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Papers authored by Rodionov DA

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Zinc-Independent Folate Biosynthesis: Genetic, Biochemical, and Structural Investigations Reveal New Metal Dependence for GTP Cyclohydrolase IB.

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Sankaran B, Bonnett SA, Shah K, Gabriel S, Reddy R, Schimmel P, Rodionov DA, de Crécy-Lagard V, Helmann JD, Iwata-Reuyl D, and Swairjo MA

Journal of bacteriology 191(22):6936-49, 2009 Nov - Who cited this? | PubMed ID: 19767425 | Fulltext

Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism.

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Huang N, De Ingeniis J, Galeazzi L, Mancini C, Korostelev YD, Rakhmaninova AB, Gelfand MS, Rodionov DA, Raffaelli N, and Zhang H

Structure (London, England : 1993) 17(7):939-51, 2009 Jul 15 - Who cited this? | PubMed ID: 19604474 | Fulltext

Engineering transcription factors with novel DNA-binding specificity using comparative genomics.

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Desai TA, Rodionov DA, Gelfand MS, Alm EJ, and Rao CV

Nucleic acids research 37(8):2493-503, 2009 May - Who cited this? | PubMed ID: 19264798 | Fulltext

Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis.

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Sorci L, Martynowski D, Rodionov DA, Eyobo Y, Zogaj X, Klose KE, Nikolaev EV, Magni G, Zhang H, and Osterman AL

Proceedings of the National Academy of Sciences of the United States of America 106(9):3083-8, 2009 Mar 3 - Who cited this? | PubMed ID: 19204287 | Fulltext

Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization.

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Pinchuk GE, Rodionov DA, Yang C, Li X, Osterman AL, Dervyn E, Geydebrekht OV, Reed SB, Romine MF, Collart FR, Scott JH, Fredrickson JK, and Beliaev AS

Proceedings of the National Academy of Sciences of the United States of America 106(8):2874-9, 2009 Feb 24 - Who cited this? | PubMed ID: 19196979 | Fulltext

Comparative genomics of regulation of Fatty Acid and branched-chain amino Acid utilization in proteobacteria.

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Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, and Gelfand MS

Journal of bacteriology 191(1):52-64, 2009 Jan - Who cited this? | PubMed ID: 18820024 | Fulltext

A novel class of modular transporters for vitamins in prokaryotes.

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Rodionov DA, Hebbeln P, Eudes A, Ter Beek J, Rodionova IA, Erkens GB, Slotboom DJ, Gelfand MS, Osterman AL, Hanson AD, and Eitinger T

Journal of bacteriology 191(1):42-51, 2009 Jan - Who cited this? | PubMed ID: 18931129 | Fulltext

Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization.

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Zhang Y, Rodionov DA, Gelfand MS, and Gladyshev VN

BMC genomics 10:78, 2009 - Who cited this? | PubMed ID: 19208259 | Fulltext

A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life.

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Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS, and de Crécy-Lagard V

BMC genomics 10:470, 2009 - Who cited this? | PubMed ID: 19822009 | Fulltext

Identification of genes encoding the folate- and thiamine-binding membrane proteins in firmicutes.

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Eudes A, Erkens GB, Slotboom DJ, Rodionov DA, Naponelli V, and Hanson AD

Journal of bacteriology 190(22):7591-4, 2008 Nov - Who cited this? | PubMed ID: 18776013 | Fulltext

Towards environmental systems biology of Shewanella.

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Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB,

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Nature reviews. Microbiology 6(8):592, 2008 Aug - Who cited this? | PubMed ID: 18604222 | Fulltext

New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'?.

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Schauer K, Rodionov DA, and de Reuse H

Trends in biochemical sciences 33(7):330-8, 2008 Jul - Who cited this? | PubMed ID: 18539464 | Fulltext

Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators.

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Rodionov DA, De Ingeniis J, Mancini C, Cimadamore F, Zhang H, Osterman AL, and Raffaelli N

Nucleic acids research 36(6):2047, 2008 Apr - Who cited this? | PubMed ID: 18276643 | Fulltext

Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon.

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Rodionov DA, Li X, Rodionova IA, Yang C, Sorci L, Dervyn E, Martynowski D, Zhang H, Gelfand MS, and Osterman AL

Nucleic acids research 36(6):2032, 2008 Apr - Who cited this? | PubMed ID: 18276644 | Fulltext

Glycerate 2-Kinase of Thermotoga maritima and Genomic Reconstruction of Related Metabolic Pathways.

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Yang C, Rodionov DA, Rodionova IA, Li X, and Osterman AL

Journal of bacteriology 190(5):1773-82, 2008 Mar - Who cited this? | PubMed ID: 18156253 | Fulltext

Comparative genomic reconstruction of transcriptional regulatory networks in bacteria.

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Rodionov DA

Chemical reviews 107(8):3467-97, 2007 Aug - Who cited this? | PubMed ID: 17636889 | Fulltext

Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria.

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Johnston AW, Todd JD, Curson AR, Lei S, Nikolaidou-Katsaridou N, Gelfand MS, and Rodionov DA

Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine 20(3-4):501-11, 2007 Jun - Who cited this? | PubMed ID: 17310401 | Fulltext

Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate.

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Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, and Osterman AL

Proceedings of the National Academy of Sciences of the United States of America 104(11):4279, 2007 Mar 13 - Who cited this? | PubMed ID: 17360515 | Fulltext

Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module.

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Hebbeln P, Rodionov DA, Alfandega A, and Eitinger T

Proceedings of the National Academy of Sciences of the United States of America 104(8):2909-14, 2007 Feb 20 - Who cited this? | PubMed ID: 17301237 | Fulltext

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation.

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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,

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Nucleic acids research 35(Database issue), 2007 Jan - Who cited this? | PubMed ID: 17145713 | Fulltext

Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria.

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Rodionov DA, Gelfand MS, Todd JD, Curson AR, and Johnston AW

PLoS computational biology 2(12):e163, 2006 Dec 15 - Who cited this? | PubMed ID: 17173478 | Fulltext

[Regulation of nitrogen metabolism in gram-positive bacteria].

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Doroshchuk NA, Gel'fand MS, and Rodionov DA

Molekuliarnaia biologiia 40(5):919 - Who cited this? | PubMed ID: 17086994 | Fulltext

Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis.

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Yang C, Rodionov DA, Li X, Laikova ON, Gelfand MS, Zagnitko OP, Romine MF, Obraztsova AY, Nealson KH, and Osterman AL

The Journal of biological chemistry 281(40):29872, 2006 Oct 6 - Who cited this? | PubMed ID: 16857666 | Fulltext

The Rhizobium leguminosarum regulator IrrA affects the transcription of a wide range of genes in response to Fe availability.

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Todd JD, Sawers G, Rodionov DA, and Johnston AW

Molecular genetics and genomics : MGG 275(6):564-77, 2006 Jun - Who cited this? | PubMed ID: 16625355 | Fulltext

Computational identification of BioR, a transcriptional regulator of biotin metabolism in Alphaproteobacteria, and of its binding signal.

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Rodionov DA and Gelfand MS

FEMS microbiology letters 255(1):102-7, 2006 Feb - Who cited this? | PubMed ID: 16436068 | Fulltext

Comparative and functional genomic analysis of prokaryotic nickel and cobalt uptake transporters: evidence for a novel group of ATP-binding cassette transporters.

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Rodionov DA, Hebbeln P, Gelfand MS, and Eitinger T

Journal of bacteriology 188(1):317, 2006 Jan - Who cited this? | PubMed ID: 16352848 | Fulltext

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.

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Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, and Gelfand MS

PLoS computational biology 1(5):e55, 2005 Oct - Who cited this? | PubMed ID: 16261196 | Fulltext

Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling.

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Rodionov DA and Gelfand MS

Trends in genetics : TIG 21(7):385-9, 2005 Jul - Who cited this? | PubMed ID: 15949864 | Fulltext

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.

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Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crécy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A,

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Nucleic acids research 33(17):5691-702, 2005 - Who cited this? | PubMed ID: 16214803 | Fulltext

Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.

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Rodionov DA, Gelfand MS, and Hugouvieux-Cotte-Pattat N

Microbiology (Reading, England) 150(Pt 11):3571, 2004 Nov - Who cited this? | PubMed ID: 15528647 | Fulltext

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.

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Rouanet C, Reverchon S, Rodionov DA, and Nasser W

The Journal of biological chemistry 279(29):30158-67, 2004 Jul 16 - Who cited this? | PubMed ID: 15140891 | Fulltext

Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems.

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Rodionov DA, Vitreschak AG, Mironov AA, and Gelfand MS

Nucleic acids research 32(11):3340, 2004 - Who cited this? | PubMed ID: 15215334 | Fulltext

Riboswitches: the oldest mechanism for the regulation of gene expression?.

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Vitreschak AG, Rodionov DA, Mironov AA, and Gelfand MS

Trends in genetics : TIG 20(1):44-50, 2004 Jan - Who cited this? | PubMed ID: 14698618 | Fulltext

Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria.

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Rodionov DA, Dubchak I, Arkin A, Alm E, and Gelfand MS

Genome biology 5(11):R90, 2004 - Who cited this? | PubMed ID: 15535866 | Fulltext

Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch?.

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Rodionov DA, Vitreschak AG, Mironov AA, and Gelfand MS

Nucleic acids research 31(23):6748, 2003 Dec 1 - Who cited this? | PubMed ID: 14627808 | Fulltext

Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes.

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Rodionov DA, Vitreschak AG, Mironov AA, and Gelfand MS

The Journal of biological chemistry 278(42):41148-59, 2003 Oct 17 - Who cited this? | PubMed ID: 12869542 | Fulltext

Regulation of the vitamin B12 metabolism and transport in bacteria by a conserved RNA structural element.

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Vitreschak AG, Rodionov DA, Mironov AA, and Gelfand MS

RNA (New York, N.Y.) 9(9):1084, 2003 Sep - Who cited this? | PubMed ID: 12923257 | Fulltext

Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms.

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Rodionov DA, Vitreschak AG, Mironov AA, and Gelfand MS

The Journal of biological chemistry 277(50):48949-59, 2002 Dec 13 - Who cited this? | PubMed ID: 12376536 | Fulltext

Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea.

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Rodionov DA, Mironov AA, and Gelfand MS

Genome research 12(10):1507-16, 2002 Oct - Who cited this? | PubMed ID: 12368242 | Fulltext

Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.

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Vitreschak AG, Rodionov DA, Mironov AA, and Gelfand MS

Nucleic acids research 30(14):3141-51, 2002 Jul 15 - Who cited this? | PubMed ID: 12136096 | Fulltext

Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria.

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Rodionov DA, Mironov AA, and Gelfand MS

FEMS microbiology letters 205(2):305-14, 2001 Dec 18 - Who cited this? | PubMed ID: 11750820 | Fulltext

Comparative approach to analysis of regulation in complete genomes: multidrug resistance systems in gamma-proteobacteria.

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Rodionov DA, Gelfand MS, Mironov AA, and Rakhmaninova AB

Journal of molecular microbiology and biotechnology 3(2):319, 2001 Apr - Who cited this? | PubMed ID: 11321589 | Fulltext

[Computer analysis of regulatory signals in bacterial genomes. Fnr binding segments].

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Gerasimova AV, Rodionov DA, Mironov AA, and Gel'fand MS

Molekuliarnaia biologiia 35(6):1001-9, 2001 - Who cited this? | PubMed ID: 11771123 | Fulltext

Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria.

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Rodionov DA, Mironov AA, Rakhmaninova AB, and Gelfand MS

Molecular microbiology 38(4):673-83, 2000 Nov - Who cited this? | PubMed ID: 11115104 | Fulltext

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