Table of Contents: July 2013


Molecular probes used to identify new druggable regions float around the epigenetic target LSD1/CoREST

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

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



Information and Efficiency in the Nervous System—A Synthesis

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

Research Articles

‘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

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

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

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

The Minimal Complexity of Adapting Agents Increases with Fitness

Nikhil J. Joshi, Giulio Tononi, Christof Koch

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

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

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