Table of Contents: July 2013

The newly developed Druggable Site Visualizer (DSV) tool enables easy inspection of druggable sites on configurational ensembles. See Robertson et al.

Image Credit: James C. Robertson and Riccardo Baron, Department of Medicinal Chemistry, The University of Utah, U.S.A


Ten Simple Rules for Writing a Literature Review

Marco Pautasso


Information and Efficiency in the Nervous System—A Synthesis

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

Research Articles

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

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

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

Co-expression Profiling of Autism Genes in the Mouse Brain

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

Spatial Stochastic Dynamics Enable Robust Cell Polarization

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

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

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

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

Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation

Justin Ritz, Joshua S. Martin, Alain Laederach

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

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

Cell-Cycle Dependence of Transcription Dominates Noise in Gene Expression

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

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

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

Shared Protein Complex Subunits Contribute to Explaining Disrupted Co-occurrence

Adrian Schneider, Michael F. Seidl, Berend Snel

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

Gain Control Network Conditions in Early Sensory Coding

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

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

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

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

Inferring Nonlinear Neuronal Computation Based on Physiologically Plausible Inputs

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

Structural Disorder Provides Increased Adaptability for Vesicle Trafficking Pathways

Natalia Pietrosemoli, Rita Pancsa, Peter Tompa

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

GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations

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

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

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

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

Consistent Estimation of Gibbs Energy Using Component Contributions

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

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