Advertisement

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

Editorial

Ten Simple Rules for Writing a Literature Review

Marco Pautasso

Review

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

Related Articles

  1. New Methods Section in PLOS Computational Biology

Optimal Dynamics for Quality Control in Spatially Distributed Mitochondrial Networks

Pinkesh K. Patel, Orian Shirihai, Kerwyn Casey Huang

The Minimal Complexity of Adapting Agents Increases with Fitness

Nikhil J. Joshi, Giulio Tononi, Christof Koch

Target Essentiality and Centrality Characterize Drug Side Effects

Xiujuan Wang, Bram Thijssen, Haiyuan Yu

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

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

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

New Universal Rules of Eukaryotic Translation Initiation Fidelity

Hadas Zur, Tamir Tuller

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

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

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

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

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

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

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