Table of Contents: January 2014

Issue Image

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.


Messages from ISCB

Building the Future of Bioinformatics through Student-Facilitated Conferencing

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

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

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


Bioinformatics Projects Supporting Life-Sciences Learning in High Schools

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


Research Articles

Robustness of DNA Repair through Collective Rate Control

Paul Verbruggen, Tim Heinemann, Erik Manders, Gesa von Bornstaedt, Roel van Driel, Thomas Höfer

De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function

Areum Han, Peter Stoilov, Anthony J. Linares, Yu Zhou, Xiang-Dong Fu, Douglas L. Black

A Division in PIN-Mediated Auxin Patterning during Organ Initiation in Grasses

Devin L. O'Connor, Adam Runions, Aaron Sluis, Jennifer Bragg, John P. Vogel, Przemyslaw Prusinkiewicz, Sarah Hake

Automated Discovery of Tissue-Targeting Enhancers and Transcription Factors from Binding Motif and Gene Function Data

Geetu Tuteja, Karen Betancourt Moreira, Tisha Chung, Jenny Chen, Aaron M. Wenger, Gill Bejerano

Global Patterns of Protein Domain Gain and Loss in Superkingdoms

Arshan Nasir, Kyung Mo Kim, Gustavo Caetano-Anollés

Modeling Within-Host Effects of Drugs on Plasmodium falciparum Transmission and Prospects for Malaria Elimination

Geoffrey L. Johnston, Peter W. Gething, Simon I. Hay, David L. Smith, David A. Fidock

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

Thibaut Jombart, Anne Cori, Xavier Didelot, Simon Cauchemez, Christophe Fraser, Neil Ferguson

Machine Learning Estimates of Natural Product Conformational Energies

Matthias Rupp, Matthias R. Bauer, Rainer Wilcken, Andreas Lange, Michael Reutlinger, Frank M. Boeckler, Gisbert Schneider

Fast Reconstruction of Compact Context-Specific Metabolic Network Models

Nikos Vlassis, Maria Pires Pacheco, Thomas Sauter

PEX5 and Ubiquitin Dynamics on Mammalian Peroxisome Membranes

Aidan I. Brown, Peter K. Kim, Andrew D. Rutenberg

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

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

Jaroslav Bendl, Jan Stourac, Ondrej Salanda, Antonin Pavelka, Eric D. Wieben, Jaroslav Zendulka, Jan Brezovsky, Jiri Damborsky

Stress and Strain Provide Positional and Directional Cues in Development

Behruz Bozorg, Pawel Krupinski, Henrik Jönsson

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

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

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

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

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