This is NCBI's Computational Biology Branch (CBB) web site, describing some of the studies of complete microbial genomes performed by Michael Y. Galperin (CV, publications, short bio) in the Eugene Koonin's research group.
The key results include:

• Clusters of Orthologous Groups (COGs)
• Recently revised COG names
• Analogous enzymes
• Census of bacterial signal transduction proteins
• Census of bacterial response regulators

References

1. The book Sequence - Evolution - Function. Computational Approaches in Comparative Genomics by E. V. Koonin and M. Y. Galperin, published in October 2002 by Kluwer Academic Publishers, Boston. The full text of the book is now freely available on the NCBI's Bookshelf.

Some relevant papers (click here for the complete list):

Genome annotation

1. Tatusov R.L., Galperin M.Y., Natale D.A. and Koonin E.V. (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28: 33-36. Abstract. Full text (PDF).

2. Galperin M.Y. and Koonin E.V. (2000) Who's your neighbor? New computational approaches for functional genomics. Nature Biotech. 18: 609-613. Abstract. Request reprint.

3. Galperin M.Y. and Koonin E.V. (2004) 'Conserved hypothetical' proteins: prioritization of targets for experimental study. Nucleic Acids Res. 32: 5452-5463. Abstract. Full text (HTML) Full text (PDF).

4. Galperin M.Y., Moroz O.V., Wilson K.S. and Murzin A.G. (2006) House cleaning, a part of good housekeeping. Mol. Microbiol. 59: 5-19. Abstract. Full text (HTML). Full text (PDF).

Evolution

1. Mulkidjanian A.Y., Cherepanov D.A. and Galperin M.Y. (2003) Survival of the fittest before the beginning of life: selection of the first oligonucleotide-like polymers by UV light. BMC Evol Biol. 3: 12. Abstract. Full text (HTML). Full text (PDF).

4. Mulkidjanian A.Y., Makarova K.S., Galperin M.Y. and Koonin E.V. (2007) Inventing the dynamo machine: the evolution of the F-type and V-type ATPases. Nature Rev. Microbiol. 5: 892-899. Abstract. Request reprint.

Signal transduction

1. Galperin M.Y. (2004) Bacterial signal transduction network in a genomic perspective. Environ. Microbiol. 6: 552-567. Abstract. Full text (HTML). Full text (PDF).

2. Galperin M.Y. (2005) A census of membrane-bound and intracellular signal transduction proteins in bacteria: Bacterial IQ, extroverts and introverts. BMC Microbiol. 5: 35. Abstract. Full text (HTML). Full text (PDF).

3. Galperin M.Y. and Gomelsky M. (2005) Bacterial signal transduction modules: from genomics to biology. ASM News 71: 326-333. Full text (HTML on ASM web site). Full text (PDF).

4. Romling U., Gomelsky M. and Galperin M.Y. (2005) C-di-GMP: the dawning of a novel bacterial signalling system. Mol. Microbiol. 57: 629-639. Abstract. Full text (HTML). Full text (PDF).

5. Amikam D. and Galperin M.Y. (2006) PilZ domain is part of the bacterial c-di-GMP binding protein. Bioinformatics 22: 3-6. Abstract. Full text (HTML). Full text (PDF).

6. Galperin M.Y. (2006) Structural classification of bacterial response regulators: Diversity of output domains and domain combinations. J. Bacteriol. 188: 4169-4182. Abstract. Full text (HTML). Full text (PDF). Supplementary Table.

Address

Michael Y. Galperin, PhD
National Center for Biotechnology Information (NCBI)
National Library of Medicine (NLM)
National Institutes of Health (NIH)
Building 38A, Room 5N507
8600 Rockville Pike, MSC 3830
Bethesda, MD 20894, USA
Tel.: (301) 435-5910
Fax: (301) 435-7793
E-mail galperin@ncbi.nlm.nih.gov

Revised: January 2, 2008.