{"id":"https://openalex.org/W3037604406","doi":"https://doi.org/10.1093/bioinformatics/btaa575","title":"Programmatic access to bacterial regulatory networks with <i>regutools</i>","display_name":"Programmatic access to bacterial regulatory networks with <i>regutools</i>","publication_year":2020,"publication_date":"2020-06-15","ids":{"openalex":"https://openalex.org/W3037604406","doi":"https://doi.org/10.1093/bioinformatics/btaa575","mag":"3037604406","pmid":"https://pubmed.ncbi.nlm.nih.gov/32573705"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4532/33965599/btaa575.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4532/33965599/btaa575.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036343557","display_name":"Joselyn Ch\u00e1vez","orcid":"https://orcid.org/0000-0002-4974-4591"},"institutions":[{"id":"https://openalex.org/I4210146045","display_name":"Instituto de Biotecnolog\u00eda de Le\u00f3n","ror":"https://ror.org/03ry8wj79","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I4210146045"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Joselyn Ch\u00e1vez","raw_affiliation_strings":["Departamento de Microbiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda"],"affiliations":[{"raw_affiliation_string":"Departamento de Microbiolog\u00eda Molecular, Instituto de Biotecnolog\u00eda","institution_ids":["https://openalex.org/I4210146045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007971858","display_name":"Carmina Barberena-Jonas","orcid":"https://orcid.org/0000-0001-7413-638X"},"institutions":[{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]},{"id":"https://openalex.org/I68368234","display_name":"Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional","ror":"https://ror.org/009eqmr18","country_code":"MX","type":"facility","lineage":["https://openalex.org/I59361560","https://openalex.org/I68368234"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["IT","MX"],"is_corresponding":false,"raw_author_name":"Carmina Barberena-Jonas","raw_affiliation_strings":["Licenciatura de Ciencias Gen\u00f3micas, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Cuernavaca, Morelos, Mexico 62210","National Laboratory of Genomics for Biodiversity, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional , Irapuato, Guanajuato 36821, Mexico","Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas"],"affiliations":[{"raw_affiliation_string":"Licenciatura de Ciencias Gen\u00f3micas, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Cuernavaca, Morelos, Mexico 62210","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"National Laboratory of Genomics for Biodiversity, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional , Irapuato, Guanajuato 36821, Mexico","institution_ids":["https://openalex.org/I68368234"]},{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas","institution_ids":["https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075275334","display_name":"Jes\u00fas Emiliano Sotelo-Fonseca","orcid":"https://orcid.org/0000-0003-1600-2396"},"institutions":[{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]},{"id":"https://openalex.org/I68368234","display_name":"Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional","ror":"https://ror.org/009eqmr18","country_code":"MX","type":"facility","lineage":["https://openalex.org/I59361560","https://openalex.org/I68368234"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["IT","MX"],"is_corresponding":false,"raw_author_name":"Jesus E Sotelo-Fonseca","raw_affiliation_strings":["Licenciatura de Ciencias Gen\u00f3micas, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Cuernavaca, Morelos, Mexico 62210","National Laboratory of Genomics for Biodiversity, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional , Irapuato, Guanajuato 36821, Mexico","Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas"],"affiliations":[{"raw_affiliation_string":"Licenciatura de Ciencias Gen\u00f3micas, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico , Cuernavaca, Morelos, Mexico 62210","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"National Laboratory of Genomics for Biodiversity, Centro de Investigaci\u00f3n y de Estudios Avanzados del Instituto Polit\u00e9cnico Nacional , Irapuato, Guanajuato 36821, Mexico","institution_ids":["https://openalex.org/I68368234"]},{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas","institution_ids":["https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060505830","display_name":"Jos\u00e9 Alquicira-Hern\u00e1ndez","orcid":"https://orcid.org/0000-0002-9049-7780"},"institutions":[{"id":"https://openalex.org/I136750679","display_name":"Garvan Institute of Medical Research","ror":"https://ror.org/01b3dvp57","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I136750679","https://openalex.org/I4210087284"]},{"id":"https://openalex.org/I165143802","display_name":"The University of Queensland","ror":"https://ror.org/00rqy9422","country_code":"AU","type":"education","lineage":["https://openalex.org/I165143802"]},{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["AU","IT"],"is_corresponding":false,"raw_author_name":"Jos\u00e9 Alquicira-Hern\u00e1ndez","raw_affiliation_strings":["Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research , Darlinghurst, Sydney, NSW 2010, Australia","Institute for Molecular Bioscience, University of Queensland , Brisbane, QLD 4072, Australia","Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas"],"affiliations":[{"raw_affiliation_string":"Garvan Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research , Darlinghurst, Sydney, NSW 2010, Australia","institution_ids":["https://openalex.org/I136750679"]},{"raw_affiliation_string":"Institute for Molecular Bioscience, University of Queensland , Brisbane, QLD 4072, Australia","institution_ids":["https://openalex.org/I165143802"]},{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas","institution_ids":["https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091338305","display_name":"Heladia Salgado","orcid":"https://orcid.org/0000-0002-3166-5801"},"institutions":[{"id":"https://openalex.org/I4210151238","display_name":"Center for Genomic Science","ror":"https://ror.org/04xbkmk86","country_code":"IT","type":"facility","lineage":["https://openalex.org/I30771326","https://openalex.org/I4210151238"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Heladia Salgado","raw_affiliation_strings":["Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas"],"affiliations":[{"raw_affiliation_string":"Programa de Gen\u00f3mica Computacional, Centro de Ciencias Gen\u00f3micas","institution_ids":["https://openalex.org/I4210151238"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075979341","display_name":"Leonardo Collado\u2010Torres","orcid":"https://orcid.org/0000-0003-2140-308X"},"institutions":[{"id":"https://openalex.org/I4210151493","display_name":"Lieber Institute for Brain Development","ror":"https://ror.org/04q36wn27","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151493"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Leonardo Collado-Torres","raw_affiliation_strings":["Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD 21205, USA"],"affiliations":[{"raw_affiliation_string":"Lieber Institute for Brain Development, Johns Hopkins Medical Campus , Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I4210151493"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025595162","display_name":"Alejandro Reyes","orcid":"https://orcid.org/0000-0001-8717-6612"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210117453","display_name":"Dana-Farber Cancer Institute","ror":"https://ror.org/02jzgtq86","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210117453"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alejandro Reyes","raw_affiliation_strings":["Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston, MA 02215, USA","Department of Data Sciences, Dana-Farber Cancer Institute , Boston, MA 02215, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston, MA 02215, USA","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Department of Data Sciences, Dana-Farber Cancer Institute , Boston, MA 02215, USA","institution_ids":["https://openalex.org/I4210117453"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5025595162","https://openalex.org/A5075979341"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I4210117453","https://openalex.org/I4210151493"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1669,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.4977792,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"36","issue":"16","first_page":"4532","last_page":"4534"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9879999756813049,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9879999756813049,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9448000192642212,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9257000088691711,"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/computer-science","display_name":"Computer science","score":0.4998619556427002}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4998619556427002}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017753","descriptor_name":"Ecosystem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D048168","descriptor_name":"Escherichia coli K12","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4532/33965599/btaa575.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32573705","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32573705","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7575047","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7575047","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa575","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa575","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/16/4532/33965599/btaa575.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5187590161","display_name":null,"funder_award_id":"5RO1-GM110597-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320323401","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3037604406.pdf","grobid_xml":"https://content.openalex.org/works/W3037604406.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W2056218698","https://openalex.org/W2131478115","https://openalex.org/W2145825942","https://openalex.org/W2232370058","https://openalex.org/W2411397641","https://openalex.org/W2740924955","https://openalex.org/W2900007277","https://openalex.org/W2951718885","https://openalex.org/W2980543550","https://openalex.org/W4238928355"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"regutools":[0],"is":[1],"an":[2],"R":[3],"package":[4],"available":[5],"through":[6],"Bioconductor":[7],"at":[8],"bioconductor.org/packages/regutools.":[9]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2020-07-02T00:00:00"}