This web site is currently maintained by Michael Y. Galperin (CV, publications, short bio) and describes some of the studies of complete microbial genomes performed by the Eugene Koonin's research group at the NCBI's Computational Biology Branch (CBB).

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 (Jan. 2011 update)
• Census of c-di-GMP-related proteins(Sept. 2016 update)
• Listing of LytTR domain proteins

References

1. The book Sequence - Evolution - Function. Computational Approaches in Comparative Genomics by E. V. Koonin and M. Y. Galperin was published in October 2002 by Kluwer Academic Publishers, Boston (currently Springer).
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., 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).

5. Galperin M.Y., Makarova K.S., Wolf Y.I. and Koonin E.V. (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 43: D261-D269. Abstract. Full text.

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).

3. Mulkidjanian A.Y. and Galperin M.Y. (2009) On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biology Direct 4: 27. Abstract. Full text.

4. Omelchenko M.V., Galperin M.Y., Wolf Y.I., and Koonin E.V. (2010) Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biology Direct 5: 31. Abstract. Full text.

5. Mulkidjanian A.Y,, Bychkov A.Y., Dibrova D.V., Galperin M.Y. and Koonin E.V. (2012) Origin of first cells at terrestrial, anoxic geothermal fields Proc Natl Acad Sci USA 109: E821-E830. Abstract. Full text.

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 (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). Supplementary Table.

7. Galperin M.Y. (2010) Diversity of structure and function of response regulator output domains. Curr. Opin. Microbiol. 13: 150-159. Abstract. Article outline. Full text (PDF). Supplementary Table.

8. Römling U., Galperin M.Y. and Gomelsky M. (2013) Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev. 77: 1-52. Abstract. Full text (HTML). Full text (PDF).

9. Chou S.-H. and Galperin M.Y. (2016) Diversity of cyclic di-GMP-binding proteins and mechanisms. J Bacteriol. 198: 32-46. Abstract. Full text. Request reprint.

10. Wang Y.C., Chin K.H., Tu Z.L., He J., Jones C.J., Zamorano Sanchez D., Yildiz F.H., Galperin M.Y. and Chou S.-H. (2016) Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain. Nature Commun. 7: 12481. Abstract. Full text (HTML). Full text (PDF).

Address

Michael Y. Galperin, PhD
NCBI, NLM, National Institutes of Health
8600 Rockville Pike, MSC 3830
Bethesda, Maryland 20894, USA
Tel.: (301) 435-5910
Fax: (301) 435-7793
E-mail: [email protected]

Please use E-mail [email protected] for all correspondence regarding the Nucleic Acids Research Database Issue and [email protected] for correspondence regarding Environmental Microbiology Genome Updates.

Revised: Sept 1, 2016.