Publications

2013

Novichkov P.S., Kazakov A., 170, Leyn S., Kovaleva G., Sutormin R.A., Kazanov M., Riehl W., Arkin A.P., Dubchak I., Rodionov D., RegPrecise 3.0 -- A resource for genome-scale exploration of transcriptional regulation in bacteria, BMC Genomics, 14(1):745, 2013.
Sun E.I., Leyn S., Kazanov M., Saier M.H., Rodionov D., Novichkov P.S., Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria, BMC Genomics, 2013, 14:597.
Leyn S., Kazanov M., Sernova N.V., Ermakova E., Novichkov P.S., Rodionov D., Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis, J Bacteriol. 2013 Jun;195(11):2463-73.
170, Best A.A., Sernova N.V., Kazanov M., Novichkov P.S., Rodionov D., Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria, BMC Genomics. 2013 Feb 12;14:94.

2012

Kazanov M., Li X., Gelfand M., L. Osterman A., Rodionov D., Functional diversification of ROK-family transcriptional regulators of sugar catabolism in the Thermotogae phylum. Nucleic Acids Res. 2012 Dec 2. http://nar.oxfordjournals.org/content/early/2012/12/02/nar.gks1184.long

2011

Rodionov D., Novichkov P.S., Stavrovskaya E., Rodionova I.A., Li X, Kazanov M., 170, Gerasimova A.V., Kazakov A., Kovaleva G., Permina E.A., Laikova O.N., Overbeek R, Romine M.F., Fredrickson J.K., Arkin A.P., Dubchak I, Osterman A.L., Gelfand M., Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus. BMC Genomics. 2011 Jun 15;12 Suppl 1:S3. http://www.biomedcentral.com/1471-2164/12/S1/S3

2010

Rodionov D., Schroeder J., Jochmann N., Tauch A., The Zur regulon of Corynebacterium glutamicum ATCC 13032. BMC Genomics, 11: 12.
Novichkov P.S., Laikova O., Novichkova E., Gelfand M., Arkin A., Dubchak I., Rodionov D., RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res. 2010, http://www.rtcb.iitp.ru/PDF/19884135.pdf
Gorbunov K., Laikova O.N., Rodionov D., Gelfand M., Lyubetsky V., “Evolution of regulatory motifs of bacterial transcription factors” In Silico Biology, 2010, 10, 0012. http://www.bioinfo.de/isb/2010/10/0012/

2009

Zhang Y., Rodionov D., Gelfand M., Gladyshev V.N., Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics. 2009, 10: 78. http://www.rtcb.iitp.ru/PDF/19208259.pdf
Desai T., Rodionov D., Gelfand M., Alm E.J., Rao C., Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res. 2009, 37: 2493-503. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677863/pdf/gkp079.pdf
Gelfand M., Kazakov A., Korostelev Y., Laikova O., Mironov A., Rakhmaninova A., 170, Rodionov D., Vitreschak A., Evolution of Regulatory Systems in Bacteria. Lecture Notes in Bioinformatics. 2009; 5542 (ISBRA 2009): 1-4.
Huang N., De Ingeniis J., Galeazzi L., Mancini C., Korostelev Y.D., Rakhmaninova A., Gelfand M., Rodionov D., Raffaelli N., Zhang H., Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism. Structure. 2009, 17: 939-51. http://www.rtcb.iitp.ru/PDF/19604474.pdf