{"id":"https://openalex.org/W2833943491","doi":"https://doi.org/10.1371/journal.pcbi.1006302","title":"COBRAme: A computational framework for genome-scale models of metabolism and gene expression","display_name":"COBRAme: A computational framework for genome-scale models of metabolism and gene expression","publication_year":2018,"publication_date":"2018-07-05","ids":{"openalex":"https://openalex.org/W2833943491","doi":"https://doi.org/10.1371/journal.pcbi.1006302","mag":"2833943491","pmid":"https://pubmed.ncbi.nlm.nih.gov/29975681"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006302","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006302","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006302&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006302&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008123229","display_name":"Colton J. Lloyd","orcid":"https://orcid.org/0000-0001-6556-6345"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colton J. Lloyd","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101406018","display_name":"Ali Ebrahim","orcid":"https://orcid.org/0000-0002-4009-2128"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ali Ebrahim","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080751595","display_name":"Laurence Yang","orcid":"https://orcid.org/0000-0001-6663-7643"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laurence Yang","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075454403","display_name":"Zachary A. King","orcid":"https://orcid.org/0000-0003-1238-1499"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]},{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]}],"countries":["DK","US"],"is_corresponding":false,"raw_author_name":"Zachary A. King","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020518995","display_name":"Edward Catoiu","orcid":"https://orcid.org/0000-0001-8680-7291"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward Catoiu","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051432302","display_name":"Edward J. O\u2019Brien","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Edward J. O\u2019Brien","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045539808","display_name":"Joanne K. Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joanne K. Liu","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, United States of America"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051097609","display_name":"Bernhard \u00d8. Palsson","orcid":"https://orcid.org/0000-0003-2357-6785"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]},{"id":"https://openalex.org/I36258959","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["DK","US"],"is_corresponding":true,"raw_author_name":"Bernhard O. Palsson","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5051097609"],"corresponding_institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I36258959","https://openalex.org/I96673099"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":8.4378,"has_fulltext":true,"cited_by_count":173,"citation_normalized_percentile":{"value":0.98452628,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"14","issue":"7","first_page":"e1006302","last_page":"e1006302"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9998999834060669,"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":0.9998999834060669,"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9836999773979187,"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":0.6605777144432068},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5575980544090271},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5016531944274902},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46212953329086304},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.45059120655059814},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4141843616962433},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.41191619634628296},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32862579822540283},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2771375775337219}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6605777144432068},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5575980544090271},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5016531944274902},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46212953329086304},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.45059120655059814},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4141843616962433},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.41191619634628296},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32862579822540283},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2771375775337219},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008660","descriptor_name":"Metabolism","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":10,"locations":[{"id":"doi:10.1371/journal.pcbi.1006302","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006302","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006302&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:29975681","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29975681","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:533a1c804675454ba81e419452b929d3","is_oa":true,"landing_page_url":"https://doaj.org/article/533a1c804675454ba81e419452b929d3","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 14, Iss 7, p e1006302 (2018)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt15k9w6t3","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/15k9w6t3","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLOS Computational Biology, vol 14, iss 7","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5012999","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6049947","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/6744299","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/COBRAme_A_computational_framework_for_genome-scale_models_of_metabolism_and_gene_expression/6744299","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:osti.gov:1459050","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1459050","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":"","raw_type":""},{"id":"pmh:oai:osti.gov:1460606","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1460606","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":"","raw_type":""},{"id":"pmh:oai:osti.gov:1544029","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1544029","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":"","raw_type":""},{"id":"pmh:oai:pubmedcentral.nih.gov:6049947","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6049947","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006302","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006302","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006302&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life below water","score":0.5799999833106995,"id":"https://metadata.un.org/sdg/14"}],"awards":[{"id":"https://openalex.org/G1387674867","display_name":null,"funder_award_id":"U01GM102098","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5417901379","display_name":null,"funder_award_id":"NNF10CC1016517","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G7555623405","display_name":null,"funder_award_id":"DGE-1144086","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"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/F4320317220","display_name":"National Energy Research Scientific Computing Center","ror":"https://ror.org/05v3mvq14"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320323153","display_name":"Danmarks Tekniske Universitet","ror":"https://ror.org/04qtj9h94"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2833943491.pdf","grobid_xml":"https://content.openalex.org/works/W2833943491.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W1665355332","https://openalex.org/W1754578874","https://openalex.org/W2011357920","https://openalex.org/W2014482592","https://openalex.org/W2034494369","https://openalex.org/W2044935306","https://openalex.org/W2048465561","https://openalex.org/W2081781433","https://openalex.org/W2082382448","https://openalex.org/W2085966233","https://openalex.org/W2104842437","https://openalex.org/W2109553965","https://openalex.org/W2111967267","https://openalex.org/W2114850508","https://openalex.org/W2120167281","https://openalex.org/W2121514092","https://openalex.org/W2122860350","https://openalex.org/W2124737787","https://openalex.org/W2144009916","https://openalex.org/W2144068357","https://openalex.org/W2147472054","https://openalex.org/W2148044817","https://openalex.org/W2151313241","https://openalex.org/W2152164604","https://openalex.org/W2162144833","https://openalex.org/W2170298003","https://openalex.org/W2521256720","https://openalex.org/W2538527935","https://openalex.org/W2541638185","https://openalex.org/W2760895823","https://openalex.org/W2764202526","https://openalex.org/W2870292801","https://openalex.org/W4249835868"],"related_works":["https://openalex.org/W2086525401","https://openalex.org/W2006735166","https://openalex.org/W2079327011","https://openalex.org/W2053325634","https://openalex.org/W2392243736","https://openalex.org/W3178279768","https://openalex.org/W86652014","https://openalex.org/W2888097224","https://openalex.org/W2773861473","https://openalex.org/W193851735"],"abstract_inverted_index":{"Genome-scale":[0],"models":[1,24,74],"of":[2,14,25,35,49,56,146,193,212,248],"metabolism":[3,26],"and":[4,28,43,68,81,97,100,123,131,144,154,196,250,258],"macromolecular":[5],"expression":[6],"(ME-models)":[7],"explicitly":[8],"compute":[9,80],"the":[10,21,50,54,191,207,246,263],"optimal":[11],"proteome":[12],"composition":[13],"a":[15,31,62,87,115,135,169,203],"growing":[16],"cell.":[17],"ME-models":[18,38,89,156,187,219,253],"expand":[19],"upon":[20],"well-established":[22],"genome-scale":[23],"(M-models),":[27],"they":[29,59],"enable":[30,158],"new":[32,116,162,264],"fundamental":[33],"understanding":[34],"cellular":[36],"growth.":[37],"have":[39,113],"increased":[40],"predictive":[41],"capabilities":[42],"accuracy":[44],"due":[45],"to":[46,79,83,151,157,167,183,224,234],"their":[47],"inclusion":[48],"biosynthetic":[51],"costs":[52],"for":[53,91,121,138,161],"machinery":[55],"life,":[57],"but":[58],"come":[60],"with":[61],"significant":[63],"increase":[64],"in":[65,73,129,198,217,232,237,240],"model":[66,178],"size":[67],"complexity.":[69],"This":[70,176,243],"challenge":[71],"results":[72],"which":[75],"are":[76,101],"both":[77],"difficult":[78],"challenging":[82],"understand":[84],"conceptually.":[85],"As":[86],"result,":[88],"exist":[90],"only":[92],"two":[93],"organisms":[94],"(Escherichia":[95],"coli":[96,172,186],"Thermotoga":[98],"maritima)":[99],"still":[102],"used":[103,165],"by":[104],"relatively":[105],"few":[106],"researchers.":[107],"To":[108],"address":[109],"these":[110],"challenges,":[111],"we":[112],"developed":[114],"software":[117,265],"framework":[118],"called":[119,174],"COBRAme":[120,141,166,249],"building":[122],"simulating":[124],"ME-models.":[125,147],"It":[126,148],"is":[127],"coded":[128],"Python":[130],"built":[132],"on":[133],"COBRApy,":[134],"popular":[136],"platform":[137],"using":[139,189,262],"M-models.":[140],"streamlines":[142],"computation":[143],"analysis":[145],"provides":[149],"tools":[150],"simplify":[152],"constructing":[153],"editing":[155],"ME-model":[159,173,214],"reconstructions":[160],"organisms.":[163],"We":[164],"reconstruct":[168],"condensed":[170],"E.":[171,185],"iJL1678b-ME.":[175],"reformulated":[177],"gives":[179],"functionally":[180],"identical":[181],"solutions":[182],"previous":[184,213,218],"while":[188],"1/6":[190],"number":[192],"free":[194],"variables":[195],"solving":[197],"less":[199],"than":[200],"10":[201],"minutes,":[202],"marked":[204],"improvement":[205],"over":[206],"6":[208],"hour":[209],"solve":[210],"time":[211],"formulations.":[215],"Errors":[216],"were":[220],"also":[221],"corrected":[222],"leading":[223],"52":[225],"additional":[226],"genes":[227],"that":[228],"must":[229],"be":[230,255],"expressed":[231],"iJL1678b-ME":[233],"grow":[235],"aerobically":[236],"glucose":[238],"minimal":[239],"silico":[241],"media.":[242],"manuscript":[244],"outlines":[245],"architecture":[247],"demonstrates":[251],"how":[252],"can":[254],"created,":[256],"modified,":[257],"shared":[259],"most":[260],"efficiently":[261],"framework.":[266]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":33},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":19},{"year":2021,"cited_by_count":35},{"year":2020,"cited_by_count":25},{"year":2019,"cited_by_count":26},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-03-08T08:50:53.379069","created_date":"2025-10-10T00:00:00"}
