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Table of Contents

June 2016

Microbes can use self-produced molecules to coordinate their actions and perform collective tasks. We present a mathematical model to describe the mechanism driving social motility in the gram-negative bacterium M. xanthus. Our model, which was confirmed by long-term colony expansion experiments, reveals that exopolysaccharide production allows the cells to move collectively across surfaces as a coherent group. Expansion of a M. xanthus colony incubated on a nutrient agar surface for 4 days at 32°C is shown in this stereo-microscope image. Patra et al.

Image Credit: Kimberley Kissoon and Heidi B. Kaplan

Editorials

Ten Simple Rules for Effective Statistical Practice

Robert E. Kass, Brian S. Caffo, Marie Davidian, Xiao-Li Meng, Bin Yu, Nancy Reid

Message from ISCB

Program Bytes: Satellite Meetings, SIGs, and AKEs at ISMB 2016

Christiana N. Fogg, Diane E. Kovats

Education Articles

Training in High-Throughput Sequencing: Common Guidelines to Enable Material Sharing, Dissemination, and Reusability

Bastian Schiffthaler, Myrto Kostadima, NGS Trainer Consortium, Nicolas Delhomme, Gabriella Rustici

Continuing Education Workshops in Bioinformatics Positively Impact Research and Careers

Michelle D. Brazas, B. F. Francis Ouellette

An Introduction to Programming for Bioscientists: A Python-Based Primer

Berk Ekmekci, Charles E. McAnany, Cameron Mura

Perspective

The Context-Dependence of Mutations: A Linkage of Formalisms

Frank J. Poelwijk, Vinod Krishna, Rama Ranganathan

Review

Revealing Atomic-Level Mechanisms of Protein Allostery with Molecular Dynamics Simulations

Samuel Hertig, Naomi R. Latorraca, Ron O. Dror

Research Articles

Inferring Strain Mixture within Clinical Plasmodium falciparum Isolates from Genomic Sequence Data

John D. O’Brien, Zamin Iqbal, Jason Wendler, Lucas Amenga-Etego

Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks

Anthony Szedlak, Nicholas Smith, Li Liu, Giovanni Paternostro, Carlo Piermarocchi

Colony Expansion of Socially Motile Myxococcus xanthus Cells Is Driven by Growth, Motility, and Exopolysaccharide Production

Pintu Patra, Kimberley Kissoon, Isabel Cornejo, Heidi B. Kaplan, Oleg A. Igoshin

Constrained Allocation Flux Balance Analysis

Matteo Mori, Terence Hwa, Olivier C. Martin, Andrea De Martino, Enzo Marinari

Rare Variants Association Analysis in Large-Scale Sequencing Studies at the Single Locus Level

Xinge Jessie Jeng, Zhongyin John Daye, Wenbin Lu, Jung-Ying Tzeng

A Crowdsourcing Approach to Developing and Assessing Prediction Algorithms for AML Prognosis

David P. Noren, Byron L. Long, Raquel Norel, Kahn Rrhissorrakrai, Kenneth Hess, Chenyue Wendy Hu, Alex J. Bisberg, Andre Schultz, Erik Engquist, Li Liu, Xihui Lin, Gregory M. Chen, Honglei Xie, Geoffrey A. M. Hunter, Paul C. Boutros, Oleg Stepanov, DREAM 9 AML-OPC Consortium, Thea Norman, Stephen H. Friend, Gustavo Stolovitzky, Steven Kornblau, Amina A. Qutub

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

Edward J. O’Brien, Jose Utrilla, Bernhard O. Palsson

Model Constrained by Visual Hierarchy Improves Prediction of Neural Responses to Natural Scenes

Ján Antolík, Sonja B. Hofer, James A. Bednar, Thomas D. Mrsic-Flogel

Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering

Elisa Boari de Lima, Wagner Meira Júnior, Raquel Cardoso de Melo-Minardi

How to Estimate Epidemic Risk from Incomplete Contact Diaries Data?

Rossana Mastrandrea, Alain Barrat

Prospective Coding by Spiking Neurons

Johanni Brea, Alexisz Tamás Gaál, Robert Urbanczik, Walter Senn

Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments

Olof Leimar, Sasha R. X. Dall, Peter Hammerstein, John M. McNamara

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

Daniel L. Parton, Patrick B. Grinaway, Sonya M. Hanson, Kyle A. Beauchamp, John D. Chodera

QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks

Asa Thibodeau, Eladio J. Márquez, Oscar Luo, Yijun Ruan, Francesca Menghi, Dong-Guk Shin, Michael L. Stitzel, Paola Vera-Licona, Duygu Ucar

Electrophysiology of Heart Failure Using a Rabbit Model: From the Failing Myocyte to Ventricular Fibrillation

Aditya V. S. Ponnaluri, Luigi E. Perotti, Michael Liu, Zhilin Qu, James N. Weiss, Daniel B. Ennis, William S. Klug, Alan Garfinkel

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

Raquel Bromberg, Nick V. Grishin, Zbyszek Otwinowski

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

Andra Waagmeester, Martina Kutmon, Anders Riutta, Ryan Miller, Egon L. Willighagen, Chris T. Evelo, Alexander R. Pico

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases

David Lee, Sayoni Das, Natalie L. Dawson, Dragana Dobrijevic, John Ward, Christine Orengo

A Mathematical Model of Neonatal Rat Atrial Monolayers with Constitutively Active Acetylcholine-Mediated K+ Current

Rupamanjari Majumder, Wanchana Jangsangthong, Iolanda Feola, Dirk L. Ypey, Daniël A. Pijnappels, Alexander V. Panfilov

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

Daniel H. Huson, Sina Beier, Isabell Flade, Anna Górska, Mohamed El-Hadidi, Suparna Mitra, Hans-Joachim Ruscheweyh, Rewati Tappu

Filopodial-Tension Model of Convergent-Extension of Tissues

Julio M. Belmonte, Maciej H. Swat, James A. Glazier

The Computational Development of Reinforcement Learning during Adolescence

Stefano Palminteri, Emma J. Kilford, Giorgio Coricelli, Sarah-Jayne Blakemore

Roles for Coincidence Detection in Coding Amplitude-Modulated Sounds

Go Ashida, Jutta Kretzberg, Daniel J. Tollin

Pervasive Selection for Cooperative Cross-Feeding in Bacterial Communities

Sebastian Germerodt, Katrin Bohl, Anja Lück, Samay Pande, Anja Schröter, Christoph Kaleta, Stefan Schuster, Christian Kost

GRAbB: Selective Assembly of Genomic Regions, a New Niche for Genomic Research

Balázs Brankovics, Hao Zhang, Anne D. van Diepeningen, Theo A. J. van der Lee, Cees Waalwijk, G. Sybren de Hoog

Learning Universal Computations with Spikes

Dominik Thalmeier, Marvin Uhlmann, Hilbert J. Kappen, Raoul-Martin Memmesheimer

Predicting Achievable Fundamental Frequency Ranges in Vocalization Across Species

Ingo Titze, Tobias Riede, Ted Mau

Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis

Rebeca Campos-Sánchez, Marzia A. Cremona, Alessia Pini, Francesca Chiaromonte, Kateryna D. Makova

Mechanistic Mathematical Modeling Tests Hypotheses of the Neurovascular Coupling in fMRI

Karin Lundengård, Gunnar Cedersund, Sebastian Sten, Felix Leong, Alexander Smedberg, Fredrik Elinder, Maria Engström

Graded, Dynamically Routable Information Processing with Synfire-Gated Synfire Chains

Zhuo Wang, Andrew T. Sornborger, Louis Tao

Formal Models of the Network Co-occurrence Underlying Mental Operations

Danilo Bzdok, Gaël Varoquaux, Olivier Grisel, Michael Eickenberg, Cyril Poupon, Bertrand Thirion

Adaptive Spike Threshold Enables Robust and Temporally Precise Neuronal Encoding

Chao Huang, Andrey Resnik, Tansu Celikel, Bernhard Englitz

Progression of Diabetic Capillary Occlusion: A Model

Xiao Fu, John Scott Gens, James A. Glazier, Stephen A. Burns, Thomas J. Gast

Phylogenetic Analysis Reveals That ERVs "Die Young" but HERV-H Is Unusually Conserved

Patrick Gemmell, Jotun Hein, Aris Katzourakis

Large Scale Chromosome Folding Is Stable against Local Changes in Chromatin Structure

Ana-Maria Florescu, Pierre Therizols, Angelo Rosa

Reservoir Computing Properties of Neural Dynamics in Prefrontal Cortex

Pierre Enel, Emmanuel Procyk, René Quilodran, Peter Ford Dominey

Theory and Experimental Validation of a Spatio-temporal Model of Chemotherapy Transport to Enhance Tumor Cell Kill

Zhihui Wang, Romica Kerketta, Yao-Li Chuang, Prashant Dogra, Joseph D. Butner, Terisse A. Brocato, Armin Day, Rong Xu, Haifa Shen, Eman Simbawa, A. S. AL-Fhaid, S. R. Mahmoud, Steven A. Curley, Mauro Ferrari, Eugene J. Koay, Vittorio Cristini

The Evolutionary Origins of Hierarchy

Henok Mengistu, Joost Huizinga, Jean-Baptiste Mouret, Jeff Clune

Computing Average Passive Forces in Sarcomeres in Length-Ramp Simulations

Gudrun Schappacher-Tilp, Timothy Leonard, Gertrud Desch, Walter Herzog

Towards Identifying and Reducing the Bias of Disease Information Extracted from Search Engine Data

Da-Cang Huang, Jin-Feng Wang, Ji-Xia Huang, Daniel Z. Sui, Hong-Yan Zhang, Mao-Gui Hu, Cheng-Dong Xu

Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space

Yu Toyoshima, Terumasa Tokunaga, Osamu Hirose, Manami Kanamori, Takayuki Teramoto, Moon Sun Jang, Sayuri Kuge, Takeshi Ishihara, Ryo Yoshida, Yuichi Iino

FamPipe: An Automatic Analysis Pipeline for Analyzing Sequencing Data in Families for Disease Studies

Ren-Hua Chung, Wei-Yun Tsai, Chen-Yu Kang, Po-Ju Yao, Hui-Ju Tsai, Chia-Hsiang Chen

The Role of Adaptation in Bacterial Speed Races

Jérôme Wong-Ng, Anna Melbinger, Antonio Celani, Massimo Vergassola

Evolution-Based Functional Decomposition of Proteins

Olivier Rivoire, Kimberly A. Reynolds, Rama Ranganathan

Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design

Arun Chandramohan, Srinath Krishnamurthy, Andreas Larsson, Paer Nordlund, Anna Jansson, Ganesh S. Anand

Non-degradative Ubiquitination of Protein Kinases

K. Aurelia Ball, Jeffrey R. Johnson, Mary K. Lewinski, John Guatelli, Erik Verschueren, Nevan J. Krogan, Matthew P. Jacobson

EGFR Signal-Network Reconstruction Demonstrates Metabolic Crosstalk in EMT

Kumari Sonal Choudhary, Neha Rohatgi, Skarphedinn Halldorsson, Eirikur Briem, Thorarinn Gudjonsson, Steinn Gudmundsson, Ottar Rolfsson

Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches

Tobias Sikosek, Heinrich Krobath, Hue Sun Chan

Validated Predictions of Metabolic Energy Consumption for Submaximal Effort Movement

George A. Tsianos, Lisa N. MacFadden

Stochastic Simulation of Biomolecular Networks in Dynamic Environments

Margaritis Voliotis, Philipp Thomas, Ramon Grima, Clive G. Bowsher