{"id":"https://openalex.org/W2106533616","doi":"https://doi.org/10.1093/nar/gkq531","title":"RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach","display_name":"RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach","publication_year":2010,"publication_date":"2010-06-11","ids":{"openalex":"https://openalex.org/W2106533616","doi":"https://doi.org/10.1093/nar/gkq531","mag":"2106533616","pmid":"https://pubmed.ncbi.nlm.nih.gov/20542910"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkq531","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq531","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/nar/gkq531","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5007293969","display_name":"Pavel S. Novichkov","orcid":"https://orcid.org/0000-0002-1102-007X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"P. S. Novichkov","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. psnovichkov@lbl.org","Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. psnovichkov@lbl.org","institution_ids":["https://openalex.org/I148283060"]},{"raw_affiliation_string":"Lawrence Berkeley National Laboratory Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041084611","display_name":"Dmitry A. Rodionov","orcid":"https://orcid.org/0000-0002-0939-390X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. A. Rodionov","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, United States"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077174410","display_name":"Elena Stavrovskaya","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E. D. Stavrovskaya","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, United States"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001036471","display_name":"E. S. Novichkova","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"E. S. Novichkova","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, United States"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036895850","display_name":"Alexey E. Kazakov","orcid":"https://orcid.org/0000-0001-7245-857X"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. E. Kazakov","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, United States"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016957787","display_name":"Mikhail S. Gelfand","orcid":"https://orcid.org/0000-0003-4181-0846"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. S. Gelfand","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, United States"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066623854","display_name":"Adam P. Arkin","orcid":"https://orcid.org/0000-0002-4999-2931"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. P. Arkin","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, United States"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048046634","display_name":"Andrey A. Mironov","orcid":"https://orcid.org/0000-0003-2888-8358"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. A. Mironov","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, United States"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, United States","institution_ids":["https://openalex.org/I148283060"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5107834893","display_name":"Inna Dubchak","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"I. Dubchak","raw_affiliation_strings":["Lawrence Berkeley National Laboratory, Berkeley, United States"],"affiliations":[{"raw_affiliation_string":"Lawrence Berkeley National Laboratory, Berkeley, United States","institution_ids":["https://openalex.org/I148283060"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5007293969"],"corresponding_institution_ids":["https://openalex.org/I148283060"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":6.235,"has_fulltext":false,"cited_by_count":135,"citation_normalized_percentile":{"value":0.97323667,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"Web Server","first_page":"W299","last_page":"W307"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9990000128746033,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/regulon","display_name":"Regulon","score":0.984792172908783},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7668598294258118},{"id":"https://openalex.org/keywords/comparative-genomics","display_name":"Comparative genomics","score":0.7225478887557983},{"id":"https://openalex.org/keywords/operon","display_name":"Operon","score":0.6897717118263245},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5590004324913025},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.5548975467681885},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5425037741661072},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4592127799987793},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4368158280849457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3119277358055115},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.25532519817352295},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.2063383162021637},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.12663519382476807}],"concepts":[{"id":"https://openalex.org/C62361671","wikidata":"https://www.wikidata.org/wiki/Q1754612","display_name":"Regulon","level":4,"score":0.984792172908783},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7668598294258118},{"id":"https://openalex.org/C105176652","wikidata":"https://www.wikidata.org/wiki/Q1147112","display_name":"Comparative genomics","level":5,"score":0.7225478887557983},{"id":"https://openalex.org/C203075996","wikidata":"https://www.wikidata.org/wiki/Q139677","display_name":"Operon","level":4,"score":0.6897717118263245},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5590004324913025},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.5548975467681885},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5425037741661072},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4592127799987793},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4368158280849457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3119277358055115},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25532519817352295},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.2063383162021637},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12663519382476807},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009876","descriptor_name":"Operon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018085","descriptor_name":"Regulon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040141","descriptor_name":"Staphylococcaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D040141","descriptor_name":"Staphylococcaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D040141","descriptor_name":"Staphylococcaceae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/nar/gkq531","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq531","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:20542910","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20542910","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic acids research","raw_type":null},{"id":"pmh:info:ark/67531/metadc1012843","is_oa":false,"landing_page_url":"https://digital.library.unt.edu/ark:/67531/metadc1012843/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400792","display_name":"University of North Texas Digital Library (University of North Texas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I123534392","host_organization_name":"University of North Texas","host_organization_lineage":["https://openalex.org/I123534392"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal Name: Nucleic Acids Research; Journal Volume: 38","raw_type":"Article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt11v6h6pk","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/11v6h6pk","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"article"},{"id":"pmh:oai:open-archive.highwire.org:nar:38/suppl_2/W299","is_oa":false,"landing_page_url":"http://nar.oxfordjournals.org/cgi/content/short/38/suppl_2/W299","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:osti.gov:986246","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/986246","pdf_url":null,"source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2896116","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2896116","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"},{"id":"pmh:qt11v6h6pk","is_oa":false,"landing_page_url":"http://www.escholarship.org/uc/item/11v6h6pk","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Novichkov, Pavel S.(2010). RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Lawrence Berkeley National Laboratory. Lawrence Berkeley National Laboratory: Lawrence Berkeley National Laboratory. Retrieved from: http://www.escholarship.org/uc/item/11v6h6pk","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkq531","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkq531","pdf_url":null,"source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.4399999976158142,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1337544421","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3944918260","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G425189044","display_name":null,"funder_award_id":"DE-AC02-05CH","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4565140552","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4610648879","display_name":null,"funder_award_id":"DE-AC02-05CH112","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G4841871747","display_name":null,"funder_award_id":"DE_AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G4979187122","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5315912995","display_name":null,"funder_award_id":"11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G5719112107","display_name":"Extending the RAST Server to Support Reconstruction and Modeling of Cellular Networks","funder_award_id":"0850546","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5802748842","display_name":null,"funder_award_id":"DE-AC02-05CH112","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G6330738325","display_name":null,"funder_award_id":"DE_AC02_05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6348972864","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6429026066","display_name":null,"funder_award_id":"DE-AC02-05CH112","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G6558272803","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7233692708","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7340683655","display_name":null,"funder_award_id":"E-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7354628648","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G7406122311","display_name":null,"funder_award_id":"AC02-05CH1123","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7629237052","display_name":null,"funder_award_id":"DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G7664691372","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G7787287669","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G7825954517","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7908228807","display_name":null,"funder_award_id":"Molecular","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8306346728","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320338292","funder_display_name":"Lawrence Berkeley National Laboratory"},{"id":"https://openalex.org/G8413608756","display_name":null,"funder_award_id":"DE-AC02-05CH1123","funder_id":"https://openalex.org/F4320337509","funder_display_name":"Biological and Environmental Research"},{"id":"https://openalex.org/G8414908677","display_name":null,"funder_award_id":"DE-AC0","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8673401335","display_name":null,"funder_award_id":"08-04","funder_id":"https://openalex.org/F4320334801","funder_display_name":"Russian Academy of Sciences"},{"id":"https://openalex.org/G897164627","display_name":null,"funder_award_id":"DE-AC02_05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320334801","display_name":"Russian Academy of Sciences","ror":"https://ror.org/05qrfxd25"},{"id":"https://openalex.org/F4320337509","display_name":"Biological and Environmental Research","ror":"https://ror.org/0114b2m14"},{"id":"https://openalex.org/F4320338292","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":25,"referenced_works":["https://openalex.org/W1969630923","https://openalex.org/W1976021976","https://openalex.org/W1994328828","https://openalex.org/W1999309464","https://openalex.org/W2029112298","https://openalex.org/W2073661767","https://openalex.org/W2078034546","https://openalex.org/W2101292724","https://openalex.org/W2104704368","https://openalex.org/W2104867459","https://openalex.org/W2105222452","https://openalex.org/W2105305331","https://openalex.org/W2107522712","https://openalex.org/W2114034054","https://openalex.org/W2119958068","https://openalex.org/W2127057035","https://openalex.org/W2136292095","https://openalex.org/W2137285295","https://openalex.org/W2139324374","https://openalex.org/W2152269861","https://openalex.org/W2154386202","https://openalex.org/W2159588654","https://openalex.org/W2165335121","https://openalex.org/W2166894101","https://openalex.org/W2168786813"],"related_works":["https://openalex.org/W2132790938","https://openalex.org/W2171972144","https://openalex.org/W1796329565","https://openalex.org/W1976388816","https://openalex.org/W2004986663","https://openalex.org/W1544013284","https://openalex.org/W2038893582","https://openalex.org/W2106533616","https://openalex.org/W2336564134","https://openalex.org/W2104867459"],"abstract_inverted_index":{"RegPredict":[0,79,108,140,158],"web":[1,137,156],"server":[2,22],"is":[3,123,159],"designed":[4],"to":[5,26,56,64],"provide":[6],"comparative":[7,18,67],"genomics":[8,19],"tools":[9],"for":[10,84,101],"reconstruction":[11,83],"and":[12,33,63,89,129,142,146],"analysis":[13,59,68],"of":[14,31,40,46,49,60,69,94,104,113,119,139],"microbial":[15],"regulons":[16,32,62],"using":[17,98],"approach.":[20],"The":[21,43],"allows":[23,53],"the":[24,54,58,66,102,133,150],"user":[25,55],"rapidly":[27],"generate":[28],"reference":[29],"sets":[30],"regulatory":[34,87,120],"motif":[35,88],"profiles":[36],"in":[37,78],"a":[38,47,85,95,110],"group":[39],"prokaryotic":[41],"genomes.":[42],"new":[44],"concept":[45],"cluster":[48],"co-regulated":[50],"orthologous":[51],"operons":[52],"distribute":[57],"large":[61],"perform":[65],"multiple":[70],"clusters":[71],"independently.":[72],"Two":[73],"major":[74],"workflows":[75],"currently":[76],"implemented":[77],"are:":[80],"(i)":[81],"regulon":[82,97,152],"known":[86],"(ii)":[90],"ab":[91],"initio":[92],"inference":[93],"novel":[96],"several":[99,155],"scenarios":[100],"generation":[103],"starting":[105],"gene":[106],"sets.":[107],"provides":[109],"comprehensive":[111],"collection":[112],"manually":[114],"curated":[115],"positional":[116],"weight":[117],"matrices":[118],"motifs.":[121],"It":[122],"based":[124],"on":[125],"genomic":[126,145],"sequences,":[127],"ortholog":[128],"operon":[130],"predictions":[131],"from":[132,154],"MicrobesOnline.":[134],"An":[135],"interactive":[136],"interface":[138],"integrates":[141],"presents":[143],"diverse":[144],"functional":[147],"information":[148],"about":[149],"candidate":[151],"members":[153],"resources.":[157],"freely":[160],"accessible":[161],"at":[162],"http://regpredict.lbl.gov.":[163]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":7},{"year":2017,"cited_by_count":10},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":17},{"year":2014,"cited_by_count":14},{"year":2013,"cited_by_count":21},{"year":2012,"cited_by_count":13}],"updated_date":"2026-04-14T08:04:32.555800","created_date":"2025-10-10T00:00:00"}