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RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach.
Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I. Novichkov PS, et al. Among authors: Kazakov AE. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W299-307. doi: 10.1093/nar/gkq531. Epub 2010 Jun 11. Nucleic Acids Res. 2010. PMID: 20542910 Free PMC article.
Comparative genomics of the dormancy regulons in mycobacteria.
Gerasimova A, Kazakov AE, Arkin AP, Dubchak I, Gelfand MS. Gerasimova A, et al. Among authors: Kazakov AE. J Bacteriol. 2011 Jul;193(14):3446-52. doi: 10.1128/JB.00179-11. Epub 2011 May 20. J Bacteriol. 2011. PMID: 21602344 Free PMC article.
Comparative genomic reconstruction of transcriptional networks controlling central metabolism in the Shewanella genus.
Rodionov DA, Novichkov PS, Stavrovskaya ED, Rodionova IA, Li X, Kazanov MD, Ravcheev DA, Gerasimova AV, Kazakov AE, Kovaleva GY, Permina EA, Laikova ON, Overbeek R, Romine MF, Fredrickson JK, Arkin AP, Dubchak I, Osterman AL, Gelfand MS. Rodionov DA, et al. Among authors: Kazakov AE. BMC Genomics. 2011 Jun 15;12 Suppl 1(Suppl 1):S3. doi: 10.1186/1471-2164-12-S1-S3. BMC Genomics. 2011. PMID: 21810205 Free PMC article.
RegTransBase--a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes.
Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I. Cipriano MJ, et al. Among authors: Kazakov AE. BMC Genomics. 2013 Apr 2;14:213. doi: 10.1186/1471-2164-14-213. BMC Genomics. 2013. PMID: 23547897 Free PMC article.
New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.
Kazakov AE, Rajeev L, Luning EG, Zane GM, Siddartha K, Rodionov DA, Dubchak I, Arkin AP, Wall JD, Mukhopadhyay A, Novichkov PS. Kazakov AE, et al. J Bacteriol. 2013 Oct;195(19):4466-75. doi: 10.1128/JB.00679-13. Epub 2013 Aug 2. J Bacteriol. 2013. PMID: 23913324 Free PMC article.
Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.
Kuehl JV, Price MN, Ray J, Wetmore KM, Esquivel Z, Kazakov AE, Nguyen M, Kuehn R, Davis RW, Hazen TC, Arkin AP, Deutschbauer A. Kuehl JV, et al. Among authors: Kazakov AE. mBio. 2014 May 27;5(3):e01041-14. doi: 10.1128/mBio.01041-14. mBio. 2014. PMID: 24865553 Free PMC article.
σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.
Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS. Kazakov AE, et al. BMC Genomics. 2015 Nov 10;16:919. doi: 10.1186/s12864-015-2176-y. BMC Genomics. 2015. PMID: 26555820 Free PMC article.
Comparative genomics and evolution of transcriptional regulons in Proteobacteria.
Leyn SA, Suvorova IA, Kazakov AE, Ravcheev DA, Stepanova VV, Novichkov PS, Rodionov DA. Leyn SA, et al. Among authors: Kazakov AE. Microb Genom. 2016 Jul 11;2(7):e000061. doi: 10.1099/mgen.0.000061. eCollection 2016 Jul. Microb Genom. 2016. PMID: 28348857 Free PMC article.
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