Table of Contents: October 2005

Protein molecular function annotation methods can incorporate evolutionary information, such as the phylogenic tree shown here, to improve their performance. This figure represents the predictions of one such method, SIFTER, for proteins in the adenosine-5-monophosphate/adenosine deaminase family, including confidence values for the predicted functional annotations (see Engelhardt et al).

Image Credit: Designed by Steven Chan ( Created in Blender ( and composited in Adobe Photoshop. Phylogeny image by ATV, created by C. Zmasek (


Ten Simple Rules for Getting Published

Philip E Bourne

Message from ISCB

The ISCB: Growing and Evolving in Step with Science

Michael Gribskov

Research Articles

Protein Molecular Function Prediction by Bayesian Phylogenomics

Barbara E Engelhardt, Michael I Jordan, Kathryn E Muratore, Steven E Brenner

Flux Balance Analysis of Mycolic Acid Pathway: Targets for Anti-Tubercular Drugs

Karthik Raman, Preethi Rajagopalan, Nagasuma Chandra

Structural Evolution of the Protein Kinase–Like Superfamily

Eric D Scheeff, Philip E Bourne

SNPdetector: A Software Tool for Sensitive and Accurate SNP Detection

Jinghui Zhang, David A Wheeler, Imtiaz Yakub, Sharon Wei, Raman Sood, William Rowe, Paul P Liu, Richard A Gibbs, Kenneth H Buetow

Ultrasensitization: Switch-Like Regulation of Cellular Signaling by Transcriptional Induction

Stefan Legewie, Nils Blüthgen, Reinhold Schäfer, Hanspeter Herzel

Dissimilatory Metabolism of Nitrogen Oxides in Bacteria: Comparative Reconstruction of Transcriptional Networks

Dmitry A Rodionov, Inna L Dubchak, Adam P Arkin, Eric J Alm, Mikhail S Gelfand