Dmitry Rodionov, PhD

    Fields of my scientific interest are various aspects of Bioinformatics and Microbial Genomics:

·    Methods and algorithms for identification of regulatory signals;

·   Comparative genomics analysis of regulatory elements (transcription factor-binding sites, RNA secondary structures, riboswitches);

·   Identification of missing genes in metabolic pathways using regulatory characteristics and genome context;

·   Functional annotation of genes and proteins;

·   Reconstruction of metabolic pathways and regulatory networks in bacteria; 

·   Phylogenetic analysis of protein families;

·   Evolution of metabolic pathways and regulatory systems

·       M.S., Biophysics, Moscow Engineer Physics Institute, Moscow, Russia, 2000;

·       Ph.D., Molecular Biology, State Scientific Center for Biotechnology GosNIIGenetika, Moscow, Russia, 2003

·        Graduate student, Moscow Engineer Physics Institute, Moscow, Russia (1994-2000);

·        Laboratory assistant, Laboratory of Bioinformatics, State Scientific Center for Biotechnology GosNIIGenetika, Moscow, Russia (1999–2000);

·        Visiting fellow at National Center for Biotechnology Information, NIH, Bethesda, MD (March-May, 2000);

·        Post-graduate student, State Scientific Center for Biotechnology GosNIIGenetika, Moscow, Russia (2000-2003);

·        Visitor scientist at Microbiology Lab of Dr. Cotte-Patat in INSA, Lyon, France (autumn 2003)

·        Temporary position of Software Developer 2 in the Physical Biosciences Division at the Lawrence Berkeley National Laboratory, Berkeley, CA (April-June 2004);

·        Research Scientist in the Institute for Information Transmission Problems of Russian Academy of Science (2004 -2005).

·        Visitor scientist at Microbiology Lab of Dr. Eitinger in Humboldt University, Berlin, Germany (spring 2005)

·        The Burnham Institute for Biomedical Research (2006 -present)

1.      Yang C, Rodionov DA, Li X, Laikova ON, Gelfand MS, Zagnitko OP, Romine MF, Obraztsova AY, Nealson KH, Osterman AL. (2006) Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis. J Biol Chem. 281(40): 29872-85.

2.      Todd JD, Sawers G, Rodionov DA, Johnston AW. (2006) The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability. Mol Genet Genomics. 275(6): 564-77.

3.      Rodionov DA, Gelfand MS. (2006) Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal. FEMS Microbiol Lett. 255(1): 102-7.

4.      Rodionov DA, Hebbeln P, Gelfand MS, Eitinger T. (2006) Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters. J Bacteriol. 188(1): 317-27.

5.      Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS. (2005) Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks. PLoS Comput Biol. 1(5):e55. Faculty of 1000 Evaluation

6.      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. (2005) The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33(17): 5691-702.

7.      Rodionov DA, and Gelfand MS. (2005) Identification of a Bacterial Regulatory System for Ribonucleotide Reductases by Phylogenetic Profiling. Trends in Genetics, 21(7): 385-9.

8.      Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biology, 5(11): R90.

9.      Rodionov DA, Gelfand MS, Hugouvieux-Cotte-Pattat N. (2004) Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria. Microbiology, 150(11): 3571-90.

10.   Rouanet C, Reverchon S, Rodionov DA, Nasser W. (2004) 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. Journal of Biological Chemistry, 279(29): 30158-67.

11.   Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. (2004) Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems. Nucleic Acids Research, 32(11): 3340-53.

12.   Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. (2004) Riboswitches: the oldest mechanism for the regulation of gene expression? Trends in Genetics, 20(1): 44-50.

13.   Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. (2003) Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Research 31(23): 6748-57.

14.   Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. (2003) Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element. RNA, 9(9): 1084-1097.

15.   Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. (2003) Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. Journal of Biological Chemistry, 278(42): 41148-59.

16.   Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. (2002) Comparative genomics of thiamin biosynthesis in procaryotes: new genes and regulatory mechanisms. Journal of Biological Chemistry, 277(50): 48949-59.

17.   Rodionov DA, Mironov AA, Gelfand MS. (2002) Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea. Genome Research 12(10): 1507-16.

18.   Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. (2002) Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. Nucleic Acids Research 30(14): 3141-51.

19.   Rodionov DA, Mironov AA, Gelfand MS. (2001) Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria.  FEMS Microbiology Letters  205(2): 305-14.

20.   Rodionov DA, Gelfand MS, Mironov AA, Rakhmaninova AB. (2001) Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria.  Journal of Molecular Microbiology and Biotechnology 3(2): 319-24.

21.   Gerasimova AV, Rodionov DA, Mironov AA, Gelfand MS. (2001) Computer analysis of regulatory signals in bacterial genomes. FNR binding sites. Molecular Biology (Moscow) 6: 853-861.

22.  Rodionov DA, Mironov AA, Rakhmaninova AB, Gelfand MS. (2000) Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria. Molecular Microbiology 38: 673-83.