{"id":"https://openalex.org/W2139896722","doi":"https://doi.org/10.1093/bib/bbs071","title":"Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models","display_name":"Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models","publication_year":2013,"publication_date":"2013-02-18","ids":{"openalex":"https://openalex.org/W2139896722","doi":"https://doi.org/10.1093/bib/bbs071","mag":"2139896722","pmid":"https://pubmed.ncbi.nlm.nih.gov/23422247"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbs071","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbs071","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://repositorium.uminho.pt/bitstreams/796509fd-ce7b-4084-9bce-d0ac4a4aaa6d/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057203488","display_name":"Jos\u00e9 P. Faria","orcid":"https://orcid.org/0000-0001-9302-7250"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"J. P. Faria","raw_affiliation_strings":["University of MInho"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of MInho","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085138988","display_name":"Ross Overbeek","orcid":null},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]},{"id":"https://openalex.org/I4210145583","display_name":"Bioengineering Center","ror":"https://ror.org/04f0ydx59","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I4210145583"]},{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT","RU","US"],"is_corresponding":false,"raw_author_name":"R. Overbeek","raw_affiliation_strings":["Argonne National Laboratory, the University of Chicago and Northwestern University","MIT Portugal Program in Bioengineering Systems","Institute for Biotechnology and Bioengineering at the University of Minho, Portugal","Centre of Biological Engineering at the University of Minho, Portugal under the scope of the","Argonne National Laboratory","University of Minho, Portugal,","Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Argonne National Laboratory, the University of Chicago and Northwestern University","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"MIT Portugal Program in Bioengineering Systems","institution_ids":["https://openalex.org/I4210145583"]},{"raw_affiliation_string":"Institute for Biotechnology and Bioengineering at the University of Minho, Portugal","institution_ids":["https://openalex.org/I4210167387"]},{"raw_affiliation_string":"Centre of Biological Engineering at the University of Minho, Portugal under the scope of the","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"Argonne National Laboratory","institution_ids":["https://openalex.org/I1282105669"]},{"raw_affiliation_string":"University of Minho, Portugal,","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"Argonne National Laboratory, Mathematics and Computer Science Division, Argonne, IL, USA","institution_ids":["https://openalex.org/I1282105669"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100781183","display_name":"Fang Xia","orcid":"https://orcid.org/0000-0002-0676-8606"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"F. Xia","raw_affiliation_strings":["University-of Chicago"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University-of Chicago","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"M. Rocha","raw_affiliation_strings":["University of MInho"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of MInho","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079343705","display_name":"Isabel Rocha","orcid":"https://orcid.org/0000-0001-9494-3410"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"I. Rocha","raw_affiliation_strings":["University of MInho"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of MInho","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017949757","display_name":"Christopher S. Henry","orcid":"https://orcid.org/0000-0001-8058-9123"},"institutions":[{"id":"https://openalex.org/I1282105669","display_name":"Argonne National Laboratory","ror":"https://ror.org/05gvnxz63","country_code":"US","type":"facility","lineage":["https://openalex.org/I1282105669","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"C. S. Henry","raw_affiliation_strings":["argonne national laboratory"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"argonne national laboratory","institution_ids":["https://openalex.org/I1282105669"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.6509,"has_fulltext":true,"cited_by_count":33,"citation_normalized_percentile":{"value":0.83785472,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"15","issue":"4","first_page":"592","last_page":"611"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9987999796867371,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976999759674072,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6486274003982544},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5423293113708496},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5166594982147217},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5063656568527222},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.49126261472702026},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"Transcriptional regulation","score":0.4267337918281555},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.3998880982398987},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39730843901634216},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3242897391319275},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22270312905311584},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1630193591117859}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6486274003982544},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5423293113708496},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5166594982147217},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5063656568527222},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.49126261472702026},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.4267337918281555},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.3998880982398987},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39730843901634216},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3242897391319275},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22270312905311584},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1630193591117859}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","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":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbs071","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbs071","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23422247","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23422247","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/32872","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/32872","pdf_url":"https://repositorium.uminho.pt/bitstreams/796509fd-ce7b-4084-9bce-d0ac4a4aaa6d/download","source":{"id":"https://openalex.org/S4306401240","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},{"id":"pmh:oai:repositorium.uminho.pt:1822/32872","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/32872","pdf_url":null,"source":{"id":"https://openalex.org/S4306402433","display_name":"Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT)","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"}],"best_oa_location":{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/32872","is_oa":true,"landing_page_url":"http://hdl.handle.net/1822/32872","pdf_url":"https://repositorium.uminho.pt/bitstreams/796509fd-ce7b-4084-9bce-d0ac4a4aaa6d/download","source":{"id":"https://openalex.org/S4306401240","display_name":"Reposit\u00f3riUM (Universidade do Minho)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99682543","host_organization_name":"University of Minho","host_organization_lineage":["https://openalex.org/I99682543"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"journal article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6848031779","display_name":null,"funder_award_id":"06CH11357","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G7067800823","display_name":null,"funder_award_id":"DE-ACO2-06CH11357","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G8868700560","display_name":null,"funder_award_id":"FCOMP-01-0124-FEDER","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"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/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2139896722.pdf","grobid_xml":"https://content.openalex.org/works/W2139896722.grobid-xml"},"referenced_works_count":199,"referenced_works":["https://openalex.org/W46105055","https://openalex.org/W176253898","https://openalex.org/W195865777","https://openalex.org/W574923274","https://openalex.org/W1481919380","https://openalex.org/W1529414772","https://openalex.org/W1544923801","https://openalex.org/W1547075801","https://openalex.org/W1553833389","https://openalex.org/W1574079093","https://openalex.org/W1591722906","https://openalex.org/W1644055901","https://openalex.org/W1657934012","https://openalex.org/W1893022572","https://openalex.org/W1965201359","https://openalex.org/W1967078918","https://openalex.org/W1969630923","https://openalex.org/W1972764318","https://openalex.org/W1972793193","https://openalex.org/W1976136586","https://openalex.org/W1978394237","https://openalex.org/W1979622547","https://openalex.org/W1981509058","https://openalex.org/W1982309495","https://openalex.org/W1984096521","https://openalex.org/W1984708728","https://openalex.org/W1986688807","https://openalex.org/W1992306474","https://openalex.org/W1993891546","https://openalex.org/W1994692113","https://openalex.org/W1994996846","https://openalex.org/W1995031758","https://openalex.org/W1995117714","https://openalex.org/W1996529795","https://openalex.org/W1996695434","https://openalex.org/W1998544165","https://openalex.org/W1998633945","https://openalex.org/W1998757083","https://openalex.org/W1999309464","https://openalex.org/W2000964393","https://openalex.org/W2002880495","https://openalex.org/W2003835605","https://openalex.org/W2006998897","https://openalex.org/W2009940763","https://openalex.org/W2010888033","https://openalex.org/W2012696764","https://openalex.org/W2013297302","https://openalex.org/W2018591360","https://openalex.org/W2020350008","https://openalex.org/W2020541351","https://openalex.org/W2021836418","https://openalex.org/W2022684902","https://openalex.org/W2023348596","https://openalex.org/W2025172803","https://openalex.org/W2025206606","https://openalex.org/W2026089579","https://openalex.org/W2026882865","https://openalex.org/W2029670310","https://openalex.org/W2031512086","https://openalex.org/W2032062076","https://openalex.org/W2034324557","https://openalex.org/W2038012561","https://openalex.org/W2038622868","https://openalex.org/W2044525257","https://openalex.org/W2046254395","https://openalex.org/W2047228180","https://openalex.org/W2053126761","https://openalex.org/W2054331129","https://openalex.org/W2054613021","https://openalex.org/W2056182651","https://openalex.org/W2056754810","https://openalex.org/W2058221907","https://openalex.org/W2059126588","https://openalex.org/W2060350133","https://openalex.org/W2061163312","https://openalex.org/W2062029454","https://openalex.org/W2062245653","https://openalex.org/W2064034649","https://openalex.org/W2065020503","https://openalex.org/W2066580949","https://openalex.org/W2070072684","https://openalex.org/W2070350400","https://openalex.org/W2071921819","https://openalex.org/W2076372398","https://openalex.org/W2076382102","https://openalex.org/W2076513103","https://openalex.org/W2078034546","https://openalex.org/W2078149659","https://openalex.org/W2081468394","https://openalex.org/W2081781433","https://openalex.org/W2081875512","https://openalex.org/W2082948758","https://openalex.org/W2084018951","https://openalex.org/W2084833542","https://openalex.org/W2084908610","https://openalex.org/W2086206983","https://openalex.org/W2087430129","https://openalex.org/W2089449076","https://openalex.org/W2090974286","https://openalex.org/W2091879895","https://openalex.org/W2094678200","https://openalex.org/W2096192437","https://openalex.org/W2096328440","https://openalex.org/W2099269203","https://openalex.org/W2100084634","https://openalex.org/W2100471807","https://openalex.org/W2100850281","https://openalex.org/W2101029276","https://openalex.org/W2101292724","https://openalex.org/W2102456970","https://openalex.org/W2103009708","https://openalex.org/W2103184043","https://openalex.org/W2104704368","https://openalex.org/W2104877015","https://openalex.org/W2105129830","https://openalex.org/W2105222452","https://openalex.org/W2106533616","https://openalex.org/W2106927126","https://openalex.org/W2106945333","https://openalex.org/W2107333582","https://openalex.org/W2107474451","https://openalex.org/W2107522712","https://openalex.org/W2107888921","https://openalex.org/W2109880272","https://openalex.org/W2111148192","https://openalex.org/W2112933558","https://openalex.org/W2113320904","https://openalex.org/W2114034054","https://openalex.org/W2114650383","https://openalex.org/W2115108153","https://openalex.org/W2115851903","https://openalex.org/W2117379303","https://openalex.org/W2118628540","https://openalex.org/W2121150592","https://openalex.org/W2121530190","https://openalex.org/W2121695897","https://openalex.org/W2124967403","https://openalex.org/W2125508747","https://openalex.org/W2125631472","https://openalex.org/W2126175129","https://openalex.org/W2126176298","https://openalex.org/W2129265801","https://openalex.org/W2129389248","https://openalex.org/W2129795133","https://openalex.org/W2130313341","https://openalex.org/W2133636765","https://openalex.org/W2137285295","https://openalex.org/W2137993400","https://openalex.org/W2139070508","https://openalex.org/W2139915240","https://openalex.org/W2139997707","https://openalex.org/W2140055849","https://openalex.org/W2141408320","https://openalex.org/W2142400903","https://openalex.org/W2143076232","https://openalex.org/W2143517204","https://openalex.org/W2143754608","https://openalex.org/W2148554599","https://openalex.org/W2148749184","https://openalex.org/W2152269861","https://openalex.org/W2152556351","https://openalex.org/W2152763121","https://openalex.org/W2152979636","https://openalex.org/W2154061034","https://openalex.org/W2154362705","https://openalex.org/W2154386202","https://openalex.org/W2154431984","https://openalex.org/W2154601808","https://openalex.org/W2156425900","https://openalex.org/W2157121418","https://openalex.org/W2157937275","https://openalex.org/W2158128075","https://openalex.org/W2159100436","https://openalex.org/W2159883877","https://openalex.org/W2160095931","https://openalex.org/W2160794724","https://openalex.org/W2161409973","https://openalex.org/W2161511352","https://openalex.org/W2161732139","https://openalex.org/W2161922735","https://openalex.org/W2161986541","https://openalex.org/W2164078761","https://openalex.org/W2165392091","https://openalex.org/W2165660562","https://openalex.org/W2166106382","https://openalex.org/W2167190345","https://openalex.org/W2168546553","https://openalex.org/W2168786813","https://openalex.org/W2170401183","https://openalex.org/W2170682402","https://openalex.org/W2171088586","https://openalex.org/W2171560951","https://openalex.org/W2611370172","https://openalex.org/W3099289621","https://openalex.org/W4213265720","https://openalex.org/W4213387068","https://openalex.org/W4248318091","https://openalex.org/W4253759977","https://openalex.org/W4302332334"],"related_works":["https://openalex.org/W2400150343","https://openalex.org/W2062631153","https://openalex.org/W2082736011","https://openalex.org/W3161647893","https://openalex.org/W2121264243","https://openalex.org/W2002880495","https://openalex.org/W2139199642","https://openalex.org/W1984003821","https://openalex.org/W2121995533","https://openalex.org/W2077941487"],"abstract_inverted_index":{"Advances":[0],"in":[1,6,43,164],"sequencing":[2],"technology":[3],"are":[4,113],"resulting":[5],"the":[7,40,55,68,75,78,117,157,168,176],"rapid":[8],"emergence":[9],"of":[10,13,22,34,48,57,67,77,93,119,170,172],"large":[11],"numbers":[12],"complete":[14],"genome":[15],"sequences.":[16],"High-throughput":[17],"annotation":[18],"and":[19,32,65,103,107,143,152],"metabolic":[20,146],"modeling":[21],"these":[23,111,159],"genomes":[24],"is":[25],"now":[26],"a":[27,179],"reality.":[28],"The":[29,46],"high-throughput":[30],"reconstruction":[31,118],"analysis":[33],"genome-scale":[35,82],"transcriptional":[36,69,94],"regulatory":[37,70,79,95,121,138],"networks":[38,139],"represent":[39],"next":[41,50],"frontier":[42,51],"microbial":[44],"bioinformatics.":[45],"fruition":[47],"this":[49],"will":[52],"depend":[53],"on":[54],"integration":[56,76],"numerous":[58],"data":[59,102,112],"sources":[60],"relating":[61],"to":[62,127,148,178],"mechanisms,":[63],"components":[64],"behavior":[66],"machinery,":[71],"as":[72,74],"well":[73],"machinery":[80],"into":[81],"cellular":[83],"models.":[84],"Here,":[85],"we":[86,108,135],"review":[87],"existing":[88],"repositories":[89],"for":[90,116],"different":[91],"types":[92],"data,":[96,99,134],"including":[97],"expression":[98,133],"transcription":[100],"factor":[101],"binding":[104],"site":[105],"locations":[106],"explore":[109,156],"how":[110,137],"being":[114],"used":[115],"new":[120],"networks.":[122],"From":[123],"template":[124],"network-based":[125],"methods":[126],"de":[128],"novo":[129],"reverse":[130],"engineering":[131],"from":[132],"discuss":[136],"can":[140,162],"be":[141],"reconstructed":[142],"integrated":[144,160],"with":[145],"models":[147,161],"improve":[149],"model":[150],"predictions":[151],"performance.":[153],"We":[154],"also":[155],"impact":[158],"have":[163],"simulating":[165],"phenotypes,":[166],"optimizing":[167],"production":[169],"compounds":[171],"interest":[173],"or":[174],"paving":[175],"way":[177],"whole-cell":[180],"model.":[181]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":6}],"updated_date":"2026-07-25T09:21:30.201066","created_date":"2025-10-10T00:00:00"}
