{"id":"https://openalex.org/W3116360709","doi":"https://doi.org/10.1093/bioinformatics/btaa1040","title":"<i>Atlas</i>: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages","display_name":"<i>Atlas</i>: automatic modeling of regulation of bacterial gene expression and metabolism using rule-based languages","publication_year":2020,"publication_date":"2020-12-01","ids":{"openalex":"https://openalex.org/W3116360709","doi":"https://doi.org/10.1093/bioinformatics/btaa1040","mag":"3116360709","pmid":"https://pubmed.ncbi.nlm.nih.gov/33367504"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa1040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1040","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5473/36856087/btaa1040.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5473/36856087/btaa1040.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064535301","display_name":"Rodrigo Santib\u00e1\u00f1ez","orcid":"https://orcid.org/0000-0003-0075-4921"},"institutions":[{"id":"https://openalex.org/I116419501","display_name":"Universidad Mayor","ror":"https://ror.org/00pn44t17","country_code":"CL","type":"education","lineage":["https://openalex.org/I116419501"]},{"id":"https://openalex.org/I162148367","display_name":"Pontificia Universidad Cat\u00f3lica de Chile","ror":"https://ror.org/04teye511","country_code":"CL","type":"education","lineage":["https://openalex.org/I162148367"]}],"countries":["CL"],"is_corresponding":true,"raw_author_name":"Rodrigo Santib\u00e1\u00f1ez","raw_affiliation_strings":["Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Cat\u00f3lica de Chile , Santiago 7820436, Chile","Laboratorio de Biolog\u00eda de Redes, Centro de Gen\u00f3mica y Bioinform\u00e1tica, Universidad Mayor , Santiago 8580745, Chile"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Cat\u00f3lica de Chile , Santiago 7820436, Chile","institution_ids":["https://openalex.org/I162148367"]},{"raw_affiliation_string":"Laboratorio de Biolog\u00eda de Redes, Centro de Gen\u00f3mica y Bioinform\u00e1tica, Universidad Mayor , Santiago 8580745, Chile","institution_ids":["https://openalex.org/I116419501"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039876979","display_name":"Daniel Garrido","orcid":"https://orcid.org/0000-0002-4982-134X"},"institutions":[{"id":"https://openalex.org/I162148367","display_name":"Pontificia Universidad Cat\u00f3lica de Chile","ror":"https://ror.org/04teye511","country_code":"CL","type":"education","lineage":["https://openalex.org/I162148367"]}],"countries":["CL"],"is_corresponding":false,"raw_author_name":"Daniel Garrido","raw_affiliation_strings":["Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Cat\u00f3lica de Chile , Santiago 7820436, Chile"],"affiliations":[{"raw_affiliation_string":"Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Cat\u00f3lica de Chile , Santiago 7820436, Chile","institution_ids":["https://openalex.org/I162148367"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022019480","display_name":"Alberto J. M. Mart\u00edn","orcid":"https://orcid.org/0000-0002-6147-3325"},"institutions":[{"id":"https://openalex.org/I116419501","display_name":"Universidad Mayor","ror":"https://ror.org/00pn44t17","country_code":"CL","type":"education","lineage":["https://openalex.org/I116419501"]}],"countries":["CL"],"is_corresponding":true,"raw_author_name":"Alberto J M Martin","raw_affiliation_strings":["Laboratorio de Biolog\u00eda de Redes, Centro de Gen\u00f3mica y Bioinform\u00e1tica, Universidad Mayor , Santiago 8580745, Chile"],"affiliations":[{"raw_affiliation_string":"Laboratorio de Biolog\u00eda de Redes, Centro de Gen\u00f3mica y Bioinform\u00e1tica, Universidad Mayor , Santiago 8580745, Chile","institution_ids":["https://openalex.org/I116419501"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5022019480","https://openalex.org/A5064535301"],"corresponding_institution_ids":["https://openalex.org/I116419501","https://openalex.org/I162148367"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.4183,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.81798034,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"36","issue":"22-23","first_page":"5473","last_page":"5480"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9997000098228455,"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":0.9977999925613403,"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/python","display_name":"Python (programming language)","score":0.7313085794448853},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.692389726638794},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.599895179271698},{"id":"https://openalex.org/keywords/atlas","display_name":"Atlas (anatomy)","score":0.5984038710594177},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5831236243247986},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.526943564414978},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48759689927101135},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.48089599609375},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4531540870666504},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.42629289627075195},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3909187912940979},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35484495759010315},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33673352003097534},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30268046259880066},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2629697322845459},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.258922278881073},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2087388038635254}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7313085794448853},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.692389726638794},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.599895179271698},{"id":"https://openalex.org/C2776673561","wikidata":"https://www.wikidata.org/wiki/Q655357","display_name":"Atlas (anatomy)","level":2,"score":0.5984038710594177},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5831236243247986},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.526943564414978},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48759689927101135},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.48089599609375},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4531540870666504},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.42629289627075195},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3909187912940979},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35484495759010315},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33673352003097534},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30268046259880066},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2629697322845459},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.258922278881073},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2087388038635254},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa1040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1040","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5473/36856087/btaa1040.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33367504","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33367504","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:8016457","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8016457","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/btaa1040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1040","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/22-23/5473/36856087/btaa1040.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320331146","display_name":"Agencia Nacional de Investigaci\u00f3n y Desarrollo","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3116360709.pdf","grobid_xml":"https://content.openalex.org/works/W3116360709.grobid-xml"},"referenced_works_count":84,"referenced_works":["https://openalex.org/W54517741","https://openalex.org/W645554778","https://openalex.org/W836474583","https://openalex.org/W1966786968","https://openalex.org/W1971416176","https://openalex.org/W1972277807","https://openalex.org/W1975993241","https://openalex.org/W1980970686","https://openalex.org/W1986366456","https://openalex.org/W1992204008","https://openalex.org/W1997896246","https://openalex.org/W2003916390","https://openalex.org/W2007085003","https://openalex.org/W2023325148","https://openalex.org/W2036517506","https://openalex.org/W2037645596","https://openalex.org/W2038186289","https://openalex.org/W2042321087","https://openalex.org/W2042388613","https://openalex.org/W2042509708","https://openalex.org/W2069941324","https://openalex.org/W2081781433","https://openalex.org/W2083786039","https://openalex.org/W2085966233","https://openalex.org/W2086928685","https://openalex.org/W2097240335","https://openalex.org/W2100084634","https://openalex.org/W2114104545","https://openalex.org/W2114870653","https://openalex.org/W2121264243","https://openalex.org/W2121490181","https://openalex.org/W2126176298","https://openalex.org/W2128601422","https://openalex.org/W2136770506","https://openalex.org/W2138793275","https://openalex.org/W2140470365","https://openalex.org/W2142055951","https://openalex.org/W2142836135","https://openalex.org/W2146704473","https://openalex.org/W2159675211","https://openalex.org/W2160453515","https://openalex.org/W2163493106","https://openalex.org/W2165700291","https://openalex.org/W2168465568","https://openalex.org/W2180334400","https://openalex.org/W2186373804","https://openalex.org/W2206933645","https://openalex.org/W2559180185","https://openalex.org/W2560707317","https://openalex.org/W2566157169","https://openalex.org/W2586192494","https://openalex.org/W2612519453","https://openalex.org/W2749464300","https://openalex.org/W2755275228","https://openalex.org/W2770082463","https://openalex.org/W2790753957","https://openalex.org/W2807744179","https://openalex.org/W2859249641","https://openalex.org/W2885439034","https://openalex.org/W2887194058","https://openalex.org/W2902840690","https://openalex.org/W2919850041","https://openalex.org/W2925263260","https://openalex.org/W2944969418","https://openalex.org/W2949379258","https://openalex.org/W2950427239","https://openalex.org/W2952117162","https://openalex.org/W2952117952","https://openalex.org/W2952755768","https://openalex.org/W2952850685","https://openalex.org/W2966850388","https://openalex.org/W2970732621","https://openalex.org/W2973177496","https://openalex.org/W2981538024","https://openalex.org/W2988775587","https://openalex.org/W2989997158","https://openalex.org/W3000025696","https://openalex.org/W3003257820","https://openalex.org/W3044339796","https://openalex.org/W3103145119","https://openalex.org/W4211166049","https://openalex.org/W4213108508","https://openalex.org/W4241630616","https://openalex.org/W6818307145"],"related_works":["https://openalex.org/W2789551765","https://openalex.org/W2156421048","https://openalex.org/W2135896045","https://openalex.org/W2032799661","https://openalex.org/W2884256268","https://openalex.org/W2131025197","https://openalex.org/W2171763327","https://openalex.org/W3108451992","https://openalex.org/W2511617859","https://openalex.org/W2031892952"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":7}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2021-01-05T00:00:00"}
