{"id":"https://openalex.org/W2941440692","doi":"https://doi.org/10.1371/journal.pcbi.1006971","title":"BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data","display_name":"BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data","publication_year":2019,"publication_date":"2019-04-22","ids":{"openalex":"https://openalex.org/W2941440692","doi":"https://doi.org/10.1371/journal.pcbi.1006971","mag":"2941440692","pmid":"https://pubmed.ncbi.nlm.nih.gov/31009451"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006971","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006971","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006971&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.1006971&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035981186","display_name":"Jean\u2010Christophe Lachance","orcid":"https://orcid.org/0000-0002-3096-6995"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Jean-Christophe Lachance","raw_affiliation_strings":["D\u00e9partement de Biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada"],"raw_orcid":"https://orcid.org/0000-0002-3096-6995","affiliations":[{"raw_affiliation_string":"D\u00e9partement de Biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008123229","display_name":"Colton J. Lloyd","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":"Colton J. Lloyd","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":null,"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/A5088968927","display_name":"Jonathan M. Monk","orcid":"https://orcid.org/0000-0002-3895-8949"},"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":"Jonathan M. Monk","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":null,"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"],"raw_orcid":"https://orcid.org/0000-0001-6663-7643","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/A5047222181","display_name":"Anand V. Sastry","orcid":"https://orcid.org/0000-0002-8293-3909"},"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":"Anand V. Sastry","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-8293-3909","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/A5090742414","display_name":"Yara Seif","orcid":"https://orcid.org/0000-0001-8813-5679"},"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":"Yara Seif","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":null,"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/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/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"]}],"countries":["DK","US"],"is_corresponding":false,"raw_author_name":"Bernhard O. Palsson","raw_affiliation_strings":["Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, United States of America","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, Kemitorvet, Lyngby, Denmark"],"raw_orcid":"https://orcid.org/0000-0003-2357-6785","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"]},{"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, Kemitorvet, Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074451072","display_name":"S\u00e9bastien Rodrigue","orcid":"https://orcid.org/0000-0002-5366-7234"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"S\u00e9bastien Rodrigue","raw_affiliation_strings":["D\u00e9partement de Biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"D\u00e9partement de Biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I135117807"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062042072","display_name":"Adam M. Feist","orcid":"https://orcid.org/0000-0002-8630-4800"},"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/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"]}],"countries":["DK","US"],"is_corresponding":false,"raw_author_name":"Adam M. Feist","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, Kemitorvet, Lyngby, Denmark"],"raw_orcid":"https://orcid.org/0000-0002-8630-4800","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, Kemitorvet, Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]},{"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"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zachary A. King","raw_affiliation_strings":["Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-1238-1499","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":"last","author":{"id":"https://openalex.org/A5007050002","display_name":"Pierre\u2010\u00c9tienne Jacques","orcid":"https://orcid.org/0000-0002-3961-294X"},"institutions":[{"id":"https://openalex.org/I135117807","display_name":"Universit\u00e9 de Sherbrooke","ror":"https://ror.org/00kybxq39","country_code":"CA","type":"education","lineage":["https://openalex.org/I135117807"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Pierre-\u00c9tienne Jacques","raw_affiliation_strings":["D\u00e9partement de Biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada"],"raw_orcid":"https://orcid.org/0000-0002-3961-294X","affiliations":[{"raw_affiliation_string":"D\u00e9partement de Biologie, Universit\u00e9 de Sherbrooke, Sherbrooke, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I135117807"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5007050002","https://openalex.org/A5075454403"],"corresponding_institution_ids":["https://openalex.org/I135117807","https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":5.2121,"has_fulltext":true,"cited_by_count":115,"citation_normalized_percentile":{"value":0.96546278,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"15","issue":"4","first_page":"e1006971","last_page":"e1006971"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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":1.0,"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":0.9951000213623047,"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":0.9932000041007996,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5670831799507141},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5390360355377197},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5262854695320129},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.5208150148391724},{"id":"https://openalex.org/keywords/biomass","display_name":"Biomass (ecology)","score":0.5057985782623291},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49451157450675964},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4613959491252899},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4517672061920166},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39732807874679565},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.32885730266571045},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29168498516082764},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.16531500220298767},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1504688560962677},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09825509786605835}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5670831799507141},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5390360355377197},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5262854695320129},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.5208150148391724},{"id":"https://openalex.org/C115540264","wikidata":"https://www.wikidata.org/wiki/Q2945560","display_name":"Biomass (ecology)","level":2,"score":0.5057985782623291},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49451157450675964},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4613959491252899},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4517672061920166},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39732807874679565},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.32885730266571045},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29168498516082764},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.16531500220298767},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1504688560962677},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09825509786605835},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018533","descriptor_name":"Biomass","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1006971","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006971","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006971&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:31009451","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31009451","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:ark:/13030/qt8px4x4j0","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:doaj.org/article:1a370b2fe7874bbdbe6b6fc1d0f8fbb2","is_oa":true,"landing_page_url":"https://doaj.org/article/1a370b2fe7874bbdbe6b6fc1d0f8fbb2","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"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 15, Iss 4, p e1006971 (2019)","raw_type":"article"},{"id":"pmh:oai:escholarship.org/ark:/13030/qt8px4x4j0","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/8px4x4j0","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS computational biology, vol 15, iss 4","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5494291","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6497307","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":null,"raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/8021507","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/BOFdat_Generating_biomass_objective_functions_for_genome-scale_metabolic_models_from_experimental_data/8021507","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:pure.atira.dk:publications/231ab331-0114-4d98-86f5-f29b3cd5ed46","is_oa":true,"landing_page_url":"https://orbit.dtu.dk/en/publications/231ab331-0114-4d98-86f5-f29b3cd5ed46","pdf_url":null,"source":{"id":"https://openalex.org/S4306400705","display_name":"Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I96673099","host_organization_name":"Technical University of Denmark","host_organization_lineage":["https://openalex.org/I96673099"],"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":"Lachance , J C , Lloyd , C J , Monk , J M , Yang , L , Sastry , A V , Seif , Y , Palsson , B O , Rodrigue , S , Feist , A M , King , Z A & Jacques , P \u00c9 2019 , ' BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data ' , PLOS Computational Biology , vol. 15 , no. 4 , e1006971 . https://doi.org/10.1371/journal.pcbi.1006971","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006971","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006971","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006971&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":[{"score":0.6800000071525574,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G3222081907","display_name":null,"funder_award_id":"206064","funder_id":"https://openalex.org/F4320334841","funder_display_name":"Fonds de recherche du Qu\u00e9bec \u2013 Nature et technologies"}],"funders":[{"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/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320334841","display_name":"Fonds de recherche du Qu\u00e9bec \u2013 Nature et technologies","ror":"https://ror.org/00b9f9778"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2941440692.pdf","grobid_xml":"https://content.openalex.org/works/W2941440692.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W54998723","https://openalex.org/W315903372","https://openalex.org/W1843350440","https://openalex.org/W1884756073","https://openalex.org/W1952732684","https://openalex.org/W1969253588","https://openalex.org/W1985161570","https://openalex.org/W1986656046","https://openalex.org/W1999938932","https://openalex.org/W2003409413","https://openalex.org/W2029403511","https://openalex.org/W2039419058","https://openalex.org/W2041115195","https://openalex.org/W2047632644","https://openalex.org/W2048465561","https://openalex.org/W2073837631","https://openalex.org/W2078355959","https://openalex.org/W2085236271","https://openalex.org/W2085993965","https://openalex.org/W2104619491","https://openalex.org/W2107459209","https://openalex.org/W2109042184","https://openalex.org/W2115069651","https://openalex.org/W2148044817","https://openalex.org/W2154146618","https://openalex.org/W2163433435","https://openalex.org/W2165899056","https://openalex.org/W2191824721","https://openalex.org/W2202347610","https://openalex.org/W2225078051","https://openalex.org/W2394694036","https://openalex.org/W2399597196","https://openalex.org/W2407174002","https://openalex.org/W2560293523","https://openalex.org/W2560707317","https://openalex.org/W2620760558","https://openalex.org/W2734603555","https://openalex.org/W2764202526","https://openalex.org/W2801253816","https://openalex.org/W2804515387","https://openalex.org/W2865919386","https://openalex.org/W6676279030","https://openalex.org/W6753660873"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W2618286804","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380","https://openalex.org/W3193760048","https://openalex.org/W2789551765"],"abstract_inverted_index":{"Genome-scale":[0],"metabolic":[1,85,149],"models":[2],"(GEMs)":[3],"are":[4,131,138,152,209],"mathematically":[5],"structured":[6],"knowledge":[7],"bases":[8],"of":[9,20,28,98,169],"metabolism":[10],"that":[11,34,111],"provide":[12],"phenotypic":[13],"predictions":[14,19],"from":[15,103,159],"genomic":[16],"information.":[17],"GEM-guided":[18],"growth":[21,193],"phenotypes":[22],"rely":[23],"on":[24,220],"the":[25,45,84,96,113,126,146,167,170,179,188,212,215],"accurate":[26],"definition":[27,97,115],"a":[29,75,92,99,108,175],"biomass":[30,41,71,150,191],"objective":[31,72],"function":[32],"(BOF)":[33],"is":[35,65,218],"designed":[36],"to":[37,68,165,202],"include":[38],"key":[39],"cellular":[40],"components":[42],"such":[43],"as":[44,123],"major":[46,129],"macromolecules":[47,130],"(DNA,":[48],"RNA,":[49],"proteins),":[50],"lipids,":[51],"coenzymes,":[52],"inorganic":[53,136],"ions":[54,137],"and":[55,135,140,195,214],"species-specific":[56,70,148],"components.":[57],"Despite":[58],"its":[59],"importance,":[60],"no":[61],"standardized":[62],"computational":[63],"platform":[64],"currently":[66],"available":[67,210,219],"generate":[69],"functions":[73],"in":[74,83,155,178,187,211],"data-driven,":[76],"unbiased":[77,157],"fashion.":[78],"To":[79],"fill":[80],"this":[81],"gap":[82],"modeling":[86],"software":[87],"ecosystem,":[88],"we":[89],"implemented":[90],"BOFdat,":[91],"Python":[93],"package":[94],"for":[95,128,207],"Biomass":[100],"Objective":[101],"Function":[102],"experimental":[104,160],"data.":[105,161],"BOFdat":[106,164,185,208],"has":[107],"modular":[109],"implementation":[110],"divides":[112],"BOF":[114,168,182],"process":[116],"into":[117],"three":[118],"independent":[119],"modules":[120],"defined":[121],"here":[122],"steps:":[124],"1)":[125],"coefficients":[127,143],"calculated,":[132],"2)":[133],"coenzymes":[134],"identified":[139],"their":[141],"stoichiometric":[142],"estimated,":[144],"3)":[145],"remaining":[147],"precursors":[151],"algorithmically":[153],"extracted":[154],"an":[156],"way":[158],"We":[162],"used":[163],"reconstruct":[166],"Escherichia":[171],"coli":[172],"model":[173],"iML1515,":[174],"gold":[176],"standard":[177],"field.":[180],"The":[181],"generated":[183],"by":[184],"resulted":[186],"most":[189],"concordant":[190],"composition,":[192],"rate,":[194],"gene":[196],"essentiality":[197],"prediction":[198],"accuracy":[199],"when":[200],"compared":[201],"other":[203],"methods.":[204],"Installation":[205],"instructions":[206],"documentation":[213],"source":[216],"code":[217],"GitHub":[221],"(https://github.com/jclachance/BOFdat).":[222]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":24},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":25},{"year":2020,"cited_by_count":14},{"year":2019,"cited_by_count":7}],"updated_date":"2026-05-20T08:49:12.498775","created_date":"2025-10-10T00:00:00"}