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Table of Contents: January 2010

COVER

The checkerboard strategy.

Image Credit: Gur Yaari (Yale University)
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Many experiments suggest that the sustainability of an ecosystem depends on its spatial structure; when a local subpopulation goes extinct the empty habitat patch is "rescued" by immigrants from nearby patches. Trying to protect endangered species via the construction of conservation corridors, the engineer faces a Goldilocks problem: weak migration does not allow for the rescue of empty patches; strong migration leads to spatial coherence and global extinction. In this work, the authors show that maximum sustainability is achieved when the migration rate is tuned to the value that yields a checkerboard spatial pattern (see Ben Zion et al., doi:10.1371/journal.pcbi.1000643).

Messages from ISCB

Live Coverage of Intelligent Systems for Molecular Biology/European Conference on Computational Biology (ISMB/ECCB) 2009

Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider

Perspective

Live Coverage of Scientific Conferences Using Web Technologies

Allyson L. Lister, Ruchira S. Datta, Oliver Hofmann, Roland Krause, Michael Kuhn, Bettina Roth, Reinhard Schneider

Research Articles

Modeling Magnification and Anisotropy in the Primate Foveal Confluence

Mark M. Schira, Christopher W. Tyler, Branka Spehar, Michael Breakspear

Functional Characterization of Transcription Factor Motifs Using Cross-species Comparison across Large Evolutionary Distances

Jaebum Kim, Ryan Cunningham, Brian James, Stefan Wyder, Joshua D. Gibson, Oliver Niehuis, Evgeny M. Zdobnov, Hugh M. Robertson, Gene E. Robinson, John H. Werren, Saurabh Sinha

FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model

Dennis L. Chao, M. Elizabeth Halloran, Valerie J. Obenchain, Ira M. Longini Jr

A Reaction-Diffusion Model of ROS-Induced ROS Release in a Mitochondrial Network

Lufang Zhou, Miguel A. Aon, Tabish Almas, Sonia Cortassa, Raimond L. Winslow, Brian O'Rourke

Acute Effects of Sex Steroid Hormones on Susceptibility to Cardiac Arrhythmias: A Simulation Study

Pei-Chi Yang, Junko Kurokawa, Tetsushi Furukawa, Colleen E. Clancy

Protein Interaction Networks—More Than Mere Modules

Stefan Pinkert, Jörg Schultz, Jörg Reichardt

Automatic Assignment of EC Numbers

Volker Egelhofer, Ida Schomburg, Dietmar Schomburg

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

Isabella Daidone, Hannes Neuweiler, Sören Doose, Markus Sauer, Jeremy C. Smith

Quantitative Modeling of GRK-Mediated β2AR Regulation

Sharat J. Vayttaden, Jacqueline Friedman, Tuan M. Tran, Thomas C. Rich, Carmen W. Dessauer, Richard B. Clark

A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology

Jacob D. Durrant, Rommie E. Amaro, Lei Xie, Michael D. Urbaniak, Michael A. J. Ferguson, Antti Haapalainen, Zhijun Chen, Anne Marie Di Guilmi, Frank Wunder, Philip E. Bourne, J. Andrew McCammon

How Synchronization Protects from Noise

Nicolas Tabareau, Jean-Jacques Slotine, Quang-Cuong Pham

Associating Genes and Protein Complexes with Disease via Network Propagation

Oron Vanunu, Oded Magger, Eytan Ruppin, Tomer Shlomi, Roded Sharan

Network-Free Inference of Knockout Effects in Yeast

Tal Peleg, Nir Yosef, Eytan Ruppin, Roded Sharan

Identification of Networks of Co-Occurring, Tumor-Related DNA Copy Number Changes Using a Genome-Wide Scoring Approach

Christiaan Klijn, Jan Bot, David J. Adams, Marcel Reinders, Lodewyk Wessels, Jos Jonkers

Modeling Mitochondrial Bioenergetics with Integrated Volume Dynamics

Jason N. Bazil, Gregery T. Buzzard, Ann E. Rundell