Ph.D. (biol.), Researcher |
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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
Sun EI, Leyn SA, Kazanov MD, Saier MH Jr, Novichkov PS, Rodionov DA. Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. BMC Genomics. 2013 Sep 2;14:597.PubMed PDF
Leyn S.A., Kazanov M.D., Sernova N.V., Ermakova E.O., Novichkov P.S., Rodionov D.A. Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis. J Bacteriol 2013 195(11): 2463-2473. 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
Kazanov M.D., Li X., Gelfand M.S., Osterman A.L., Rodionov D.A. Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res 2013 41(2): 790-803. PubMed PDF
Gorbunov K.Y., Laikova O.N., Rodionov D.A., Gelfand M.S., Lyubetsky V.A. Evolution of regulatory motifs of bacterial transcription factors. In Silico Biol 2010 10(3): 163-183. 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
Leyn S.A., Li X., Zheng Q., Novichkov P.S., Reed S., Romine M.F., Fredrickson J.K., Yang C., Osterman A.L., Rodionov D.A. Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis. J Biol Chem 2011 286(41): 35782-35794. 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
Blaby-Haas C.E, Furman R, Rodionov D.A, Artsimovitch I, de Crecy-Lagard V. Role of a Zn-independent DksA in Zn homeostasis and stringent response. Mol Microbiol. 2011, 79: 700-15. PubMed PDF
Novichkov P.S, Rodionov D.A, Stavrovskaya E.D, Novichkova E.S, Kazakov A.E, Gelfand M.S, Arkin A.P, Mironov A.A, Dubchak I. RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res. 2010, 38: W299-307. PubMed PDF
Eitinger T, Rodionov D.A, Grote M, Schneider E. Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions. FEMS Microbiol Rev. 2011, 35: 3-67. PubMed PDF
Gu Y, Ding Y, Ren C, Sun Z, Rodionov D.A, Zhang W, Yang S, Yang C, Jiang W. Reconstruction of xylose utilization pathway and regulons in Firmicutes. BMC Genomics. 2010, 11: 255. PubMed PDF
J. Schroder, N. Jochmann, D.A. Rodionov, A. Tauch. The Zur regulon of Corynebacterium glutamicum ATCC 13032. BMC Genomics. 2010, 11: 12. PubMed PDF
Novichkov P.S, Laikova O.N, Novichkova E.S, Gelfand M.S, Arkin A.P, Dubchak I, Rodionov D.A. RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010, 38: D111-8. PubMed PDF
Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev Y.D, Rakhmaninova A.B, Gelfand M.S, Rodionov D.A, Raffaelli N, Zhang H. Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure. 2009, 17: 939-51. PubMed PDF
Haas C.E, Rodionov D.A, Kropat J, Malasarn D, Merchant S.S, de Crecy-Lagard V. A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics. 2009, 10: 470. PubMed PDF
Sankaran B, Bonnett S.A, Shah K, Gabriel S, Reddy R, Schimmel P, Rodionov D.A, de Crecy-Lagard V, Helmann J.D, Iwata-Reuyl D, Swairjo M.A. Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. J Bacteriol. 2009, 191: 6936-49. 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
Sorci L, Martynowski D, Rodionov D.A, Eyobo Y, Zogaj X, Klose K.E, Nikolaev E.V, Magni G, Zhang H, Osterman A.L. Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis. Proc Natl Acad Sci U S A. 2009, 106: 3083-8. PubMed PDF
Desai T.A, Rodionov D.A, Gelfand M.S, Alm E.J, Rao C.V. Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res. 2009, 37: 2493-503. PubMed PDF
Zhang Y, Rodionov D.A, Gelfand M.S, Gladyshev V.N. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics. 2009, 10: 78. PubMed PDF
A. Eudes, G.B. Erkens, D.J. Slotboom, D.A. Rodionov, V. Naponelli, A.D. Hanson. Identification of genes encoding the folate- and thiamine-binding membrane proteins in Firmicutes. J Bacteriol. 2008, 190: 7591-4. PubMed PDF
A.E. Kazakov, D.A. Rodionov, E. Alm, A.P. Arkin, I. Dubchak, M.S. Gelfand. Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria. J Bacteriol. 2009, 191: 52-64. PubMed PDF
D.A. Rodionov, P. Hebbeln, A. Eudes, J. ter Beek, I.A. Rodionova, G.B. Erkens, D.J. Slotboom, M.S. Gelfand, A.L. Osterman, A.D. Hanson, T. Eitinger. A novel class of modular transporters for vitamins in prokaryotes. J Bacteriol. 2009, 191: 42-51. PubMed PDF
G.E. Pinchuk, D.A. Rodionov, C. Yang, X. Li, A.L. Osterman, E. Dervyn, O.V. Geydebrekht, S.B. Reed, M.F. Romine, F.R. Collart, J.H. Scott, J.K. Fredrickson, A.S. Beliaev. Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci U S A. 2009, 106: 2874-9. PubMed PDF
D.A. Rodionov, J. De Ingeniis, C. Mancini, F. Cimadamore, H. Zhang, A.L. Osterman, N. Raffaelli. Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators. Nucleic Acids Res. 2008, 36: 2047-59. PubMed PDF
D.A. Rodionov, X. Li, I.A. Rodionova, C. Yang, L. Sorci, E. Dervyn, D. Martynowski, H. Zhang, M.S. Gelfand, A.L. Osterman. Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon. Nucleic Acids Res. 2008, 36: 2032-46. PubMed PDF
J.K. Fredrickson, M.F. Romine, A.S. Beliaev, J.M. Auchtung, M.E. Driscoll, T.S. Gardner, K.H. Nealson, A.L. Osterman, G. Pinchuk, J.L. Reed, D.A. Rodionov, J.L. Rodrigues, D.A. Saffarini, M.H. Serres, A.M. Spormann, I.B. Zhulin, J.M. Tiedje. Towards environmental systems biology of Shewanella. Nat Rev Microbiol. 2008, 6: 592-603. PubMed PDF
Schauer K, Rodionov D.A, H. de Reuse. New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'? Trends Biochem Sci. 2008, 33: 330-8. PubMed PDF
Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways. J Bacteriol. 2008, 190(5):1773-82 PubMed PDF
Rodionov DA, Gelfand MS. Comparative genomics and functional annotation of bacterial transporters. Physics of Life Reviews, 2008, 5: 22-49. PDF
Rodionov DA. Comparative Genomic Reconstruction of Transcriptional Regulatory Networks in Bacteria. Chem Rev. 2007, 107(8):3467-97. PubMed PDF
Premkumar L, Rife CL, Sri Krishna S, McMullan D, Miller MD, Abdubek P, Ambing E, Astakhova T, Axelrod HL, Canaves JM, Carlton D, Chiu HJ, Clayton T, DiDonato M, Duan L, Elsliger MA, Feuerhelm J, Floyd R, Grzechnik SK, Hale J, Hampton E, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Koesema E, Kovarik JS, Kreusch A, Levin I, McPhillips TM, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Quijano K, Reyes R, Rezezadeh F, Rodionov D, Schwarzenbacher R, Spraggon G, van den Bedem H, White A, Wolf G, Xu Q, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA. Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function. Proteins. 2007, 68(1):418-24. PubMed PDF
McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman A, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko O, Xia F, Zinner J, Overbeek R, Stevens R. The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.Nucleic Acids Res. 2007, 35: D347-53. PubMed PDF
Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL. Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. Proc Natl Acad Sci U S A. 2007, 104(11):4279-84. PubMed PDF
Hebbeln P, Rodionov DA, Alfandega A, Eitinger T. Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. Proc Natl Acad Sci U S A. 2007 104(8):2909-14. PubMed PDF
Johnston AW, Todd JD, Curson AR, Lei S, Nikolaidou-Katsaridou N, Gelfand MS, Rodionov DA. Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria. Biometals. 2007, 20(3-4):501-11 PubMed PDF
Rodionov DA, Gelfand MS, Todd JD, Curson A.R.J, Johnston A.W.B. Computational Reconstruction of Iron- and Manganese-Responsive Transcriptional Networks in alfa-Proteobacteria. PLoS Comput Biol. 2006, 444:240. PubMed PDF
Doroshchuk NA, Gelfand MS, Rodionov DA. Regulation of nitrogen metabolism in gram-positive bacteria. Molecular Biology. 2006, 40 (5): 829-836
Yang C, Rodionov DA, Li X, Laikova ON, Gelfand MS, Zagnitko OP, Romine MF, Obraztsova AY, Nealson KH, Osterman AL. Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem. 2006, 281(40):29872-85. PubMed PDF
Todd JD, Sawers G, Rodionov DA, Johnston AW. The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability. Mol Genet Genomics. 2006, 275(6):564-77 PubMed PDF
Giel JL, Rodionov DA, Liu M, Blattner FR, Kiley PJ. IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli. Molecular Microbiology. 2006, 60(4):1058-75 PubMed PDF
Rodionov DA, Gelfand MS. Computational identification of BioR, a transcriptional regulator of biotin metabolism in alpha-proteobacteria, and of its binding signal. FEMS Microbiol Lett. 2006, 255(1):102-7. PubMed PDF
Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T. Comparative and Functional Genomic Analysis of Prokaryotic Nickel and Cobalt Uptake Transporters: Evidence for a Novel Group of ATP-Binding Cassette Transporters. J Bacteriol. 2006, 188(1):317-27. PubMed PDF
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. Print 2005. PubMed PDF
Rodionov D.A, Dubchak I.L, Arkin A.P, Alm E.J, Gelfand M.S. Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput Biol. 2005, 1(5):e55. PubMed PDF
Rodionov D.A, Gelfand M.S. Identification of a Bacterial Regulatory System for Ribonucleotide Reductases by Phylogenetic Profiling. Trends in.Genetics. 2005, 21 (7): 385-389. PubMed PDF
Gelfand M.S, Gerasimova A.V, Kotelnikova E.A, Laikova O.N, Makeev V.Yu, Mironov A.A, Panina E.M, Ravcheev D.A, Rodionov D.A, Vitreschak A.G
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.
Rodionov DA, Gelfand MS, Hugouvieux-Cotte-Pattat N. Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria. Microbiology. 2004, 150(Pt 11):3571-90. PubMed PDF
Rouanet C, Reverchon S, Rodionov DA, Nasser W. Definition of a consensus DNA-binding site for PecS, a global regulator of virulence gene expression in Erwinia chrysanthemi and identification of new members of the PecS regulon. J Biol Chem. 2004, 279(29):30158-67 PubMed PDF
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Res. 2004, 32(11):3340-53. Print 2004. PubMed PDF
Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol. 2004; 5(11):R90 PubMed PDF
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 2004, 20(1):44-50. PubMed PDF
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res. 2003, 31(23):6748-57. PubMed PDF
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem. 2003, 278(42):41148-59 PubMed PDF
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA. 2003, 9(9):1084-97. PubMed PDF
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms. J Biol Chem. 2002, 277(50):48949-59 PubMed PDF
Rodionov DA, Mironov AA, Gelfand MS. Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res. 2002, 12(10):1507-16. PubMed PDF
Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Res. 2002, 30(14):3141-51. PubMed PDF
Rodionov DA, Mironov AA, Gelfand MS. Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria. FEMS Microbiol Lett. 2001, 205(2):305-14. PubMed PDF
Gerasimova AV, Rodionov DA, Mironov AA, Gel'fand MS. [Computer analysis of regulatory signals in bacterial genomes. Fnr binding segments] Mol Biol (Mosk). 2001, 35(6):1001-9. Russian. PubMed PDF
Rodionov DA, Gelfand MS, Mironov AA, Rakhmaninova AB. Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria. J Mol Microbiol Biotechnol. 2001, 3(2):319-24. PubMed PDF
Rodionov DA, Mironov AA, Rakhmaninova AB, Gelfand MS. Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria. Mol Microbiol. 2000, 38(4):673-83. PubMed PDF