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Items: 26

1.

Anion transport as a target of adaption to perchlorate in sulfate-reducing communities.

Stoeva MK, Kuehl J, Kazakov AE, Wang O, Rushton-Green R, Coates JD.

ISME J. 2020 Feb;14(2):450-462. doi: 10.1038/s41396-019-0540-7. Epub 2019 Oct 28.

PMID:
31659234
2.

LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species.

Rajeev L, Luning EG, Zane GM, Juba TR, Kazakov AE, Novichkov PS, Wall JD, Mukhopadhyay A.

PLoS One. 2019 Apr 9;14(4):e0214960. doi: 10.1371/journal.pone.0214960. eCollection 2019.

3.

A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport.

Rajeev L, Garber ME, Zane GM, Price MN, Dubchak I, Wall JD, Novichkov PS, Mukhopadhyay A, Kazakov AE.

Environ Microbiol. 2019 Feb;21(2):784-799. doi: 10.1111/1462-2920.14500. Epub 2019 Jan 16.

PMID:
30536693
4.

Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs.

Garber ME, Rajeev L, Kazakov AE, Trinh J, Masuno D, Thompson MG, Kaplan N, Luk J, Novichkov PS, Mukhopadhyay A.

Mol Microbiol. 2018 Mar;107(6):704-717. doi: 10.1111/mmi.13909. Epub 2018 Jan 23.

5.

Draft Genome Sequences of Two Janthinobacteriumlividum Strains, Isolated from Pristine Groundwater Collected from the Oak Ridge Field Research Center.

Wu X, Deutschbauer AM, Kazakov AE, Wetmore KM, Cwick BA, Walker RM, Novichkov PS, Arkin AP, Chakraborty R.

Genome Announc. 2017 Jun 29;5(26). pii: e00582-17. doi: 10.1128/genomeA.00582-17.

6.

Comparative genomics and evolution of transcriptional regulons in Proteobacteria.

Leyn SA, Suvorova IA, Kazakov AE, Ravcheev DA, Stepanova VV, Novichkov PS, Rodionov DA.

Microb Genom. 2016 Jul 11;2(7):e000061. doi: 10.1099/mgen.0.000061. eCollection 2016 Jul.

7.

Novel Metal Cation Resistance Systems from Mutant Fitness Analysis of Denitrifying Pseudomonas stutzeri.

Vaccaro BJ, Lancaster WA, Thorgersen MP, Zane GM, Younkin AD, Kazakov AE, Wetmore KM, Deutschbauer A, Arkin AP, Novichkov PS, Wall JD, Adams MW.

Appl Environ Microbiol. 2016 Sep 16;82(19):6046-56. doi: 10.1128/AEM.01845-16. Print 2016 Oct 1.

8.

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.

Kazakov AE, Rajeev L, Chen A, Luning EG, Dubchak I, Mukhopadhyay A, Novichkov PS.

BMC Genomics. 2015 Nov 10;16:919. doi: 10.1186/s12864-015-2176-y.

9.

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium.

Rajeev L, Chen A, Kazakov AE, Luning EG, Zane GM, Novichkov PS, Wall JD, Mukhopadhyay A.

J Bacteriol. 2015 Nov;197(21):3400-8. doi: 10.1128/JB.00319-15. Epub 2015 Aug 17.

10.

Rex (encoded by DVU_0916) in Desulfovibrio vulgaris Hildenborough is a repressor of sulfate adenylyl transferase and is regulated by NADH.

Christensen GA, Zane GM, Kazakov AE, Li X, Rodionov DA, Novichkov PS, Dubchak I, Arkin AP, Wall JD.

J Bacteriol. 2015 Jan 1;197(1):29-39. doi: 10.1128/JB.02083-14. Epub 2014 Oct 13.

11.

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.

mBio. 2014 May 27;5(3):e01041-14. doi: 10.1128/mBio.01041-14.

12.

RegPrecise 3.0--a resource for genome-scale exploration of transcriptional regulation in bacteria.

Novichkov PS, Kazakov AE, Ravcheev DA, Leyn SA, Kovaleva GY, Sutormin RA, Kazanov MD, Riehl W, Arkin AP, Dubchak I, Rodionov DA.

BMC Genomics. 2013 Nov 1;14:745. doi: 10.1186/1471-2164-14-745.

13.

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.

J Bacteriol. 2013 Oct;195(19):4466-75. doi: 10.1128/JB.00679-13. Epub 2013 Aug 2.

14.

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.

BMC Genomics. 2013 Apr 2;14:213. doi: 10.1186/1471-2164-14-213.

15.

Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes.

Kazakov AE, Rodionov DA, Price MN, Arkin AP, Dubchak I, Novichkov PS.

J Bacteriol. 2013 Jan;195(1):29-38. doi: 10.1128/JB.01977-12. Epub 2012 Oct 19.

16.

Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex.

Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov PS, Osterman AL, Rodionov DA.

J Bacteriol. 2012 Mar;194(5):1145-57. doi: 10.1128/JB.06412-11. Epub 2011 Dec 30.

17.

[Regulation of multidrug resistance genes by transcriptional factors from the BltR subfamily].

Zharov IA, Gel'fand MS, Kazakov AE.

Mol Biol (Mosk). 2011 Jul-Aug;45(4):715-23. Russian.

PMID:
21954605
18.

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.

BMC Genomics. 2011 Jun 15;12 Suppl 1:S3. doi: 10.1186/1471-2164-12-S1-S3.

19.

Comparative genomics of the dormancy regulons in mycobacteria.

Gerasimova A, Kazakov AE, Arkin AP, Dubchak I, Gelfand MS.

J Bacteriol. 2011 Jul;193(14):3446-52. doi: 10.1128/JB.00179-11. Epub 2011 May 20.

20.

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.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W299-307. doi: 10.1093/nar/gkq531. Epub 2010 Jun 11.

21.

Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria.

Kazakov AE, Rodionov DA, Alm E, Arkin AP, Dubchak I, Gelfand MS.

J Bacteriol. 2009 Jan;191(1):52-64. doi: 10.1128/JB.01175-08. Epub 2008 Sep 26.

22.

RegTransBase--a database of regulatory sequences and interactions in a wide range of prokaryotic genomes.

Kazakov AE, Cipriano MJ, Novichkov PS, Minovitsky S, Vinogradov DV, Arkin A, Mironov AA, Gelfand MS, Dubchak I.

Nucleic Acids Res. 2007 Jan;35(Database issue):D407-12. Epub 2006 Nov 16.

23.

Comparative genomics of regulation of heavy metal resistance in Eubacteria.

Permina EA, Kazakov AE, Kalinina OV, Gelfand MS.

BMC Microbiol. 2006 Jun 5;6:49.

24.

Interspersed repeats are found predominantly in the "old" alpha satellite families.

Kazakov AE, Shepelev VA, Tumeneva IG, Alexandrov AA, Yurov YB, Alexandrov IA.

Genomics. 2003 Dec;82(6):619-27.

PMID:
14611803
25.

Bioinformatics classification and functional analysis of PhoH homologs.

Kazakov AE, Vassieva O, Gelfand MS, Osterman A, Overbeek R.

In Silico Biol. 2003;3(1-2):3-15. Epub 2002 Dec 30.

PMID:
12762842
26.

[DNA-diagnosis of bulbospinal muscular atrophy (Kennedy's disease)].

Malygina NA, Kazakov AE, Dubchak LV.

Zh Nevrol Psikhiatr Im S S Korsakova. 1997;97(12):35-8. Russian.

PMID:
9591063

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