Table of Contents

February 2016

Most bacteria live in colonies, where they often express different cell types. The ecological significance of these cell types and their evolutionary origin are often unknown. Here, we study the evolution of cell differentiation in the context of surface colonization. We particularly focus on the evolution of a 'sticky' cell type that is required for surface attachment, but is costly to express. van Gestel et al.

Image Credit: van Gestel et al.


Ten Simple Rules for Selecting a Bio-ontology

James Malone, Robert Stevens, Simon Jupp, Tom Hancocks, Helen Parkinson, Cath Brooksbank

Message from ISCB

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

Nomi L. Harris, Peter J. A. Cock, Hilmar Lapp, Brad Chapman, Rob Davey, Christopher Fields, Karsten Hokamp, Monica Munoz-Torres


Practical Approaches for Detecting Selection in Microbial Genomes

Jessica Hedge, Daniel J. Wilson


The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt

Nicola J. Mulder, Alan Christoffels, Tulio de Oliveira, Junaid Gamieldien, Scott Hazelhurst, Fourie Joubert, Judit Kumuthini, Ché S. Pillay, Jacky L. Snoep, Özlem Tastan Bishop, Nicki Tiffin

Computational Cancer Biology: An Evolutionary Perspective

Niko Beerenwinkel, Chris D. Greenman, Jens Lagergren

Research Articles

Oligomers of Heat-Shock Proteins: Structures That Don’t Imply Function

William M. Jacobs, Tuomas P. J. Knowles, Daan Frenkel

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers

Yasin Şenbabaoğlu, Selçuk Onur Sümer, Francisco Sánchez-Vega, Debra Bemis, Giovanni Ciriello, Nikolaus Schultz, Chris Sander

Evolution of Cooperation in Social Dilemmas on Complex Networks

Swami Iyer, Timothy Killingback

Feedbacks, Bifurcations, and Cell Fate Decision-Making in the p53 System

Beata Hat, Marek Kochańczyk, Marta N. Bogdał, Tomasz Lipniacki

Training Excitatory-Inhibitory Recurrent Neural Networks for Cognitive Tasks: A Simple and Flexible Framework

H. Francis Song, Guangyu R. Yang, Xiao-Jing Wang

A Sensory-Driven Trade-Off between Coordinated Motion in Social Prey and a Predator’s Visual Confusion

Bertrand H. Lemasson, Colby J. Tanner, Eric Dimperio

Cortical Resonance Frequencies Emerge from Network Size and Connectivity

Caroline A. Lea-Carnall, Marcelo A. Montemurro, Nelson J. Trujillo-Barreto, Laura M. Parkes, Wael El-Deredy

Enhanced Sensitivity to Rapid Input Fluctuations by Nonlinear Threshold Dynamics in Neocortical Pyramidal Neurons

Skander Mensi, Olivier Hagens, Wulfram Gerstner, Christian Pozzorini

Control of βAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons

Andrew Chay, Ilaria Zamparo, Andreas Koschinski, Manuela Zaccolo, Kim T. Blackwell

Non-monotonic Response to Monotonic Stimulus: Regulation of Glyoxylate Shunt Gene-Expression Dynamics in Mycobacterium tuberculosis

Joao A. Ascensao, Pratik Datta, Baris Hancioglu, Eduardo Sontag, Maria L. Gennaro, Oleg A. Igoshin

Model-Driven Understanding of Palmitoylation Dynamics: Regulated Acylation of the Endoplasmic Reticulum Chaperone Calnexin

Tiziano Dallavilla, Laurence Abrami, Patrick A. Sandoz, Georgios Savoglidis, Vassily Hatzimanikatis, F. Gisou van der Goot

Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles

Jordi van Gestel, Martin A. Nowak

BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data

Juntao Liu, Guojun Li, Zheng Chang, Ting Yu, Bingqiang Liu, Rick McMullen, Pengyin Chen, Xiuzhen Huang

Quantifying Transmission Investment in Malaria Parasites

Megan A. Greischar, Nicole Mideo, Andrew F. Read, Ottar N. Bjørnstad

Developing a Physiologically-Based Pharmacokinetic Model Knowledgebase in Support of Provisional Model Construction

Jingtao Lu, Michael-Rock Goldsmith, Christopher M. Grulke, Daniel T. Chang, Raina D. Brooks, Jeremy A. Leonard, Martin B. Phillips, Ethan D. Hypes, Matthew J. Fair, Rogelio Tornero-Velez, Jeffre Johnson, Curtis C. Dary, Yu-Mei Tan

Structural and Functional Characterization of a Caenorhabditis elegans Genetic Interaction Network within Pathways

Benjamin Boucher, Anna Y. Lee, Michael Hallett, Sarah Jenna

FastGGM: An Efficient Algorithm for the Inference of Gaussian Graphical Model in Biological Networks

Ting Wang, Zhao Ren, Ying Ding, Zhou Fang, Zhe Sun, Matthew L. MacDonald, Robert A. Sweet, Jieru Wang, Wei Chen

Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction

Yong Liu, Min Wu, Chunyan Miao, Peilin Zhao, Xiao-Li Li

Inferring Growth Control Mechanisms in Growing Multi-cellular Spheroids of NSCLC Cells from Spatial-Temporal Image Data

Nick Jagiella, Benedikt Müller, Margareta Müller, Irene E. Vignon-Clementel, Dirk Drasdo

Non-monotonic Temporal-Weighting Indicates a Dynamically Modulated Evidence-Integration Mechanism

Zohar Z. Bronfman, Noam Brezis, Marius Usher

Using an Insect Mushroom Body Circuit to Encode Route Memory in Complex Natural Environments

Paul Ardin, Fei Peng, Michael Mangan, Konstantinos Lagogiannis, Barbara Webb

On the Origins and Control of Community Types in the Human Microbiome

Travis E. Gibson, Amir Bashan, Hong-Tai Cao, Scott T. Weiss, Yang-Yu Liu

Radial Frequency Analysis of Contour Shapes in the Visual Cortex

Viljami R. Salmela, Linda Henriksson, Simo Vanni

Muscle Synergies Heavily Influence the Neural Control of Arm Endpoint Stiffness and Energy Consumption

Joshua M. Inouye, Francisco J. Valero-Cuevas

What Population Reveals about Individual Cell Identity: Single-Cell Parameter Estimation of Models of Gene Expression in Yeast

Artémis Llamosi, Andres M. Gonzalez-Vargas, Cristian Versari, Eugenio Cinquemani, Giancarlo Ferrari-Trecate, Pascal Hersen, Gregory Batt

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

Rory M. Donovan, Jose-Juan Tapia, Devin P. Sullivan, James R. Faeder, Robert F. Murphy, Markus Dittrich, Daniel M. Zuckerman

Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns

Benjamin D. Dalziel, Ottar N. Bjørnstad, Willem G. van Panhuis, Donald S. Burke, C. Jessica E. Metcalf, Bryan T. Grenfell

Ensemble Tractography

Hiromasa Takemura, Cesar F. Caiafa, Brian A. Wandell, Franco Pestilli

Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories

Harendra Guturu, Sandeep Chinchali, Shoa L. Clarke, Gill Bejerano

MicroRNAs Form Triplexes with Double Stranded DNA at Sequence-Specific Binding Sites; a Eukaryotic Mechanism via which microRNAs Could Directly Alter Gene Expression

Steven W. Paugh, David R. Coss, Ju Bao, Lucas T. Laudermilk, Christy R. Grace, Antonio M. Ferreira, M. Brett Waddell, Granger Ridout, Deanna Naeve, Michael Leuze, Philip F. LoCascio, John C. Panetta, Mark R. Wilkinson, Ching-Hon Pui, Clayton W. Naeve, Edward C. Uberbacher, Erik J. Bonten, William E. Evans

Somato-dendritic Synaptic Plasticity and Error-backpropagation in Active Dendrites

Mathieu Schiess, Robert Urbanczik, Walter Senn

Molecular Mechanisms of Glutamine Synthetase Mutations that Lead to Clinically Relevant Pathologies

Benedikt Frieg, Boris Görg, Nadine Homeyer, Verena Keitel, Dieter Häussinger, Holger Gohlke

Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia

Javier Macia, Romilde Manzoni, Núria Conde, Arturo Urrios, Eulàlia de Nadal, Ricard Solé, Francesc Posas

Recovery of Dynamics and Function in Spiking Neural Networks with Closed-Loop Control

Ioannis Vlachos, Taşkin Deniz, Ad Aertsen, Arvind Kumar

Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection

Victor Garcia, Marcus W. Feldman, Roland R. Regoes

Food Web Assembly Rules for Generalized Lotka-Volterra Equations

Jan O. Haerter, Namiko Mitarai, Kim Sneppen

Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution

Ivana Bozic, Jeffrey M. Gerold, Martin A. Nowak

PSAMM: A Portable System for the Analysis of Metabolic Models

Jon Lund Steffensen, Keith Dufault-Thompson, Ying Zhang

Kernel Architecture of the Genetic Circuitry of the Arabidopsis Circadian System

Mathias Foo, David E. Somers, Pan-Jun Kim