April 19, 2012 | https://doi.org/10.1371/journal.pcbi.1002471

Ligand-Dependent Conformations and Dynamics of the Serotonin 5-HT_2A Receptor Determine Its Activation and Membrane-Driven Oligomerization Properties

Jufang Shan, George Khelashvili, Sayan Mondal, Ernest L. Mehler, Harel Weinstein

PLOS Computational Biology: published April 19, 2012 | https://doi.org/10.1371/journal.pcbi.1002473

Persisting Viral Sequences Shape Microbial CRISPR-based Immunity

Ariel D. Weinberger, Christine L. Sun, Mateusz M. Pluciński, Vincent J. Denef, Brian C. Thomas, Philippe Horvath, Rodolphe Barrangou, Michael S. Gilmore, Wayne M. Getz, Jillian F. Banfield

PLOS Computational Biology: published April 19, 2012 | https://doi.org/10.1371/journal.pcbi.1002475

Computational Design of a PDZ Domain Peptide Inhibitor that Rescues CFTR Activity

Kyle E. Roberts, Patrick R. Cushing, Prisca Boisguerin, Dean R. Madden, Bruce R. Donald

PLOS Computational Biology: published April 19, 2012 | https://doi.org/10.1371/journal.pcbi.1002477

Inference of Genotype–Phenotype Relationships in the Antigenic Evolution of Human Influenza A (H3N2) Viruses

Lars Steinbrück, Alice Carolyn McHardy

PLOS Computational Biology: published April 19, 2012 | https://doi.org/10.1371/journal.pcbi.1002492

The Effects of NMDA Subunit Composition on Calcium Influx and Spike Timing-Dependent Plasticity in Striatal Medium Spiny Neurons

Rebekah C. Evans, Teresa Morera-Herreras, Yihui Cui, Kai Du, Tom Sheehan, Jeanette Hellgren Kotaleski, Laurent Venance, Kim T. Blackwell

PLOS Computational Biology: published April 19, 2012 | https://doi.org/10.1371/journal.pcbi.1002493

Evolution of the Multi-Domain Structures of Virulence Genes in the Human Malaria Parasite, Plasmodium falciparum

Caroline O. Buckee, Mario Recker

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002451

A New Perceptual Bias Reveals Suboptimal Population Decoding of Sensory Responses

Tom Putzeys, Matthias Bethge, Felix Wichmann, Johan Wagemans, Robbe Goris

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002453

Quantifying Type-Specific Reproduction Numbers for Nosocomial Pathogens: Evidence for Heightened Transmission of an Asian Sequence Type 239 MRSA Clone

Ben S. Cooper, Theodore Kypraios, Rahul Batra, Duncan Wyncoll, Olga Tosas, Jonathan D. Edgeworth

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002454

Warm Body Temperature Facilitates Energy Efficient Cortical Action Potentials

Yuguo Yu, Adam P. Hill, David A. McCormick

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002456

Power-Law Inter-Spike Interval Distributions Infer a Conditional Maximization of Entropy in Cortical Neurons

Yasuhiro Tsubo, Yoshikazu Isomura, Tomoki Fukai

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002461

Optimization of Muscle Activity for Task-Level Goals Predicts Complex Changes in Limb Forces across Biomechanical Contexts

J. Lucas McKay, Lena H. Ting

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002465

Differences in Cell Division Rates Drive the Evolution of Terminal Differentiation in Microbes

João F. Matias Rodrigues, Daniel J. Rankin, Valentina Rossetti, Andreas Wagner, Homayoun C. Bagheri

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002468

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The Impact of Imitation on Vaccination Behavior in Social Contact Networks

Martial L. Ndeffo Mbah, Jingzhou Liu, Chris T. Bauch, Yonas I. Tekel, Jan Medlock, Lauren Ancel Meyers, Alison P. Galvani

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002469

Optimizing Provider Recruitment for Influenza Surveillance Networks

Samuel V. Scarpino, Nedialko B. Dimitrov, Lauren Ancel Meyers

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002472

Geometric Theory Predicts Bifurcations in Minimal Wiring Cost Trees in Biology Are Flat

Yihwa Kim, Robert Sinclair, Nol Chindapol, Jaap A. Kaandorp, Erik De Schutter

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002474

Impact of Adaptation Currents on Synchronization of Coupled Exponential Integrate-and-Fire Neurons

Josef Ladenbauer, Moritz Augustin, LieJune Shiau, Klaus Obermayer

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002478

Establishment and Validation of Computational Model for MT1-MMP Dependent ECM Degradation and Intervention Strategies

Daisuke Hoshino, Naohiko Koshikawa, Takashi Suzuki, Vito Quaranta, Alissa M. Weaver, Motoharu Seiki, Kazuhisa Ichikawa

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002479

Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit

Dmitry Nevozhay, Rhys M. Adams, Elizabeth Van Itallie, Matthew R. Bennett, Gábor Balázsi

PLOS Computational Biology: published April 12, 2012 | https://doi.org/10.1371/journal.pcbi.1002480

Replication Fork Polarity Gradients Revealed by Megabase-Sized U-Shaped Replication Timing Domains in Human Cell Lines

Antoine Baker, Benjamin Audit, Chun-Long Chen, Benoit Moindrot, Antoine Leleu, Guillaume Guilbaud, Aurélien Rappailles, Cédric Vaillant, Arach Goldar, Fabien Mongelard, Yves d'Aubenton-Carafa, Olivier Hyrien, Claude Thermes, Alain Arneodo

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002443

Molecular Machines in the Synapse: Overlapping Protein Sets Control Distinct Steps in Neurosecretion

L. Niels Cornelisse, Evgeni Tsivtsivadze, Marieke Meijer, Tjeerd M. H. Dijkstra, Tom Heskes, Matthijs Verhage

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002450

Evolutionary Game Theory and Social Learning Can Determine How Vaccine Scares Unfold

Chris T. Bauch, Samit Bhattacharyya

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002452

Automatic Filtering and Substantiation of Drug Safety Signals

Anna Bauer-Mehren, Erik M. van Mullingen, Paul Avillach, María del Carmen Carrascosa, Ricard Garcia-Serna, Janet Piñero, Bharat Singh, Pedro Lopes, José L. Oliveira, Gayo Diallo, Ernst Ahlberg Helgee, Scott Boyer, Jordi Mestres, Ferran Sanz, Jan A. Kors, Laura I. Furlong

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002457

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1. Correction: Automatic Filtering and Substantiation of Drug Safety Signals

What Can Causal Networks Tell Us about Metabolic Pathways?

Rachael Hageman Blair, Daniel J. Kliebenstein, Gary A. Churchill

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002458

Parameters in Dynamic Models of Complex Traits are Containers of Missing Heritability

Yunpeng Wang, Arne B. Gjuvsland, Jon Olav Vik, Nicolas P. Smith, Peter J. Hunter, Stig W. Omholt

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002459

Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142

Trang T. Vu, Sergey M. Stolyar, Grigoriy E. Pinchuk, Eric A. Hill, Leo A. Kucek, Roslyn N. Brown, Mary S. Lipton, Andrei Osterman, Jim K. Fredrickson, Allan E. Konopka, Alexander S. Beliaev, Jennifer L. Reed

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002460

Energetic Selection of Topology in Ferredoxins

J. Dongun Kim, Agustina Rodriguez-Granillo, David A. Case, Vikas Nanda, Paul G. Falkowski

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002463

RNA-Seq Mapping and Detection of Gene Fusions with a Suffix Array Algorithm

Onur Sakarya, Heinz Breu, Milan Radovich, Yongzhi Chen, Yulei N. Wang, Catalin Barbacioru, Sowmi Utiramerur, Penn P. Whitley, Joel P. Brockman, Paolo Vatta, Zheng Zhang, Liviu Popescu, Matthew W. Muller, Vidya Kudlingar, Nriti Garg, Chieh-Yuan Li, Benjamin S. Kong, John P. Bodeau, Robert C. Nutter, Jian Gu, Kelli S. Bramlett, Jeffrey K. Ichikawa, Fiona C. Hyland, Asim S. Siddiqui

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002464

On Conduction in a Bacterial Sodium Channel

Simone Furini, Carmen Domene

PLOS Computational Biology: published April 5, 2012 | https://doi.org/10.1371/journal.pcbi.1002476