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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:
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).
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). 4. Galperin M.Y. and Koonin E.V. (2010) From complete genome sequence to 'complete' understanding? Trends Biotech. 28: 398-406. Abstract. Article outline 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). 2. Mulkidjanian A.Y., Koonin E.V., Makarova K.S., Mekhedov S.L., Sorokin A., Wolf Y.I., Dufresne A., Partensky F., Burd H., Kaznadzey D., Haselkorn R. and Galperin M.Y. (2006) The cyanobacterial genome core and the origin of photosynthesis. Proc. Natl. Acad. Sci. USA 103: 13126-13131. Abstract. Full text (HTML). Full text (PDF). 3. 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.4. 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 (HTML). Full text (PDF). 5. 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 (HTML). Full text (PDF).
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.
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.
Michael Y. Galperin, PhD
Please use E-mail nardatabase@gmail.com for all correspondence regarding the Nucleic Acids Research Database Issue and mygalperin@gmail.com for correspondence regarding Environmental Microbiology or FEMS Microbiology Letters. Revised: Jan 25, 2011. |