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Items: 1 to 20 of 22

1.

Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria.

Tsoy OV, Ravcheev DA, ÄŒuklina J, Gelfand MS.

Front Microbiol. 2016 Aug 26;7:1343. doi: 10.3389/fmicb.2016.01343. eCollection 2016.

2.

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis.

Ravcheev DA, Thiele I.

Front Microbiol. 2016 Feb 9;7:128. doi: 10.3389/fmicb.2016.00128. eCollection 2016.

3.

Two novel regulators of N-acetyl-galactosamine utilization pathway and distinct roles in bacterial infections.

Zhang H, Ravcheev DA, Hu D, Zhang F, Gong X, Hao L, Cao M, Rodionov DA, Wang C, Feng Y.

Microbiologyopen. 2015 Dec;4(6):983-1000. doi: 10.1002/mbo3.307. Epub 2015 Nov 5.

4.

Paracoccus denitrificans possesses two BioR homologs having a role in regulation of biotin metabolism.

Feng Y, Kumar R, Ravcheev DA, Zhang H.

Microbiologyopen. 2015 Aug;4(4):644-59. doi: 10.1002/mbo3.270. Epub 2015 Jun 2.

5.

Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota.

Ravcheev DA, Thiele I.

Front Microbiol. 2014 Dec 5;5:674. doi: 10.3389/fmicb.2014.00674. eCollection 2014.

6.

Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum.

Zhang L, Nie X, Ravcheev DA, Rodionov DA, Sheng J, Gu Y, Yang S, Jiang W, Yang C.

J Bacteriol. 2014 Nov;196(22):3949-63. doi: 10.1128/JB.02037-14. Epub 2014 Sep 2.

7.

Comparative genomics and evolution of regulons of the LacI-family transcription factors.

Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA.

Front Microbiol. 2014 Jun 11;5:294. doi: 10.3389/fmicb.2014.00294. eCollection 2014.

8.

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks.

Ravcheev DA, Godzik A, Osterman AL, Rodionov DA.

BMC Genomics. 2013 Dec 12;14:873. doi: 10.1186/1471-2164-14-873.

9.

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.

10.

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.

Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL.

Front Microbiol. 2013 Aug 23;4:244. doi: 10.3389/fmicb.2013.00244. eCollection 2013.

11.

Genomic reconstruction of transcriptional regulatory networks in lactic acid bacteria.

Ravcheev DA, Best AA, Sernova NV, Kazanov MD, Novichkov PS, Rodionov DA.

BMC Genomics. 2013 Feb 12;14:94. doi: 10.1186/1471-2164-14-94.

12.

Regulation and evolution of malonate and propionate catabolism in proteobacteria.

Suvorova IA, Ravcheev DA, Gelfand MS.

J Bacteriol. 2012 Jun;194(12):3234-40. doi: 10.1128/JB.00163-12. Epub 2012 Apr 13.

13.

Temporal regulation of gene expression of the Escherichia coli bacteriophage phiEco32.

Pavlova O, Lavysh D, Klimuk E, Djordjevic M, Ravcheev DA, Gelfand MS, Severinov K, Akulenko N.

J Mol Biol. 2012 Feb 24;416(3):389-99. doi: 10.1016/j.jmb.2012.01.002. Epub 2012 Jan 10.

14.

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.

15.

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.

16.

Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria.

Suvorova IA, Tutukina MN, Ravcheev DA, Rodionov DA, Ozoline ON, Gelfand MS.

J Bacteriol. 2011 Aug;193(15):3956-63. doi: 10.1128/JB.00277-11. Epub 2011 May 27.

17.

Inference of the transcriptional regulatory network in Staphylococcus aureus by integration of experimental and genomics-based evidence.

Ravcheev DA, Best AA, Tintle N, Dejongh M, Osterman AL, Novichkov PS, Rodionov DA.

J Bacteriol. 2011 Jul;193(13):3228-40. doi: 10.1128/JB.00350-11. Epub 2011 Apr 29.

18.

[Regulation of respiration in enterobacteria: comparison of microarray and comparative genomic data].

Tsyganova MO, Gel'fand MS, Ravcheev DA.

Mol Biol (Mosk). 2007 May-Jun;41(3):556-71. Russian.

PMID:
17685233
20.

[Comparative genomics analysis of nitrate and nitrite respiration in gamma proteobacteria].

Ravcheev DA, Rakhmaninova AB, Mironov AA, Gel'fand MS.

Mol Biol (Mosk). 2005 Sep-Oct;39(5):832-46. Russian.

PMID:
16240717
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