Ten Simple Rules for Writing a Literature Review

Marco Pautasso

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003149

Information and Efficiency in the Nervous System—A Synthesis

Biswa Sengupta, Martin B. Stemmler, Karl J. Friston

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003157

Models of Self-Peptide Sampling by Developing T Cells Identify Candidate Mechanisms of Thymic Selection

Iren Bains, Hisse M. van Santen, Benedict Seddon, Andrew J. Yates

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003102

‘HypothesisFinder:’ A Strategy for the Detection of Speculative Statements in Scientific Text

Ashutosh Malhotra, Erfan Younesi, Harsha Gurulingappa, Martin Hofmann-Apitius

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003117

Co-expression Profiling of Autism Genes in the Mouse Brain

Idan Menashe, Pascal Grange, Eric C. Larsen, Sharmila Banerjee-Basu, Partha P. Mitra

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003128

Spatial Stochastic Dynamics Enable Robust Cell Polarization

Michael J. Lawson, Brian Drawert, Mustafa Khammash, Linda Petzold, Tau-Mu Yi

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003139

Efficient Partitioning of Memory Systems and Its Importance for Memory Consolidation

Alex Roxin, Stefano Fusi

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003146

Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures

Jaeyun Sung, Pan-Jun Kim, Shuyi Ma, Cory C. Funk, Andrew T. Magis, Yuliang Wang, Leroy Hood, Donald Geman, Nathan D. Price

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003148

A Mixture of Delta-Rules Approximation to Bayesian Inference in Change-Point Problems

Robert C. Wilson, Matthew R. Nassar, Joshua I. Gold

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003150

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Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

Justin Ritz, Joshua S. Martin, Alain Laederach

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003152

Insertion of the Ca²⁺-Independent Phospholipase A₂ into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations

Denis Bucher, Yuan-Hao Hsu, Varnavas D. Mouchlis, Edward A. Dennis, J. Andrew McCammon

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003156

Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria

Nadine Veith, Anna Feldman-Salit, Vlad Cojocaru, Stefan Henrich, Ursula Kummer, Rebecca C. Wade

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003159

Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression

C. J. Zopf, Katie Quinn, Joshua Zeidman, Narendra Maheshri

PLOS Computational Biology: published July 25, 2013 | https://doi.org/10.1371/journal.pcbi.1003161

A Family of Algorithms for Computing Consensus about Node State from Network Data

Eleanor R. Brush, David C. Krakauer, Jessica C. Flack

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003109

The Role of Multiple Marks in Epigenetic Silencing and the Emergence of a Stable Bivalent Chromatin State

Swagatam Mukhopadhyay, Anirvan M. Sengupta

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003121

Shared Protein Complex Subunits Contribute to Explaining Disrupted Co-occurrence

Adrian Schneider, Michael F. Seidl, Berend Snel

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003124

A Model for the Self-Organization of Vesicular Flux and Protein Distributions in the Golgi Apparatus

Iaroslav Ispolatov, Anne Müsch

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003125

Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM

Jonathan M. Dreyfuss, Jeremy D. Zucker, Heather M. Hood, Linda R. Ocasio, Matthew S. Sachs, James E. Galagan

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003126

Gain Control Network Conditions in Early Sensory Coding

Eduardo Serrano, Thomas Nowotny, Rafael Levi, Brian H. Smith, Ramón Huerta

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003133

Charles Bonnet Syndrome: Evidence for a Generative Model in the Cortex?

David P. Reichert, Peggy Seriès, Amos J. Storkey

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003134

Frequency Dependence of Signal Power and Spatial Reach of the Local Field Potential

Szymon Łęski, Henrik Lindén, Tom Tetzlaff, Klas H. Pettersen, Gaute T. Einevoll

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003137

Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein

Burcu Aykaç Fas, Yusuf Tutar, Türkan Haliloğlu

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003141

Epidemiologically Optimal Static Networks from Temporal Network Data

Petter Holme

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003142

Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs

James M. McFarland, Yuwei Cui, Daniel A. Butts

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003143

Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways

Natalia Pietrosemoli, Rita Pancsa, Peter Tompa

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003144

Statistical Analysis of Molecular Signal Recording

Joshua I. Glaser, Bradley M. Zamft, Adam H. Marblestone, Jeffrey R. Moffitt, Keith Tyo, Edward S. Boyden, George Church, Konrad P. Kording

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003145

Improving Pharmacokinetic-Pharmacodynamic Modeling to Investigate Anti-Infective Chemotherapy with Application to the Current Generation of Antimalarial Drugs

Katherine Kay, Ian M. Hastings

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003151

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

Umadevi Paila, Brad A. Chapman, Rory Kirchner, Aaron R. Quinlan

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003153

A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications

Drazen Petrov, Christian Margreitter, Melanie Grandits, Chris Oostenbrink, Bojan Zagrovic

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003154

Variations within Class-A β-Lactamase Physiochemical Properties Reflect Evolutionary and Environmental Patterns, but not Antibiotic Specificity

Deeptak Verma, Donald J. Jacobs, Dennis R. Livesay

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003155

Expanding the Druggable Space of the LSD1/CoREST Epigenetic Target: New Potential Binding Regions for Drug-Like Molecules, Peptides, Protein Partners, and Chromatin

James C. Robertson, Nate C. Hurley, Marcello Tortorici, Giuseppe Ciossani, Maria Teresa Borrello, Nadeem A. Vellore, A. Ganesan, Andrea Mattevi, Riccardo Baron

PLOS Computational Biology: published July 18, 2013 | https://doi.org/10.1371/journal.pcbi.1003158

Consistent Estimation of Gibbs Energy Using Component Contributions

Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003098

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Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks

Pinkesh K. Patel, Orian Shirihai, Kerwyn Casey Huang

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003108

The Minimal Complexity of Adapting Agents Increases with Fitness

Nikhil J. Joshi, Giulio Tononi, Christof Koch

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003111

Target Essentiality and Centrality Characterize Drug Side Effects

Xiujuan Wang, Bram Thijssen, Haiyuan Yu

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003119

Towards Predicting the Response of a Solid Tumour to Chemotherapy and Radiotherapy Treatments: Clinical Insights from a Computational Model

Gibin G. Powathil, Douglas J. A. Adamson, Mark A. J. Chaplain

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003120

Hierarchical Modeling for Rare Event Detection and Cell Subset Alignment across Flow Cytometry Samples

Andrew Cron, Cécile Gouttefangeas, Jacob Frelinger, Lin Lin, Satwinder K. Singh, Cedrik M. Britten, Marij J. P. Welters, Sjoerd H. van der Burg, Mike West, Cliburn Chan

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003130

Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs

Chao Cheng, Matthew Ung, Gavin D. Grant, Michael L. Whitfield

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003132

Genetic Selection for Context-Dependent Stochastic Phenotypes: Sp1 and TATA Mutations Increase Phenotypic Noise in HIV-1 Gene Expression

Kathryn Miller-Jensen, Ron Skupsky, Priya S. Shah, Adam P. Arkin, David V. Schaffer

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003135

New Universal Rules of Eukaryotic Translation Initiation Fidelity

Hadas Zur, Tamir Tuller

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003136

Successful Reconstruction of a Physiological Circuit with Known Connectivity from Spiking Activity Alone

Felipe Gerhard, Tilman Kispersky, Gabrielle J. Gutierrez, Eve Marder, Mark Kramer, Uri Eden

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003138

Distinct Allelic Patterns of Nanog Expression Impart Embryonic Stem Cell Population Heterogeneity

Jincheng Wu, Emmanuel S. Tzanakakis

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003140

Dynamics of SIN Asymmetry Establishment

Archana Bajpai, Anna Feoktistova, Jun-Song Chen, Dannel McCollum, Masamitsu Sato, Rafael E. Carazo-Salas, Kathleen L. Gould, Attila Csikász-Nagy

PLOS Computational Biology: published July 11, 2013 | https://doi.org/10.1371/journal.pcbi.1003147

Interaction of Motility, Directional Sensing, and Polarity Modules Recreates the Behaviors of Chemotaxing Cells

Changji Shi, Chuan-Hsiang Huang, Peter N. Devreotes, Pablo A. Iglesias

PLOS Computational Biology: published July 4, 2013 | https://doi.org/10.1371/journal.pcbi.1003122

Predicting Network Activity from High Throughput Metabolomics

Shuzhao Li, Youngja Park, Sai Duraisingham, Frederick H. Strobel, Nooruddin Khan, Quinlyn A. Soltow, Dean P. Jones, Bali Pulendran

PLOS Computational Biology: published July 4, 2013 | https://doi.org/10.1371/journal.pcbi.1003123

Pathway-based Screening Strategy for Multitarget Inhibitors of Diverse Proteins in Metabolic Pathways

Kai-Cheng Hsu, Wen-Chi Cheng, Yen-Fu Chen, Wen-Ching Wang, Jinn-Moon Yang

PLOS Computational Biology: published July 4, 2013 | https://doi.org/10.1371/journal.pcbi.1003127

Engineering a More Thermostable Blue Light Photo Receptor Bacillus subtilis YtvA LOV Domain by a Computer Aided Rational Design Method

Xiangfei Song, Yefei Wang, Zhiyu Shu, Jingbo Hong, Tong Li, Lishan Yao

PLOS Computational Biology: published July 4, 2013 | https://doi.org/10.1371/journal.pcbi.1003129

Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach

Joshua T. Schiffer, Dave A. Swan, Daniel Stone, Keith R. Jerome

PLOS Computational Biology: published July 4, 2013 | https://doi.org/10.1371/journal.pcbi.1003131