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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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


The Microbe browser for comparative genomics.

Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W296-9. doi: 10.1093/nar/gkp268.


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.


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.


iCR: a web tool to identify conserved targets of a regulatory protein across the multiple related prokaryotic species.

Ranjan S, Seshadri J, Vindal V, Yellaboina S, Ranjan A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W584-7.


MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level.

Chiapello H, Gendrault A, Caron C, Blum J, Petit MA, El Karoui M.

BMC Bioinformatics. 2008 Nov 27;9:498. doi: 10.1186/1471-2105-9-498.


MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.

Cruveiller S, Le Saux J, Vallenet D, Lajus A, Bocs S, M├ędigue C.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W471-9.


DAVID-WS: a stateful web service to facilitate gene/protein list analysis.

Jiao X, Sherman BT, Huang da W, Stephens R, Baseler MW, Lane HC, Lempicki RA.

Bioinformatics. 2012 Jul 1;28(13):1805-6. doi: 10.1093/bioinformatics/bts251.

20. an on-line community resource for innate immunity research.

Robert C, Lu X, Law A, Freeman TC, Hume DA.

Immunobiology. 2011 Nov;216(11):1203-11. doi: 10.1016/j.imbio.2011.07.025.

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