List of publications
Underlying list of references represents selected publications on the identification and reconstruction of transcriptional regulons using the comparative genomic approach.
1. 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. Mol Microbiol, 38: 673-83.
2. Rodionov DA, Mironov AA, Gelfand MS. (2001)
Transcriptional regulation of pentose utilisation systems in the Bacillus/Clostridium group of bacteria. FEMS Microbiol Lett, 205(2): 305-14.
3. Gerasimova AV, Rodionov DA, Mironov AA, Gelfand MS. (2001)
Computer analysis of regulatory signals in bacterial genomes. FNR binding sites. Mol Biol (Moscow), 6: 853-861.
4. Rodionov DA, Mironov AA, Gelfand MS. (2002)
Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea. Genome Res, 12: 1507?16.
5. 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.
6. 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.
7. 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.
8. Rodionov DA, and Gelfand MS. (2005)
Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling. Trends Genet, 21: 385?9.
9. 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.
10. 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.
11. 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.
12. 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.
13. Doroshchuk NA, Gelfand MS, Rodionov DA. (2006)
Regulation of nitrogen metabolism in gram-positive bacteria. Mol Biol (Mosk), 40: 919?26.
14. 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.
15. 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.
- NrtR - Shewanellaceae
- NrtR - Actinobacteria-1
- NrtR - Actinobacteria-2
- NrtR - Actinobacteria-3
- NrtR - Actinobacteria-4
- NrtR - Bacteroidetes-1
- NrtR - Bacteroidetes-2
- NrtR - Bacteroidetes-3
- NrtR - Chloroflexi
- NrtR - Cyanobacteria
- NrtR - Cytophaga
- NrtR - Firmicutes-1
- NrtR - Firmicutes-2
- NrtR - Firmicutes-3
- NrtR - Firmicutes-4
- NrtR - Gammaproteobacteria-1
- NrtR - Gammaproteobacteria-2
- NrtR - Gammaproteobacteria-3
- NrtR - Pirellula
16. 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.
17. Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS. (2008)
Comparative Genomics of Regulation of Fatty Acid and Branched-chain Amino Acid Utilization in Proteobacteria. J Bacteriol, 190: Sep 26.
- PsrA - Shewanellaceae
- LiuR - Shewanellaceae
- FadR - Shewanellaceae
- PsrA - Alphaproteobacteria
- LiuR - Alteromonadales
- PsrA - Alteromonadales
- LiuR - Betaproteobacteria
- PsrA - Betaproteobacteria
- FadP - Burkholderiales
- LiuQ - Burkholderiales
- LiuR - Burkholderiales
- LiuR - Caulobacterales
- LiuR - Oceanospirillales
- PsrA - Oceanospirillales
- LiuR - Pseudomonadales
- PsrA - Pseudomonadales
- LiuR - Rhizobiales
- LiuR - Rhodobacterales
- LiuR - Rhodocyclales
- LiuR - Rhodospirillales
- LiuR - Sphingomonadales
- LiuR - Vibrionales
- PsrA - Vibrionales
- PsrA - Xanthomonadales
18. Rodionov DA. (2007)
Comparative genomic reconstruction of transcriptional regulatory networks in bacteria. Chem Rev, 107(8): 3467-97.
19. Rodionov DA, Yang C, Li X, Rodionova IA, Wang Y, Obraztsova AY, Zagnitko OP, Overbeek R, Romine MF, Reed S, Fredrickson JK, Nealson KH, Osterman AL. (2009)
Comparative genomic reconstruction of carbohydrate utilization pathways in the Shewanella genus. in preparation,
20. Makarova KS, Mironov AA, Gelfand MS. (2001)
Conservation of the binding site for the arginine repressor in all bacterial lineages. Genome Biol, 2(4):RESEARCH0013.
21. Permina EA, Kazakov AE, Kalinina OV, Gelfand MS. (2006)
Comparative genomics of regulation of heavy metal resistance in Eubacteria. BMC Microbiol, 6:4
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Collection of Manually Curated Inferences of Regulons in Prokaryotic Genomes