Table of Contents

June 2006

Snapshot of Min protein locations in simulated filamentous (ftsZ-), wild-type and spherical (rodA-) Escherichia coli (see Fange and Elf). A stochastic reaction–diffusion model is used to account for the spatiotemporal Min oscillations in phenotypes for which a mean-field approach fails. Cytosolic proteins MinE (purple), MinDATP (green), and MinDADP( yellow) are seen in the upper part of the cells, and the membrane-bound species MinD (red) and MinDE (blue) are seen on the surface of the lower part of the cells.

Image Credit: Johan Elf and David Fange. Output from MesoRD is visualized using Matlab.


Functional Classification Using Phylogenomic Inference

Duncan Brown, Kimmen Sjölander


Immunoinformatics Comes of Age

Bette Korber, Montiago LaBute, Karina Yusim

Research Articles

The G Protein–Coupled Receptor Subset of the Chicken Genome

Malin C Lagerström, Anders R Hellström, David E Gloriam, Thomas P Larsson, Helgi B Schiöth, Robert Fredriksson

Moving Forward Moving Backward: Directional Sorting of Chemotactic Cells due to Size and Adhesion Differences

Jos Käfer, Paulien Hogeweg, Athanasius F. M Marée

Prioritizing Genomic Drug Targets in Pathogens: Application to Mycobacterium tuberculosis

Samiul Hasan, Sabine Daugelat, P. S. Srinivasa Rao, Mark Schreiber

Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses

Sergei L Kosakovsky Pond, Simon D. W Frost, Zehava Grossman, Michael B Gravenor, Douglas D Richman, Andrew J. Leigh Brown

Ultra-Fast Evaluation of Protein Energies Directly from Sequence

Gevorg Grigoryan, Fei Zhou, Steve R Lustig, Gerbrand Ceder, Dane Morgan, Amy E Keating

On Modeling HIV and T Cells In Vivo: Assessing Causal Estimators in Vaccine Trials

W. David Wick, Peter B Gilbert, Steven G Self

A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I Molecules

Bjoern Peters, Huynh-Hoa Bui, Sune Frankild, Morten Nielsen, Claus Lundegaard, Emrah Kostem, Derek Basch, Kasper Lamberth, Mikkel Harndahl, Ward Fleri, Stephen S Wilson, John Sidney, Ole Lund, Soren Buus, Alessandro Sette

Inference of Disease-Related Molecular Logic from Systems-Based Microarray Analysis

Vinay Varadan, Dimitris Anastassiou

Assessing the Accuracy of Ancestral Protein Reconstruction Methods

Paul D Williams, David D Pollock, Benjamin P Blackburne, Richard A Goldstein

Integrated Assessment and Prediction of Transcription Factor Binding

Andreas Beyer, Christopher Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, Trey Ideker

Parametric Alignment of Drosophila Genomes

Colin N Dewey, Peter M Huggins, Kevin Woods, Bernd Sturmfels, Lior Pachter

Identification and Analysis of Genes and Pseudogenes within Duplicated Regions in the Human and Mouse Genomes

Mikita Suyama, Eoghan Harrington, Peer Bork, David Torrents

Noise-Induced Min Phenotypes in E. coli

David Fange, Johan Elf