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Table of Contents

August 2015

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.

Image Credit: 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

Inflow/Outflow Boundary Conditions for Particle-Based Blood Flow Simulations: Application to Arterial Bifurcations and Trees

Kirill Lykov, Xuejin Li, Huan Lei, Igor V. Pivkin, George Em Karniadakis

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

Task-Driven Activity Reduces the Cortical Activity Space of the Brain: Experiment and Whole-Brain Modeling

Adrián Ponce-Alvarez, Biyu J. He, Patric Hagmann, Gustavo Deco

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

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

Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks

Mitchell G Newberry, Daniel B Ennis, Van M Savage

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

Mechanism for Collective Cell Alignment in Myxococcus xanthus Bacteria

Rajesh Balagam, Oleg A. Igoshin

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

Tipping the Scale from Disorder to Alpha-helix: Folding of Amphiphilic Peptides in the Presence of Macroscopic and Molecular Interfaces

Cahit Dalgicdir, Christoph Globisch, Christine Peter, Mehmet Sayar

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

Impact of School Cycles and Environmental Forcing on the Timing of Pandemic Influenza Activity in Mexican States, May-December 2009

James Tamerius, Cécile Viboud, Jeffrey Shaman, Gerardo Chowell

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

Alireza Alemi, Carlo Baldassi, Nicolas Brunel, Riccardo Zecchina

Self-Organization of Microcircuits in Networks of Spiking Neurons with Plastic Synapses

Gabriel Koch Ocker, Ashok Litwin-Kumar, Brent Doiron

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

The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans

Deborah A. Striegel, Manami Hara, Vipul Periwal

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

Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures

Brinda Vallat, Carlos Madrid-Aliste, Andras Fiser

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

Related Articles

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