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Table of Contents: December 2005

COVER

Derivation of genome trees from comparative analyses of complete genomes

Image Credit: Genome graphic representation completed with GenomeViz software, provided by Rohit Ghai. Fractal tree obtained with the FractalTrees X software, provided by Simon Woodside. Compiled by Edouard Yeramian.
Issue Image

The composition on the cover highlights the derivation of genome trees from comparative analyses of complete genomes. The circular maps are associated with two complete Listeria genomes. Beyond pairwise comparisons, protein conservation profiles (with the binary data representations in the background) allow capture of the evolutionary histories of proteins jointly through multiple genomes. The intricacies of the resulting genome trees are reflected in the artistic view associated with a fractal tree (see Tekaia and Yeramian).

Message from ISCB

The Eighth Annual Bio-Ontologies Meeting

Phillip Lord, Robert Stevens, James A Butler, Robin McEntire

Perspective

Time to Organize the Bioinformatics Resourceome

Nicola Cannata, Emanuela Merelli, Russ B Altman

Research Articles

New Maximum Likelihood Estimators for Eukaryotic Intron Evolution

Hung D Nguyen, Maki Yoshihama, Naoya Kenmochi

Functional Alignment of Regulatory Networks: A Study of Temperate Phages

Ala Trusina, Kim Sneppen, Ian B Dodd, Keith E Shearwin, J. Barry Egan

The Activity Reaction Core and Plasticity of Metabolic Networks

Eivind Almaas, Zoltán N Oltvai, Albert-László Barabási

Comparing the Dictyostelium and Entamoeba Genomes Reveals an Ancient Split in the Conosa Lineage

Jie Song, Qikai Xu, Rolf Olsen, William F Loomis, Gad Shaulsky, Adam Kuspa, Richard Sucgang

Genome Trees from Conservation Profiles

Fredj Tekaia, Edouard Yeramian

PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny

Rahul Siddharthan, Eric D Siggia, Erik van Nimwegen