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Table of Contents: October 2005

COVER

Representation of SIFTER protein molecular function annotation method

Image Credit: Designed by Steven Chan (http://www.stevenchan.us). Created in Blender (http://www.blender.org) and composited in Adobe Photoshop. Phylogeny image by ATV, created by C. Zmasek (http://www.phylogenomics.us/atv)
Issue Image

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).

Editorial

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Research Articles

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

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

Karthik Raman, Preethi Rajagopalan, Nagasuma Chandra

Protein Molecular Function Prediction by Bayesian Phylogenomics

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