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Table of Contents

January 2014

The image shows a group of dogs equipped with GPS around the owner during a free walk. We obtained high-resolution spatio-temporal GPS trajectory data from five Vizslas and a mixed breed dog belonging to the same household and their owner during fourteen walks, and identified several features of the dogs' paths (e.g., running speed or distance from the owner) that are characteristic of a given dog. A detailed analysis of motion patterns quantified leading-following interactions between pairs of dogs that run loops jointly. We found that the network constructed from the leader-follower relations was hierarchical, and the dogs' positions in the network correlated with their age, and their dominance rank order, trainability, controllability, and aggression derived from questionnaires. See Ákos et al.

Image Credit: Zsuzsa Ákos & Máté Nagy

Editorials

Ten Simple Rules for Writing Research Papers

Weixiong Zhang

Messages from ISCB

The Making of the Women in Biology Forum (WiB) at Bioclues

Reeta Rani Singhania, Dhatri Madduru, Pranathi Pappu, Sameera Panchangam, Renuka Suravajhala, Mohanalatha Chandrasekharan

Building the Future of Bioinformatics through Student-Facilitated Conferencing

Kavisha Ramdayal, Miranda D. Stobbe, Tarun Mishra, Magali Michaut

Education

Bioinformatics Projects Supporting Life-Sciences Learning in High Schools

Isabel Marques, Paulo Almeida, Renato Alves, Maria João Dias, Ana Godinho, José B. Pereira-Leal

Perspective

Current Practice in Software Development for Computational Neuroscience and How to Improve It

Marc-Oliver Gewaltig, Robert Cannon

Research Articles

A Multi-Scale Model of Hepcidin Promoter Regulation Reveals Factors Controlling Systemic Iron Homeostasis

Guillem Casanovas, Anashua Banerji, Flavia d'Alessio, Martina U. Muckenthaler, Stefan Legewie

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks

Axel von Kamp, Steffen Klamt

Encoding of Natural Sounds at Multiple Spectral and Temporal Resolutions in the Human Auditory Cortex

Roberta Santoro, Michelle Moerel, Federico De Martino, Rainer Goebel, Kamil Ugurbil, Essa Yacoub, Elia Formisano

Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting

Aaron C. Miller, Linnea A. Polgreen, Philip M. Polgreen

Environmental Influence on the Evolution of Morphological Complexity in Machines

Joshua E. Auerbach, Josh C. Bongard

Population Decoding in Rat Barrel Cortex: Optimizing the Linear Readout of Correlated Population Responses

Mehdi Adibi, James S. McDonald, Colin W. G. Clifford, Ehsan Arabzadeh

Searching for Collective Behavior in a Large Network of Sensory Neurons

Gašper Tkačik, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, Michael J. Berry II

Task-Specific Response Strategy Selection on the Basis of Recent Training Experience

Jacqueline M. Fulvio, C. Shawn Green, Paul R. Schrater

The Free Energy Landscape of Dimerization of a Membrane Protein, NanC

Thomas A. Dunton, Joseph E. Goose, David J. Gavaghan, Mark S. P. Sansom, James M. Osborne

Stress and Strain Provide Positional and Directional Cues in Development

Behruz Bozorg, Pawel Krupinski, Henrik Jönsson

Interference and Shaping in Sensorimotor Adaptations with Rewards

Ran Darshan, Arthur Leblois, David Hansel

Communication Efficiency and Congestion of Signal Traffic in Large-Scale Brain Networks

Bratislav Mišić, Olaf Sporns, Anthony R. McIntosh

Linkage of Viral Sequences among HIV-Infected Village Residents in Botswana: Estimation of Linkage Rates in the Presence of Missing Data

Nicole Bohme Carnegie, Rui Wang, Vladimir Novitsky, Victor De Gruttola

Microenvironmental Variables Must Influence Intrinsic Phenotypic Parameters of Cancer Stem Cells to Affect Tumourigenicity

Jacob G. Scott, Anita B. Hjelmeland, Prakash Chinnaiyan, Alexander R. A. Anderson, David Basanta

The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity

Sean T. Kelly, Jens Kremkow, Jianzhong Jin, Yushi Wang, Qi Wang, Jose-Manuel Alonso, Garrett B. Stanley

The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics

Moritz Helias, Tom Tetzlaff, Markus Diesmann

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

Nikos Vlassis, Maria Pires Pacheco, Thomas Sauter

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Leadership and Path Characteristics during Walks Are Linked to Dominance Order and Individual Traits in Dogs

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