RegPrecise 3.0 -- A resource for genome-scale exploration of transcriptional regulation in bacteria, BMC Genomics, 14(1):745, 2013.

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria, BMC Genomics, 2013, 14:597.

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis, J Bacteriol. 2013 Jun;195(11):2463-73.

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria, BMC Genomics. 2013 Feb 12;14:94.

Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res. 2012 Dec 2.
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Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011 Jun 15;12 Suppl 1:S3.
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The Zur regulon of Corynebacterium glutamicum ATCC 13032. BMC Genomics, 11: 12.
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RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res, 38: D111-D118.
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“Evolution of regulatory motifs of bacterial transcription factors” In Silico Biology, 2010, 10, 0012.
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Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS. (2009) Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria. J Bacteriol. 190: 52-64.
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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, Eitinger T. (2009) A Novel Class of Modular Transporters for Vitamins in Prokaryotes. J Bacteriol. 190: 42-51.
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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,Beliaev, AS. (2009) Genomic reconstruction of Shewanella oneidensis MR-1 metabolism reveals a previously uncharacterized machinery for lactate utilization. Proc Natl Acad Sci USA, 105: 2874-79.
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Sorci L, Martynowski D, Rodionov DA, Eyobo Y, Zogaj X, Klose KE, Nikolaev EV, Magni G, Zhang H, Osterman AL. (2009) Nicotinamide mononucleotide synthetase is the key enzyme for an alternative route of NAD biosynthesis in Francisella tularensis. Proc Natl Acad Sci USA, 105: 3083-88.
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Sankaran B, Bonnett S, Shah K, Gabriel S, Reddy R, Schimmel P, Rodionov DA, de Crécy-Lagard V, Helmann JD, Iwata-Reuyl D, Swairjo MA. (2009) Zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for GTP cyclohydrolase IB. J Bacteriol., 191: 6936-6949.
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Haas CE, Rodionov DA, Kropat J, Malasarn D, Merchant SS, de Crecy-Lagard V. (2009) A subset of the diverse COG0523 family of putative metal chaperones is linked to zinc homeostasis in all kingdoms of life. BMC Genomics, 10: 470.
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Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics, 2009, 10: 78.
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Desai TA, Rodionov DA, Gelfand MS, Alm EJ, Rao CV. (2009) Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res, 37: 2493-503.
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Evolution of Regulatory Systems in Bacteria. Lecture Notes in Bioinformatics. 2009; 5542 (ISBRA 2009): 1-4.

Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure. 2009, 17: 939-51.
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Yang C, Rodionov DA, Rodionova IA, Li X, Osterman AL. (2008) Glycerate 2-kinase of Thermotoga maritima and genomic reconstruction of related metabolic pathways. J Bacteriol., 190:1773–82.
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Rodionov DA, De Ingeniis J, Mancini C, Cimadamore F, Zhang H, Osterman AL, Raffaelli N. (2008) Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators. Nucleic Acids Res., 36:2047–59.
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Rodionov DA, Li X, Rodionova IA, Yang C, Sorci L, Dervyn E, Martynowski D, Zhang H, Gelfand MS, Osterman AL. (2008) Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon. Nucleic Acids Res., 36:2032–46.
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Schauer K, Rodionov DA, de Reusse H. (2008) New substrates for TonB-dependent transport: Do we only see the "tip of the iceberg"? Trends Biochem Sci, 33: 330-8
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Gelfand MS, Rodionov DA. (2008) Comparative genomics and functional annotation of bacterial transporters. Physics of Life Reviews, 5: 22-49.
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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, Tiedje JM. (2008) Towards environmental systems biology of Shewanella. Nature Reviews Microbiology. 6: 592-603.
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Eudes A, Erkens GB, Slotboom DJ, Rodionov DA, Naponelli V, Hanson AD. (2008) Identification of Genes Encoding the Folate- and Thiamine-binding Membrane Proteins in Firmicutes. J Bacteriol. 2008 190: 7591-7594.
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26. McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes S, Hwang K, Kubal M, Margaryan GR, Meyer F, 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. (2007) The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res, 35: D347–53.
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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. (2007) Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function. Proteins, 68(1): 418-24.
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Hebbeln P, Rodionov DA, Alfandega A, Eitinger T. (2007) Biotin uptake in prokaryotes by solute transporters with an optional ATP-binding cassette-containing module. Proc Natl Acad Sci USA, 104: 2909–14.
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Johnston AW, Todd JD, Curson AR, Lei S, Nikolaidou-Katsaridou N, Gelfand MS, Rodionov DA. (2007) Living without Fur: the subtlety and complexity of iron-responsive gene regulation in the symbiotic bacterium Rhizobium and other alpha-proteobacteria. Biometals, 20: 501–11.
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Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL. (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. Proc Natl Acad Sci USA, 104: 4279–84.
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Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chemical Reviews, 2007, 107(8): 3467-97.
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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: 317–27.
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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: 102–7.
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Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ. (2006) IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli. Mol Microbiol, 60(4): 1058-75.
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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: 564–77.
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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: 29872–85.
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Н.А. Дорощук, М.С. Гельфанд, Д.А. Родионов. Регуляция метаболизма азота у грамположительных бактерий. Молекулярная биология. 2006, 40 (5): 919-926.
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Rodionov DA, Gelfand MS, Todd JD, Johnston AW. (2006) Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria. PLoS Comput Biol, 2: e163.
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Rodionov DA, and Gelfand MS. (2005) Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling. Trends Genet, 21: 385–9.
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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 R, 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: 5691–702.
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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: e55.
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Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS. (2004) Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet, 20: 44–50.
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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 Res, 32: 3340–53.
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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. J Biol Chem, 279: 30158–67.
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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: 3571–90.
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Rodionov DA, Dubchak I, Arkin A, Alm E, Gelfand MS. (2004) Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria. Genome Biol, 5: R90.
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Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. (2003) Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem, 278: 41148–59.
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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: 1084–97.
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Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS. (2003) Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res 31: 6748–57.
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