{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:33:59Z","timestamp":1772138039641,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2020,6,23]],"date-time":"2020-06-23T00:00:00Z","timestamp":1592870400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100005739","name":"UNAM","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005739","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["5RO1-GM110597-04"],"award-info":[{"award-number":["5RO1-GM110597-04"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CONACyT M\u00e9xico","award":["565669"],"award-info":[{"award-number":["565669"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>RegulonDB has collected, harmonized and centralized data from hundreds of experiments for nearly two decades and is considered a point of reference for transcriptional regulation in Escherichia coli K12. Here, we present the regutools R package to facilitate programmatic access to RegulonDB data in computational biology. regutools gives researchers the possibility of writing reproducible workflows with automated queries to RegulonDB. The regutools package serves as a bridge between RegulonDB data and the Bioconductor ecosystem by reusing the data structures and statistical methods powered by other Bioconductor packages. We demonstrate the integration of regutools with Bioconductor by analyzing transcription factor DNA binding sites and transcriptional regulatory networks from RegulonDB. We anticipate that regutools will serve as a useful building block in our progress to further our understanding of gene regulatory networks.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>regutools is an R package available through Bioconductor at bioconductor.org\/packages\/regutools.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa575","type":"journal-article","created":{"date-parts":[[2020,6,15]],"date-time":"2020-06-15T15:11:41Z","timestamp":1592233901000},"page":"4532-4534","source":"Crossref","is-referenced-by-count":5,"title":["Programmatic access to bacterial regulatory networks with\n                    <i>regutools<\/i>"],"prefix":"10.1093","volume":"36","author":[{"given":"Joselyn","family":"Ch\u00e1vez","sequence":"first","affiliation":[{"name":"Departamento de Microbiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda"}]},{"given":"Carmina","family":"Barberena-Jonas","sequence":"additional","affiliation":[{"name":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas"},{"name":"Licenciatura de Ciencias Gen\u00f3micas, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Cuernavaca, Morelos, Mexico 62210"},{"name":"National Laboratory of Genomics for Biodiversity, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional , Irapuato, Guanajuato 36821, Mexico"}]},{"given":"Jesus E","family":"Sotelo-Fonseca","sequence":"additional","affiliation":[{"name":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas"},{"name":"Licenciatura de Ciencias Gen\u00f3micas, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Cuernavaca, Morelos, Mexico 62210"},{"name":"National Laboratory of Genomics for Biodiversity, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional , Irapuato, Guanajuato 36821, Mexico"}]},{"given":"Jos\u00e9","family":"Alquicira-Hern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas"},{"name":"Institute for Molecular Bioscience, University of Queensland , Brisbane, QLD 4072, Australia"},{"name":"Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research , Darlinghurst, Sydney, NSW 2010, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3166-5801","authenticated-orcid":false,"given":"Heladia","family":"Salgado","sequence":"additional","affiliation":[{"name":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2140-308X","authenticated-orcid":false,"given":"Leonardo","family":"Collado-Torres","sequence":"additional","affiliation":[{"name":"Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD 21205, USA"}]},{"given":"Alejandro","family":"Reyes","sequence":"additional","affiliation":[{"name":"Department of Data Sciences, Dana-Farber Cancer Institute , Boston, MA 02215, USA"},{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston, MA 02215, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,6,23]]},"reference":[{"key":"2023062213534271000_btaa575-B1","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"Biomart and bioconductor: a powerful link between biological databases and microarray data analysis","volume":"21","author":"Durinck","year":"2005","journal-title":"Bioinformatics"},{"key":"2023062213534271000_btaa575-B2","doi-asserted-by":"crossref","first-page":"D133","DOI":"10.1093\/nar\/gkv1156","article-title":"RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond","volume":"44","author":"Gama-Castro","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023062213534271000_btaa575-B3","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.20887.2","article-title":"RCy3: network biology using cytoscape from within R","author":"Gustavsen","year":"2019","journal-title":"F1000Research"},{"key":"2023062213534271000_btaa575-B4","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1007\/978-1-4939-3578-9_16","volume-title":"Statistical Genomics: Methods and Protocols, Chapter Visualizing Genomic Data Using Gviz and Bioconductor","author":"Hahne","year":"2016"},{"key":"2023062213534271000_btaa575-B5","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nmeth.3252","article-title":"Orchestrating high-throughput genomic analysis with Bioconductor","volume":"12","author":"Huber","year":"2015","journal-title":"Nat. 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Microbiol"},{"key":"2023062213534271000_btaa575-B8","doi-asserted-by":"crossref","first-page":"6656","DOI":"10.1093\/nar\/gkz525","article-title":"Limits to a classic paradigm: most transcription factors in e. coli regulate genes involved in multiple biological processes","volume":"47","author":"Ledezma-Tejeida","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023062213534271000_btaa575-B9","doi-asserted-by":"crossref","first-page":"D212","DOI":"10.1093\/nar\/gky1077","article-title":"RegulonDB v 10.5: tackling challenges to unify classic and high throughput knowledge of gene regulation in E. coli K-12","volume":"47","author":"Santos-Zavaleta","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2023062213534271000_btaa575-B10","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1016\/j.mib.2006.08.007","article-title":"Transcriptional regulatory networks in bacteria: from input signals to output responses","volume":"9","author":"Seshasayee","year":"2006","journal-title":"Curr. 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