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Table of Contents: June 2006

COVER

Min protein locations in simulated filamentous E. coli

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

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.

Education

Review

Immunoinformatics Comes of Age

Bette Korber, Montiago LaBute, Karina Yusim

Research Articles

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

Assessing the Accuracy of Ancestral Protein Reconstruction Methods

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

Parametric Alignment of Drosophila Genomes

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

Ultra-Fast Evaluation of Protein Energies Directly from Sequence

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

Integrated Assessment and Prediction of Transcription Factor Binding

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

How Does Cross-Reactive Stimulation Affect the Longevity of CD8+ T Cell Memory?

Vitaly V Ganusov, Sergei S Pilyugin, Rafi Ahmed, Rustom Antia

Prioritizing Genomic Drug Targets in Pathogens: Application to Mycobacterium tuberculosis

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

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

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

Correction

Correction: Spatiotemporal Expression Control Correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana

Igor V Tetko, Georg Haberer, Stephen Rudd, Blake C Meyers, Hans-Werner Mewes, Klaus F. X Mayer