{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T07:08:13Z","timestamp":1771052893796,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"suppl_1","license":[{"start":{"date-parts":[[2017,5,10]],"date-time":"2017-05-10T00:00:00Z","timestamp":1494374400000},"content-version":"vor","delay-in-days":2748,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1]]},"DOI":"10.1093\/nar\/gkp894","type":"journal-article","created":{"date-parts":[[2009,11,3]],"date-time":"2009-11-03T01:40:26Z","timestamp":1257212426000},"page":"D111-D118","source":"Crossref","is-referenced-by-count":150,"title":["RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes"],"prefix":"10.1093","volume":"38","author":[{"given":"Pavel S.","family":"Novichkov","sequence":"first","affiliation":[]},{"given":"Olga N.","family":"Laikova","sequence":"additional","affiliation":[]},{"given":"Elena S.","family":"Novichkova","sequence":"additional","affiliation":[]},{"given":"Mikhail S.","family":"Gelfand","sequence":"additional","affiliation":[]},{"given":"Adam P.","family":"Arkin","sequence":"additional","affiliation":[]},{"given":"Inna","family":"Dubchak","sequence":"additional","affiliation":[]},{"given":"Dmitry A.","family":"Rodionov","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2009,10,31]]},"reference":[{"key":"key\n\t\t\t\t20170408060131_B1","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1111\/j.1574-6976.2008.00145.x","article-title":"Regulation by transcription factors in bacteria: beyond description","volume":"33","author":"Balleza","year":"2009","journal-title":"FEMS Microbiol. Rev."},{"key":"key\n\t\t\t\t20170408060131_B2","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1016\/j.sbi.2006.04.001","article-title":"Evolution of transcriptional regulatory networks in microbial genomes","volume":"16","author":"Gelfand","year":"2006","journal-title":"Curr. Opin. Struct. Biol."},{"key":"key\n\t\t\t\t20170408060131_B3","doi-asserted-by":"crossref","first-page":"3467","DOI":"10.1021\/cr068309+","article-title":"Comparative genomic reconstruction of transcriptional regulatory networks in bacteria","volume":"107","author":"Rodionov","year":"2007","journal-title":"Chem. Rev."},{"key":"key\n\t\t\t\t20170408060131_B4","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1186\/1471-2105-8-429","article-title":"CoryneRegNet 4.0 \u2013 a reference database for corynebacterial gene regulatory networks","volume":"8","author":"Baumbach","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170408060131_B5","doi-asserted-by":"crossref","first-page":"D120","DOI":"10.1093\/nar\/gkm994","article-title":"RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation","volume":"36","author":"Gama-Castro","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B6","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkn837","article-title":"PRODORIC (release 2009): a database and tool platform for the analysis of gene regulation in prokaryotes","volume":"37","author":"Grote","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B7","doi-asserted-by":"crossref","first-page":"2563","DOI":"10.1093\/bioinformatics\/bti321","article-title":"MtbRegList, a database dedicated to the analysis of transcriptional regulation in Mycobacterium tuberculosis","volume":"21","author":"Jacques","year":"2005","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170408060131_B8","doi-asserted-by":"crossref","first-page":"D93","DOI":"10.1093\/nar\/gkm910","article-title":"DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information","volume":"36","author":"Sierro","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B9","doi-asserted-by":"crossref","first-page":"D407","DOI":"10.1093\/nar\/gkl865","article-title":"RegTransBase \u2013 a database of regulatory sequences and interactions in a wide range of prokaryotic genomes","volume":"35","author":"Kazakov","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B10","doi-asserted-by":"crossref","first-page":"D98","DOI":"10.1093\/nar\/gki054","article-title":"TRACTOR_DB: a database of regulatory networks in gamma-proteobacterial genomes","volume":"33","author":"Gonzalez","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B11","doi-asserted-by":"crossref","first-page":"e97","DOI":"10.1093\/nar\/gkp453","article-title":"From Corynebacterium glutamicum to Mycobacterium tuberculosis \u2013 towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet","volume":"37","author":"Krawczyk","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B12","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1038\/nrmicro1947","article-title":"Towards environmental systems biology of Shewanella","volume":"6","author":"Fredrickson","year":"2008","journal-title":"Nat. Rev. Microbiol."},{"key":"key\n\t\t\t\t20170408060131_B13","doi-asserted-by":"crossref","first-page":"2981","DOI":"10.1093\/nar\/27.14.2981","article-title":"Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes","volume":"27","author":"Mironov","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B14","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1016\/S0923-2508(99)00117-5","article-title":"Recognition of regulatory sites by genomic comparison","volume":"150","author":"Gelfand","year":"1999","journal-title":"Res. Microbiol."},{"key":"key\n\t\t\t\t20170408060131_B15","doi-asserted-by":"crossref","first-page":"1362","DOI":"10.1101\/gr.2242604","article-title":"Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus","volume":"14","author":"Alkema","year":"2004","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170408060131_B16","doi-asserted-by":"crossref","first-page":"7442","DOI":"10.1128\/AEM.71.11.7442-7452.2005","article-title":"Rhodopseudomonas palustris regulons detected by cross-species analysis of alphaproteobacterial genomes","volume":"71","author":"Conlan","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"key\n\t\t\t\t20170408060131_B17","doi-asserted-by":"crossref","first-page":"6617","DOI":"10.1093\/nar\/gkh996","article-title":"Differences in LexA regulon structure among Proteobacteria through in vivo assisted comparative genomics","volume":"32","author":"Erill","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B18","first-page":"209","article-title":"Complementing computationally predicted regulatory sites in Tractor_DB using a pattern matching approach","volume":"5","author":"Guia","year":"2005","journal-title":"In Silico Biol."},{"key":"key\n\t\t\t\t20170408060131_B19","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1186\/1471-2105-4-18","article-title":"Genome wide identification of regulatory motifs in Bacillus subtilis","volume":"4","author":"Mwangi","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170408060131_B20","doi-asserted-by":"crossref","first-page":"1947","DOI":"10.1093\/nar\/gkl138","article-title":"Predicting cis-acting elements of Lactobacillus plantarum by comparative genomics with different taxonomic subgroups","volume":"34","author":"Wels","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B21","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1471-2164-10-23","article-title":"Computational prediction of cAMP receptor protein (CRP) binding sites in cyanobacterial genomes","volume":"10","author":"Xu","year":"2009","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170408060131_B22","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.1093\/nar\/gkn047","article-title":"Transcriptional regulation of NAD metabolism in bacteria: NrtR family of Nudix-related regulators","volume":"36","author":"Rodionov","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B23","doi-asserted-by":"crossref","first-page":"2032","DOI":"10.1093\/nar\/gkn046","article-title":"Transcriptional regulation of NAD metabolism in bacteria: genomic reconstruction of NiaR (YrxA) regulon","volume":"36","author":"Rodionov","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B24","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1101\/gr.314502","article-title":"Conservation of the biotin regulon and the BirA regulatory signal in Eubacteria and Archaea","volume":"12","author":"Rodionov","year":"2002","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170408060131_B25","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1128\/JB.01175-08","article-title":"Comparative genomics of regulation of fatty acid and branched-chain amino acid utilization in proteobacteria","volume":"191","author":"Kazakov","year":"2009","journal-title":"J. Bacteriol."},{"key":"key\n\t\t\t\t20170408060131_B26","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2001-2-4-research0013","article-title":"Conservation of the binding site for the arginine repressor in all bacterial lineages","volume":"2","author":"Makarova","year":"2001","journal-title":"Genome Biol"},{"key":"key\n\t\t\t\t20170408060131_B27","doi-asserted-by":"crossref","first-page":"3340","DOI":"10.1093\/nar\/gkh659","article-title":"Comparative genomics of the methionine metabolism in Gram-positive bacteria: a variety of regulatory systems","volume":"32","author":"Rodionov","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170408060131_B28","doi-asserted-by":"crossref","first-page":"3571","DOI":"10.1099\/mic.0.27041-0","article-title":"Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria","volume":"150","author":"Rodionov","year":"2004","journal-title":"Microbiology"},{"key":"key\n\t\t\t\t20170408060131_B29","doi-asserted-by":"crossref","first-page":"29872","DOI":"10.1074\/jbc.M605052200","article-title":"Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis","volume":"281","author":"Yang","year":"2006","journal-title":"J. Biol. Chem."},{"key":"key\n\t\t\t\t20170408060131_B30","doi-asserted-by":"crossref","first-page":"9912","DOI":"10.1073\/pnas.1733691100","article-title":"Comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins","volume":"100","author":"Panina","year":"2003","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"key\n\t\t\t\t20170408060131_B31","doi-asserted-by":"crossref","first-page":"e163","DOI":"10.1371\/journal.pcbi.0020163","article-title":"Computational reconstruction of iron- and manganese-responsive transcriptional networks in alpha-proteobacteria","volume":"2","author":"Rodionov","year":"2006","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20170408060131_B32","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1186\/1471-2180-6-49","article-title":"Comparative genomics of regulation of heavy metal resistance in Eubacteria","volume":"6","author":"Permina","year":"2006","journal-title":"BMC Microbiol."},{"key":"key\n\t\t\t\t20170408060131_B33","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1186\/1471-2164-8-54","article-title":"Comparative genomic analysis of regulation of anaerobic respiration in ten genomes from three families of gamma-proteobacteria (Enterobacteriaceae, Pasteurellaceae, Vibrionaceae)","volume":"8","author":"Ravcheev","year":"2007","journal-title":"BMC Genomics"},{"key":"key\n\t\t\t\t20170408060131_B34","doi-asserted-by":"crossref","first-page":"e55","DOI":"10.1371\/journal.pcbi.0010055","article-title":"Dissimilatory metabolism of nitrogen oxides in bacteria: comparative reconstruction of transcriptional networks","volume":"1","author":"Rodionov","year":"2005","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20170408060131_B35","doi-asserted-by":"crossref","first-page":"R90","DOI":"10.1186\/gb-2004-5-11-r90","article-title":"Reconstruction of regulatory and metabolic pathways in metal-reducing delta-proteobacteria","volume":"5","author":"Rodionov","year":"2004","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20170408060131_B36","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.tig.2005.05.011","article-title":"Identification of a bacterial regulatory system for ribonucleotide reductases by phylogenetic profiling","volume":"21","author":"Rodionov","year":"2005","journal-title":"Trends Genet."},{"key":"key\n\t\t\t\t20170408060131_B37","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1016\/j.str.2009.05.012","article-title":"Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism","volume":"17","author":"Huang","year":"2009","journal-title":"Structure"},{"key":"key\n\t\t\t\t20170408060131_B38","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170408060131_B39","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1101\/gr.3844805","article-title":"The MicrobesOnline Web site for comparative genomics","volume":"15","author":"Alm","year":"2005","journal-title":"Genome Res."},{"key":"key\n\t\t\t\t20170408060131_B40","doi-asserted-by":"crossref","first-page":"5691","DOI":"10.1093\/nar\/gki866","article-title":"The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes","volume":"33","author":"Overbeek","year":"2005","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/38\/suppl_1\/D111\/11217910\/gkp894.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,17]],"date-time":"2024-03-17T12:04:49Z","timestamp":1710677089000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkp894"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,10,31]]},"references-count":40,"journal-issue":{"issue":"suppl_1","published-online":{"date-parts":[[2009,10,31]]},"published-print":{"date-parts":[[2010,1]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkp894","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,10,31]]}}}