Dmitry A. Ravcheev
Ph.D. (biol.), Junior Researcher

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Awards:

December 2007. Award for the best publication in Russian scientific journals in 2005 for a series of papers in "Molecular Biology" ("Nauka/Interperiodica" publishing house)

Ravcheev DA (PhD student DBB, MSU, Junior Researcher IITP RAS). 2005/2006 .

Publications:

Ravcheev D.A., Khoroshkin M.S., Laikova O.N., Tsoy O.V., Sernova N.V., Petrova S.A., Rakhmaninova A.B., Novichkov P.S., Gelfand M.S. and Rodionov D.A. Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol. 2014 Jun 11;5:294. PubMed  PDF

Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA. RegPrecise 3.0 -- A resource for genome-scale exploration of transcriptional regulation in bacteria. BMC Genomics. 2013 Nov 1;14(1):745. PubMed  PDF

Ravcheev D.A., Best A.A., Sernova N.V., Kazanov M.D., Novichkov P.S., Rodionov D.A. Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria. BMC Genomics 2013 14(94. PubMed  PDF

Suvorova I.A., Ravcheev D.A., Gelfand M.S. Regulation and evolution of malonate and propionate catabolism in proteobacteria. J Bacteriol 2012 194(12): 3234-3240. PubMed  PDF

Pavlova O., Lavysh D., Klimuk E., Djordjevic M., Ravcheev D.A., Gelfand M.S., Severinov K., Akulenko N. Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32. J Mol Biol 2012 416(3): 389-399. PubMed  PDF

Ravcheev D.A., Li X., Latif H., Zengler K., Leyn S.A., Korostelev Y.D., Kazakov A.E., Novichkov P.S., Osterman A.L., Rodionov D.A. Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex. J Bacteriol 2012 194(5): 1145-1157. PubMed  PDF

Rodionov D.A, Novichkov P.S, Stavrovskaya E.D, Rodionova I.A, Li X, Kazanov M.D, Ravcheev D.A, Gerasimova A.V, Kazakov A.E, Kovaleva G.Y, Permina E.A, Laikova O.N, Overbeek R, Romine M.F, Fredrickson J.K, Arkin A.P, Dubchak I, Osterman A.L, Gelfand M.S. Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011, 12 Suppl 1: S3. PubMed  PDF

Suvorova I.A, Tutukina M.N, Ravcheev D.A, Rodionov D.A, Ozoline O.N, Gelfand M.S. Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria. J Bacteriol. 2011, 193: 3956-63. PubMed  PDF

Tsoy O, Ravcheev D, Mushegian A. Comparative genomics of ethanolamine utilization. J Bacteriol. 2009, 191(23):7157-64 PubMed  PDF

Gelfand MS, Kazakov AE, Korostelev YD, Laikova ON, Mironov AA, Rakhmaninova AB, Ravcheev DA, Rodionov DA, Vitreschak AG. Evolution of Regulatory Systems in Bacteria. Lecture Notes in Bioinformatics. 2009; 5542 (ISBRA 2009): 1-4

Tsyganova MO, Gelfand MS, Ravcheev DA. [Regulation of respiration in enterobacteria: comparison of microarray and comparative genomic data]. Mol. Biol. (Mosk). 2007, 41(3): 556-71. Russian. PubMed  PDF

Ravcheev DA, Gerasimova AV, Mironov AA. and Gelfand MS. Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae). BMC Genomics 2007, 8:54   PDF

Ravcheev DA, Rakhmaninova AB, Mironov AA, Gelfand MS. Regulation of nitrate and nitrite respiration in gammaproteobacteria: a comparative genomics study Molecular Biology. 2005, 39(5): 727-740   PDF

Gelfand MS, Gerasimova AV, Kotelnikova EA, Laikova ON, Makeev VY, Mironov AA, Panina EM, Ravcheev DA, Rodionov DA, Vitreschak AG
Comparative genomics and evolution of bacterial regulatory systems.
Bioinformatics of Genome Regulation and Structure II (Springer Science+Business Media, Inc.) P. 111-119 (2005)
Eds. Kolchanov N. and Hofestaedt R.

Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VJ. A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length. Bioinformatics. 2005, 21(10):2240-5. PubMed  PDF

Iarovaia OV, Bystritskiy A, Ravcheev D, Hancock R, Razin SV. Visualization of individual DNA loops and a map of loop domains in the human dystrophin gene. Nucleic Acids Res. 2004 Apr 15;32(7):2079-86. Print 2004. PubMed   PDF

Ravcheev DA, Gel'fand MS, Mironov AA, Rakhmaninova AB. [Purine regulon of gamma-proteobacteria: a detailed description] Genetika. 2002, 38(9):1203-14. Russian. PubMed   PDF

Conferences:

3rd Int. Moscow Conference on Computational Molecular Biology MCCMB07 (Moscow, Russia, July 2007)
M.J.Cipriano, A.E.Kazakov, D.Ravcheev, A.Arkin, M.S.Gelfand, I.Dubchak. RegTransBase (RTB) a database of regulatory sequences and interactions in prokaryotic genomes (poster) p. 66
O.Tsoy, W.Zakirzianova, D.A.Ravcheev. Stories about the evolution of regulators: huw FruR became CRA and RbsR became PurR (talk) p. 300

Gerasimova AV, Ravcheev DA, Gelfand MS. Multiple Regulation of Respiration in Gamma-Proteobacteria: FNR, ArcA, NarP and ModE Regulons Proceedings of 5th European Conference on Computational Biology ECCB2006 (Eilat, Israel January 2007). (poster)

Ravcheev DA. Regulation of respiration in gamma-proteobacteria: Evolution of multiple regulatory systems. 4th Bertinoro Computational Biology Meeting "Evolution of and Comparative Approaches to Gene Regulation" (Bertinoro, Italy, June 2006)

Gerasimova AV, Ravcheyev DA, Gelfand MS, Rakhmaninova AB. Comparative Genomic Analysis of Respiration switch in Gamma-Proteobacteria. Proceedings of The Fourth International Conference on Bioinformatics of Genome Regulation and Structure. 2004. v.2. 195-198. PDF

Gelfand MS, Gerasimova AV, Kazakov AE, Kotelnikova EA, Laikova ON,1 Mironov AA, Permina EA, Ravcheev DA, Rodionov DA, Vitreschak AG. Comparative genomics, metabolic reconstruction, and analysis of regulation in bacterial genomes. Meeting of International Research Scholars. Program and Abstracts. 2004. 45.

Ravcheev DA, Gel'fand MS, Mironov AA, Rakhmaninova AB Comparative genomic analysis of NarP-dependent regulation of nitrate and nitrite respiration in gammaproteobacteria. Proceedings of the XI International Scientific Conference for Undergraduate and Graduate Students and Young Scientists "Lomonosov", 2004, v.1, p.27

Ravcheev DA, Rakhmaninova AB, Mironov AA, Gel'fand MS. NarP-dependent regulation of nitrate and nitrite respiration in gammaproteobacteria. Proceedings of the III Russian Biophysics Congress, 2004, p10

Gerasimova AV, Ravcheyev DA, Rakhmaninova AB, Gelfand MS. Computer Analysis of aerobic-anaerobic regulation in Gamma-Proteobacteria. Proceedings of The Third International Conference on Bioinformatics of Genome Regulation and Structure. 2002. v. 2. 38-39.

Ravcheyev DA, Gelfand MS, Mironov AA, Rakhmaninova AB. Purine regulon of gamma-proteobacteria. Proceedings of The Third International Conference on Bioinformatics of Genome Regulation and Structure. 2002. v. 2. 38-39. PDF