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Table of Contents: August 2015

COVER

Systematic Mapping of Protein Mutational Space

Image Credit: Tawfik et al.
Issue Image

Systematic mappings of the effects of all possible mutations in a given protein sequence are routinely performed, with the aim of understanding protein structure-function and evolution. Most of these experiments indicate that the majority of amino acid substitutions are neutral. Our experimental system mimicked the manner by which protein sequences diverge in nature: a prolonged, gradual accumulation of mutations while retaining the protein¹s structure and function. Unlike previous mappings, the sequence-function Œheat map¹ derived from this experiment indicates that the fraction of deleterious mutations is in the order of 80% (dark to light blue) whereas the neutral mutations (white; ~15%), let alone beneficial mutations (~2%; in red), comprise a minority. Tawfik et al.

Education

Informatics for RNA Sequencing: A Web Resource for Analysis on the Cloud

Malachi Griffith, Jason R. Walker, Nicholas C. Spies, Benjamin J. Ainscough, Obi L. Griffith

Research Articles

Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets

Songjian Lu, Kevin N. Lu, Shi-Yuan Cheng, Bo Hu, Xiaojun Ma, Nicholas Nystrom, Xinghua Lu

Do Brain Networks Evolve by Maximizing Their Information Flow Capacity?

Chris G. Antonopoulos, Shambhavi Srivastava, Sandro E. de S. Pinto, Murilo S. Baptista

Flexible Modeling of Epidemics with an Empirical Bayes Framework

Logan C. Brooks, David C. Farrow, Sangwon Hyun, Ryan J. Tibshirani, Roni Rosenfeld

Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling

Åsmund Flobak, Anaïs Baudot, Elisabeth Remy, Liv Thommesen, Denis Thieffry, Martin Kuiper, Astrid Lægreid

Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions

Assaf Amitai, Mathias Toulouze, Karine Dubrana, David Holcman

Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity

Marc Breit, Michael Netzer, Klaus M. Weinberger, Christian Baumgartner

Efficient Characterization of Parametric Uncertainty of Complex (Bio)chemical Networks

Claudia Schillings, Mikael Sunnåker, Jörg Stelling, Christoph Schwab

Functional Basis of Microorganism Classification

Chengsheng Zhu, Tom O. Delmont, Timothy M. Vogel, Yana Bromberg

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways

Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson

Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes

Jeffrey R. Johnson, Silvia D. Santos, Tasha Johnson, Ursula Pieper, Marta Strumillo, Omar Wagih, Andrej Sali, Nevan J. Krogan, Pedro Beltrao

Asymmetric Evolutionary Games

Alex McAvoy, Christoph Hauert

Structure Learning in Bayesian Sensorimotor Integration

Tim Genewein, Eduard Hez, Zeynab Razzaghpanah, Daniel A. Braun

Changes in Postural Syntax Characterize Sensory Modulation and Natural Variation of C. elegans Locomotion

Roland F. Schwarz, Robyn Branicky, Laura J. Grundy, William R. Schafer, André E. X. Brown

Formation and Dynamics of Waves in a Cortical Model of Cholinergic Modulation

James P. Roach, Eshel Ben-Jacob, Leonard M. Sander, Michal R. Zochowski

Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations

Paul M. Harrison, Laurent Badel, Mark J. Wall, Magnus J. E. Richardson

A Three-Threshold Learning Rule Approaches the Maximal Capacity of Recurrent Neural Networks

Alireza Alemi, Carlo Baldassi, Nicolas Brunel, Riccardo Zecchina

Innate Immunity and the Inter-exposure Interval Determine the Dynamics of Secondary Influenza Virus Infection and Explain Observed Viral Hierarchies

Pengxing Cao, Ada W. C. Yan, Jane M. Heffernan, Stephen Petrie, Robert G. Moss, Louise A. Carolan, Teagan A. Guarnaccia, Anne Kelso, Ian G. Barr, Jodie McVernon, Karen L. Laurie, James M. McCaw

Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes

Ariel Afek, Hila Cohen, Shiran Barber-Zucker, Raluca Gordân, David B. Lukatsky

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data

Alexey A. Gritsenko, Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder

Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

John R. Houser, Craig Barnhart, Daniel R. Boutz, Sean M. Carroll, Aurko Dasgupta, Joshua K. Michener, Brittany D. Needham, Ophelia Papoulas, Viswanadham Sridhara, Dariya K. Sydykova, Christopher J. Marx, M. Stephen Trent, Jeffrey E. Barrick, Edward M. Marcotte, Claus O. Wilke

Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers

Shaun S. Sanders, Dale D. O. Martin, Stefanie L. Butland, Mathieu Lavallée-Adam, Diego Calzolari, Chris Kay, John R. Yates III, Michael R. Hayden

The Role of Cell Volume in the Dynamics of Seizure, Spreading Depression, and Anoxic Depolarization

Ghanim Ullah, Yina Wei, Markus A Dahlem, Martin Wechselberger, Steven J Schiff

A Bayesian Attractor Model for Perceptual Decision Making

Sebastian Bitzer, Jelle Bruineberg, Stefan J. Kiebel

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction

Jonas Paulsen, Odin Gramstad, Philippe Collas

Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data

Pengyi Yang, Xiaofeng Zheng, Vivek Jayaswal, Guang Hu, Jean Yee Hwa Yang, Raja Jothi

Irradiation of Neurons with High-Energy Charged Particles: An In Silico Modeling Approach

Murat Alp, Vipan K. Parihar, Charles L. Limoli, Francis A. Cucinotta

Evolution of Self-Organized Task Specialization in Robot Swarms

Eliseo Ferrante, Ali Emre Turgut, Edgar Duéñez-Guzmán, Marco Dorigo, Tom Wenseleers

The Force at the Tip - Modelling Tension and Proliferation in Sprouting Angiogenesis

Patrícia Santos-Oliveira, António Correia, Tiago Rodrigues, Teresa M Ribeiro-Rodrigues, Paulo Matafome, Juan Carlos Rodríguez-Manzaneque, Raquel Seiça, Henrique Girão, Rui D. M. Travasso

Dynamic Allostery of the Catabolite Activator Protein Revealed by Interatomic Forces

Maxime Louet, Christian Seifert, Ulf Hensen, Frauke Gräter