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Items: 1 to 20 of 98

1.

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.

2.

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.

3.

Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis.

Leyn SA, Kazanov MD, Sernova NV, Ermakova EO, Novichkov PS, Rodionov DA.

J Bacteriol. 2013 Jun;195(11):2463-73. doi: 10.1128/JB.00140-13. Epub 2013 Mar 15.

4.

RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Novichkov PS, Brettin TS, Novichkova ES, Dehal PS, Arkin AP, Dubchak I, Rodionov DA.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W604-8. doi: 10.1093/nar/gks562. Epub 2012 Jun 14.

5.

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.

6.

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.

7.

RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.

Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA.

Nucleic Acids Res. 2010 Jan;38(Database issue):D111-8. doi: 10.1093/nar/gkp894. Epub 2009 Nov 1.

8.

Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks.

Rodionov DA, Dubchak IL, Arkin AP, Alm EJ, Gelfand MS.

PLoS Comput Biol. 2005 Oct;1(5):e55. Epub 2005 Oct 28.

9.

Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria.

Sun EI, Leyn SA, Kazanov MD, Saier MH Jr, Novichkov PS, Rodionov DA.

BMC Genomics. 2013 Sep 2;14:597. doi: 10.1186/1471-2164-14-597.

10.

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.

11.

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.

12.

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.

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15.

Novel Transcriptional Regulons for Autotrophic Cycle Genes in Crenarchaeota.

Leyn SA, Rodionova IA, Li X, Rodionov DA.

J Bacteriol. 2015 Jul;197(14):2383-91. doi: 10.1128/JB.00249-15. Epub 2015 May 4.

16.

The cis-regulatory map of Shewanella genomes.

Liu J, Xu X, Stormo GD.

Nucleic Acids Res. 2008 Sep;36(16):5376-90. doi: 10.1093/nar/gkn515. Epub 2008 Aug 13.

17.

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.

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20.

Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways.

Falord M, Mäder U, Hiron A, Débarbouillé M, Msadek T.

PLoS One. 2011;6(7):e21323. doi: 10.1371/journal.pone.0021323. Epub 2011 Jul 1.

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