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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