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Table of Contents: September 2014

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Drugs are typically developed to modulate the function of specific proteins, which are directly associated with particular disease states. Nonetheless, protein-drug interactions are rather promiscuous and the majority of pharmaceuticals exhibit activity against multiple, often unrelated targets; for instance, ATP-dependent DNA ligase and histamine N-methyltransferase shown here bind the same compound. To detect those binding sites having the capability to bind similar molecules, Michal Brylinski developed eMatchSite, which constructs local sequence order-independent alignments using computer-generated protein models. This approach opens up the possibility to investigate drug-protein interactions for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning.

Editorial

Ten Simple Rules for Better Figures

Nicolas P. Rougier, Michael Droettboom, Philip E. Bourne

Topic Page

Multi-state Modeling of Biomolecules

Melanie I. Stefan, Thomas M. Bartol, Terrence J. Sejnowski, Mary B. Kennedy

Research Articles

Quantifying the Impact and Extent of Undocumented Biomedical Synonymy

David R. Blair, Kanix Wang, Svetlozar Nestorov, James A. Evans, Andrey Rzhetsky

Characterizing Protein Interactions Employing a Genome-Wide siRNA Cellular Phenotyping Screen

Apichat Suratanee, Martin H. Schaefer, Matthew J. Betts, Zita Soons, Heiko Mannsperger, Nathalie Harder, Marcus Oswald, Markus Gipp, Ellen Ramminger, Guillermo Marcus, Reinhard Männer, Karl Rohr, Erich Wanker, Robert B. Russell, Miguel A. Andrade-Navarro, Roland Eils, Rainer König

Clique of Functional Hubs Orchestrates Population Bursts in Developmentally Regulated Neural Networks

Stefano Luccioli, Eshel Ben-Jacob, Ari Barzilai, Paolo Bonifazi, Alessandro Torcini

Identifying Cell Types from Spatially Referenced Single-Cell Expression Datasets

Jean-Baptiste Pettit, Raju Tomer, Kaia Achim, Sylvia Richardson, Lamiae Azizi, John Marioni

IDEPI: Rapid Prediction of HIV-1 Antibody Epitopes and Other Phenotypic Features from Sequence Data Using a Flexible Machine Learning Platform

N. Lance Hepler, Konrad Scheffler, Steven Weaver, Ben Murrell, Douglas D. Richman, Dennis R. Burton, Pascal Poignard, Davey M. Smith, Sergei L. Kosakovsky Pond

A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data

Qing Xie, Qi Liu, Fengbiao Mao, Wanshi Cai, Honghu Wu, Mingcong You, Zhen Wang, Bingyu Chen, Zhong Sheng Sun, Jinyu Wu

Synchronization of Isolated Downstates (K-Complexes) May Be Caused by Cortically-Induced Disruption of Thalamic Spindling

Rachel A. Mak-McCully, Stephen R. Deiss, Burke Q. Rosen, Ki-Young Jung, Terrence J. Sejnowski, Hélène Bastuji, Marc Rey, Sydney S. Cash, Maxim Bazhenov, Eric Halgren

Geometry Shapes Evolution of Early Multicellularity

Eric Libby, William Ratcliff, Michael Travisano, Ben Kerr

Spatial Heterogeneity and Peptide Availability Determine CTL Killing Efficiency In Vivo

Thea Hogan, Ulrich Kadolsky, Sim Tung, Benedict Seddon, Andrew Yates

Multidimensional Epistasis and the Transitory Advantage of Sex

Stefan Nowak, Johannes Neidhart, Ivan G. Szendro, Joachim Krug

A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks

Hojung Nam, Miguel Campodonico, Aarash Bordbar, Daniel R. Hyduke, Sangwoo Kim, Daniel C. Zielinski, Bernhard O. Palsson

NESmapper: Accurate Prediction of Leucine-Rich Nuclear Export Signals Using Activity-Based Profiles

Shunichi Kosugi, Hiroshi Yanagawa, Ryohei Terauchi, Satoshi Tabata

Genome-Scale Metabolic Network Validation of Shewanella oneidensis Using Transposon Insertion Frequency Analysis

Hong Yang, Elias W. Krumholz, Evan D. Brutinel, Nagendra P. Palani, Michael J. Sadowsky, Andrew M. Odlyzko, Jeffrey A. Gralnick, Igor G. L. Libourel

Examining Variable Domain Orientations in Antigen Receptors Gives Insight into TCR-Like Antibody Design

James Dunbar, Bernhard Knapp, Angelika Fuchs, Jiye Shi, Charlotte M. Deane

Pupil-Linked Arousal Determines Variability in Perceptual Decision Making

Peter R. Murphy, Joachim Vandekerckhove, Sander Nieuwenhuis

Strategies for Controlling Non-Transmissible Infection Outbreaks Using a Large Human Movement Data Set

Penelope A. Hancock, Yasmin Rehman, Ian M. Hall, Obaghe Edeghere, Leon Danon, Thomas A. House, Matthew J. Keeling

The Time Scale of Evolutionary Innovation

Krishnendu Chatterjee, Andreas Pavlogiannis, Ben Adlam, Martin A. Nowak

The Structural Basis of ATP as an Allosteric Modulator

Shaoyong Lu, Wenkang Huang, Qi Wang, Qiancheng Shen, Shuai Li, Ruth Nussinov, Jian Zhang

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

Jinyu Li, Giulia Rossetti, Jens Dreyer, Simone Raugei, Emiliano Ippoliti, Bernhard Lüscher, Paolo Carloni

Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops

Gaetano Invernizzi, Matteo Tiberti, Matteo Lambrughi, Kresten Lindorff-Larsen, Elena Papaleo

Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages

Tamás Székely Jr, Kevin Burrage, Marc Mangel, Michael B. Bonsall

Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma

Marti Bernardo-Faura, Stefan Massen, Christine S. Falk, Nathan R. Brady, Roland Eils

Emergence of Assortative Mixing between Clusters of Cultured Neurons

Sara Teller, Clara Granell, Manlio De Domenico, Jordi Soriano, Sergio Gómez, Alex Arenas

Revealing Molecular Mechanisms by Integrating High-Dimensional Functional Screens with Protein Interaction Data

Angela Simeone, Giovanni Marsico, Claudio Collinet, Thierry Galvez, Yannis Kalaidzidis, Marino Zerial, Andreas Beyer

Inferring on the Intentions of Others by Hierarchical Bayesian Learning

Andreea O. Diaconescu, Christoph Mathys, Lilian A. E. Weber, Jean Daunizeau, Lars Kasper, Ekaterina I. Lomakina, Ernst Fehr, Klaas E. Stephan

Phase Transitions in the Multi-cellular Regulatory Behavior of Pancreatic Islet Excitability

Thomas H. Hraha, Matthew J. Westacott, Marina Pozzoli, Aleena M. Notary, P. Mason McClatchey, Richard K. P. Benninger

Pep2Path: Automated Mass Spectrometry-Guided Genome Mining of Peptidic Natural Products

Marnix H. Medema, Yared Paalvast, Don D. Nguyen, Alexey Melnik, Pieter C. Dorrestein, Eriko Takano, Rainer Breitling

A Probabilistic Model to Predict Clinical Phenotypic Traits from Genome Sequencing

Yun-Ching Chen, Christopher Douville, Cheng Wang, Noushin Niknafs, Grace Yeo, Violeta Beleva-Guthrie, Hannah Carter, Peter D. Stenson, David N. Cooper, Biao Li, Sean Mooney, Rachel Karchin

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities

Amit Ghosh, Jerome Nilmeier, Daniel Weaver, Paul D. Adams, Jay D. Keasling, Aindrila Mukhopadhyay, Christopher J. Petzold, Héctor García Martín

Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression

Melissa M. Norström, Nazle M. Veras, Wei Huang, Mattia C. F. Proper, Jennifer Cook, Wendy Hartogensis, Frederick M. Hecht, Annika C. Karlsoon, Marco Salemi