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Table of Contents

September 2015

The future is uncertain because some forthcoming events are unpredictable and also because our ability to foresee the myriad consequences of our own actions is limited. Here we studied how humans select actions under such extrinsic and intrinsic uncertainty, in view of the exponentially expanding number of prospects on a branching multivalued visual stimulus. Gepshtein et al.

Image Credit: Gepshtein et al. and Trisha Williams of Pigeon Hole Productions



You Are Not Working for Me; I Am Working with You

Florian Markowetz

How to Grow a Computational Biology Lab

Alice Carolyn McHardy

The Problem with Phi: A Critique of Integrated Information Theory

Michael A. Cerullo

Bioinformatics in Africa: The Rise of Ghana?

Thomas K. Karikari

Research Articles

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model

Naiqian Zhang, Haiyun Wang, Yun Fang, Jun Wang, Xiaoqi Zheng, X. Shirley Liu

miRTex: A Text Mining System for miRNA-Gene Relation Extraction

Gang Li, Karen E. Ross, Cecilia N. Arighi, Yifan Peng, Cathy H. Wu, K. Vijay-Shanker

Implicit Value Updating Explains Transitive Inference Performance: The Betasort Model

Greg Jensen, Fabian Muñoz, Yelda Alkan, Vincent P. Ferrera, Herbert S. Terrace

Early Characterization of the Severity and Transmissibility of Pandemic Influenza Using Clinical Episode Data from Multiple Populations

Pete Riley, Michal Ben-Nun, Jon A. Linker, Angelia A. Cost, Jose L. Sanchez, Dylan George, David P. Bacon, Steven Riley

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity

Noah Ollikainen, René M. de Jong, Tanja Kortemme

Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding

Suhani Nagpal, Satyam Tiwari, Koyeli Mapa, Lipi Thukral

Automated Identification of Core Regulatory Genes in Human Gene Regulatory Networks

Vipin Narang, Muhamad Azfar Ramli, Amit Singhal, Pavanish Kumar, Gennaro de Libero, Michael Poidinger, Christopher Monterola

Systematic Prediction of Scaffold Proteins Reveals New Design Principles in Scaffold-Mediated Signal Transduction

Jianfei Hu, Johnathan Neiswinger, Jin Zhang, Heng Zhu, Jiang Qian

The LUX Score: A Metric for Lipidome Homology

Chakravarthy Marella, Andrew E. Torda, Dominik Schwudke

An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer

Jasmine Foo, Lin L Liu, Kevin Leder, Markus Riester, Yoh Iwasa, Christoph Lengauer, Franziska Michor

A Method to Constrain Genome-Scale Models with 13C Labeling Data

Héctor García Martín, Vinay Satish Kumar, Daniel Weaver, Amit Ghosh, Victor Chubukov, Aindrila Mukhopadhyay, Adam Arkin, Jay D. Keasling

Model-Based Reasoning in Humans Becomes Automatic with Training

Marcos Economides, Zeb Kurth-Nelson, Annika Lübbert, Marc Guitart-Masip, Raymond J. Dolan

Efficient Optimization of Stimuli for Model-Based Design of Experiments to Resolve Dynamical Uncertainty

Thembi Mdluli, Gregery T. Buzzard, Ann E. Rundell

Shaping Neuronal Network Activity by Presynaptic Mechanisms

Ayal Lavi, Omri Perez, Uri Ashery

Structural Bridges through Fold Space

Hannah Edwards, Charlotte M. Deane

The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption

Stephan Köhler, Friederike Schmid, Giovanni Settanni

Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone

Alexander Ullrich, Mathias A. Böhme, Johannes Schöneberg, Harald Depner, Stephan J. Sigrist, Frank Noé

Diversity Waves in Collapse-Driven Population Dynamics

Sergei Maslov, Kim Sneppen

Prospective Optimization with Limited Resources

Joseph Snider, Dongpyo Lee, Howard Poizner, Sergei Gepshtein

Steering Evolution with Sequential Therapy to Prevent the Emergence of Bacterial Antibiotic Resistance

Daniel Nichol, Peter Jeavons, Alexander G. Fletcher, Robert A. Bonomo, Philip K. Maini, Jerome L. Paul, Robert A. Gatenby, Alexander R.A. Anderson, Jacob G. Scott

Social Feedback and the Emergence of Rank in Animal Society

Elizabeth A. Hobson, Simon DeDeo

A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

Feixiong Cheng, Chuang Liu, Chen-Ching Lin, Junfei Zhao, Peilin Jia, Wen-Hsiung Li, Zhongming Zhao

Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms

Greet De Baets, Loic Van Doorn, Frederic Rousseau, Joost Schymkowitz

Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions

Claudio Altafini, Giuseppe Facchetti

Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome

Marco Galardini, Matteo Brilli, Giulia Spini, Matteo Rossi, Bianca Roncaglia, Alessia Bani, Manuela Chiancianesi, Marco Moretto, Kristof Engelen, Giovanni Bacci, Francesco Pini, Emanuele G. Biondi, Marco Bazzicalupo, Alessio Mengoni

A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle

Elizabeth Ortiz-Gutiérrez, Karla García-Cruz, Eugenio Azpeitia, Aaron Castillo, María de la Paz Sánchez, Elena R. Álvarez-Buylla

A Self-Organising Model of Thermoregulatory Huddling

Jonathan Glancy, Roderich Groß, James V. Stone, Stuart P. Wilson

Relating Alpha Power and Phase to Population Firing and Hemodynamic Activity Using a Thalamo-cortical Neural Mass Model

Robert Becker, Stuart Knock, Petra Ritter, Viktor Jirsa

An Emerging Allee Effect Is Critical for Tumor Initiation and Persistence

Katrin Böttger, Haralambos Hatzikirou, Anja Voss-Böhme, Elisabetta Ada Cavalcanti-Adam, Miguel A. Herrero, Andreas Deutsch

Examination of the Effects of Heterogeneous Organization of RyR Clusters, Myofibrils and Mitochondria on Ca2+ Release Patterns in Cardiomyocytes

Vijay Rajagopal, Gregory Bass, Cameron G. Walker, David J. Crossman, Amorita Petzer, Anthony Hickey, Ivo Siekmann, Masahiko Hoshijima, Mark H. Ellisman, Edmund J. Crampin, Christian Soeller

Self-organization in Balanced State Networks by STDP and Homeostatic Plasticity

Felix Effenberger, Jürgen Jost, Anna Levina

ReproPhylo: An Environment for Reproducible Phylogenomics

Amir Szitenberg, Max John, Mark L. Blaxter, David H. Lunt

Explaining the Timing of Natural Scene Understanding with a Computational Model of Perceptual Categorization

Imri Sofer, Sébastien M. Crouzet, Thomas Serre

An Integrated Framework Advancing Membrane Protein Modeling and Design

Rebecca F. Alford, Julia Koehler Leman, Brian D. Weitzner, Amanda M. Duran, Drew C. Tilley, Assaf Elazar, Jeffrey J. Gray

A Theory of Cheap Control in Embodied Systems

Guido Montúfar, Keyan Ghazi-Zahedi, Nihat Ay

Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates

Jiayu Wen, Erik Ladewig, Sol Shenker, Jaaved Mohammed, Eric C. Lai

Scalability of Asynchronous Networks Is Limited by One-to-One Mapping between Effective Connectivity and Correlations

Sacha Jennifer van Albada, Moritz Helias, Markus Diesmann