Table of Contents: February 2007

Snapshot from the end of a 100-ns simulation of a three-component lipid bilayer: POPC molecules are shown in gray, PSM in orange, CHOL in yellow, and water in cyan. The ratio of different lipids here is POPC:PSM:CHOL = 1:1:1 (see Niemelä et al).

Image Credit: Cover design by Perttu Niemelä. Created with the VMD and Raster3D software packages.


From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research

Jomol P Mathew, Barry S Taylor, Gary D Bader, Saiju Pyarajan, Marco Antoniotti, Arul M Chinnaiyan, Chris Sander, Steven J Burakoff, Bud Mishra

Research Articles

Robustness Can Evolve Gradually in Complex Regulatory Gene Networks with Varying Topology

Stefano Ciliberti, Olivier C Martin, Andreas Wagner

Automatic Extraction of Protein Point Mutations Using a Graph Bigram Association

Lawrence C Lee, Florence Horn, Fred E Cohen

Efficiency and Cost of Economical Brain Functional Networks

Sophie Achard, Ed Bullmore

Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning

Gunnar Rätsch, Sören Sonnenburg, Jagan Srinivasan, Hanh Witte, Klaus-R Müller, Ralf-J Sommer, Bernhard Schölkopf

Deprotonation by Dehydration: The Origin of Ammonium Sensing in the AmtB Channel

David L Bostick, Charles L. Brooks III

Functional Impact of Missense Variants in BRCA1 Predicted by Supervised Learning

Rachel Karchin, Alvaro N. A Monteiro, Sean V Tavtigian, Marcelo A Carvalho, Andrej Sali

Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics

Philippe Lemey, Sergei L Kosakovsky Pond, Alexei J Drummond, Oliver G Pybus, Beth Shapiro, Helena Barroso, Nuno Taveira, Andrew Rambaut

Unsupervised Learning of Visual Features through Spike Timing Dependent Plasticity

Timothée Masquelier, Simon J Thorpe

Repressor Dimerization in the Zebrafish Somitogenesis Clock

Olivier Cinquin

Assessing the Nature of Lipid Raft Membranes

Perttu S Niemelä, Samuli Ollila, Marja T Hyvönen, Mikko Karttunen, Ilpo Vattulainen


Correction: Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays

Rameen Beroukhim, Ming Lin, Yuhyun Park, Ke Hao, Xiaojun Zhao, Levi A Garraway, Edward A Fox, Ephraim P Hochberg, Ingo K Mellinghoff, Matthias D Hofer, Aurelien Descazeaud, Mark A Rubin, Matthew Meyerson, Wing Hung Wong, William R Sellers, Cheng Li

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  1. Inferring Loss-of-Heterozygosity from Unpaired Tumors Using High-Density Oligonucleotide SNP Arrays

Correction: The Genome: An Outsider's View

Carl Zimmer

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  1. The Genome: An Outsider's View