{"id":"https://openalex.org/W2165387703","doi":"https://doi.org/10.1371/journal.pcbi.1003126","title":"Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM","display_name":"Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM","publication_year":2013,"publication_date":"2013-07-18","ids":{"openalex":"https://openalex.org/W2165387703","doi":"https://doi.org/10.1371/journal.pcbi.1003126","mag":"2165387703","pmid":"https://pubmed.ncbi.nlm.nih.gov/23935467"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1003126","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003126","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003126&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.1003126&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089465175","display_name":"Jonathan M. Dreyfuss","orcid":"https://orcid.org/0000-0001-7242-3991"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan M. Dreyfuss","raw_affiliation_strings":["Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015978856","display_name":"Jeremy Zucker","orcid":"https://orcid.org/0000-0002-7276-9009"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy D. Zucker","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America","Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","Tardigrade Biotechnologies, Jamaica Plain, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Tardigrade Biotechnologies, Jamaica Plain, Massachusetts, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055566053","display_name":"Heather M. Hood","orcid":null},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heather M. Hood","raw_affiliation_strings":["Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon, United States of America"],"affiliations":[{"raw_affiliation_string":"Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon, United States of America","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085612232","display_name":"Linda R. Ocasio","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Linda R. Ocasio","raw_affiliation_strings":["Tardigrade Biotechnologies, Jamaica Plain, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Tardigrade Biotechnologies, Jamaica Plain, Massachusetts, United States of America","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083058673","display_name":"Matthew S. Sachs","orcid":"https://orcid.org/0000-0001-9891-9223"},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew S. Sachs","raw_affiliation_strings":["Department of Biology, Texas A&M University, College Station, Texas, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Texas A&M University, College Station, Texas, United States of America","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056863747","display_name":"James E. Galagan","orcid":"https://orcid.org/0000-0003-0542-3291"},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"funder","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"James E. Galagan","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America","Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America"],"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]},{"raw_affiliation_string":"Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5056863747"],"corresponding_institution_ids":["https://openalex.org/I107606265","https://openalex.org/I111088046"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.0705,"has_fulltext":true,"cited_by_count":70,"citation_normalized_percentile":{"value":0.92121527,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"9","issue":"7","first_page":"e1003126","last_page":"e1003126"},"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9961000084877014,"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":0.9955999851226807,"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/neurospora-crassa","display_name":"Neurospora crassa","score":0.8341320753097534},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.7796130180358887},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7252449989318848},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.7122300267219543},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6979566216468811},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.658867359161377},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5868204832077026},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.525256335735321},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.5245395302772522},{"id":"https://openalex.org/keywords/neurospora","display_name":"Neurospora","score":0.5180249810218811},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.44039615988731384},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.42389047145843506},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.42005935311317444},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41686946153640747},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4027978777885437},{"id":"https://openalex.org/keywords/mutant","display_name":"Mutant","score":0.10048657655715942},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.09408825635910034}],"concepts":[{"id":"https://openalex.org/C2776739539","wikidata":"https://www.wikidata.org/wiki/Q133459","display_name":"Neurospora crassa","level":4,"score":0.8341320753097534},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.7796130180358887},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7252449989318848},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.7122300267219543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6979566216468811},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.658867359161377},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5868204832077026},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.525256335735321},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.5245395302772522},{"id":"https://openalex.org/C2776769606","wikidata":"https://www.wikidata.org/wiki/Q309943","display_name":"Neurospora","level":5,"score":0.5180249810218811},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.44039615988731384},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.42389047145843506},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.42005935311317444},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41686946153640747},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4027978777885437},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.10048657655715942},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.09408825635910034},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","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":"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":"D009492","descriptor_name":"Neurospora crassa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009492","descriptor_name":"Neurospora crassa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009492","descriptor_name":"Neurospora crassa","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1003126","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003126","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003126&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:23935467","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23935467","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:dash.harvard.edu:1/11855753","is_oa":true,"landing_page_url":"http://nrs.harvard.edu/urn-3:HUL.InstRepos:11855753","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:f9cbcfc2850d44958456ecb969c51e43","is_oa":true,"landing_page_url":"https://doaj.org/article/f9cbcfc2850d44958456ecb969c51e43","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 9, Iss 7, p e1003126 (2013)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:2731327","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3730674","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/748097","is_oa":true,"landing_page_url":"https://figshare.com/articles/Reconstruction_and_Validation_of_a_Genome_Scale_Metabolic_Model_for_the_Filamentous_Fungus_Neurospora_crassa_Using_FARM/748097","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1003126","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1003126","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1003126&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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2165387703.pdf","grobid_xml":"https://content.openalex.org/works/W2165387703.grobid-xml"},"referenced_works_count":117,"referenced_works":["https://openalex.org/W68507353","https://openalex.org/W1482541033","https://openalex.org/W1486011748","https://openalex.org/W1489312705","https://openalex.org/W1496662040","https://openalex.org/W1496812201","https://openalex.org/W1540874598","https://openalex.org/W1544985773","https://openalex.org/W1558981331","https://openalex.org/W1571026908","https://openalex.org/W1574048238","https://openalex.org/W1587613092","https://openalex.org/W1741525514","https://openalex.org/W1831733120","https://openalex.org/W1875084745","https://openalex.org/W1897953275","https://openalex.org/W1967998153","https://openalex.org/W1970632218","https://openalex.org/W1971241982","https://openalex.org/W1972897978","https://openalex.org/W1978408474","https://openalex.org/W1981322987","https://openalex.org/W1982444105","https://openalex.org/W1986656046","https://openalex.org/W1994787881","https://openalex.org/W1995014717","https://openalex.org/W1998777096","https://openalex.org/W2006386982","https://openalex.org/W2009346579","https://openalex.org/W2011009521","https://openalex.org/W2011307711","https://openalex.org/W2011485738","https://openalex.org/W2012015138","https://openalex.org/W2012069696","https://openalex.org/W2013171416","https://openalex.org/W2013531208","https://openalex.org/W2015653219","https://openalex.org/W2020561965","https://openalex.org/W2022734245","https://openalex.org/W2023070887","https://openalex.org/W2025552689","https://openalex.org/W2025663053","https://openalex.org/W2026904316","https://openalex.org/W2029403511","https://openalex.org/W2031494151","https://openalex.org/W2039030574","https://openalex.org/W2042067428","https://openalex.org/W2042532809","https://openalex.org/W2042938280","https://openalex.org/W2048214825","https://openalex.org/W2051650982","https://openalex.org/W2052558315","https://openalex.org/W2053419354","https://openalex.org/W2058501095","https://openalex.org/W2062819025","https://openalex.org/W2064938664","https://openalex.org/W2069144532","https://openalex.org/W2073837631","https://openalex.org/W2076262841","https://openalex.org/W2078355959","https://openalex.org/W2080766885","https://openalex.org/W2082382448","https://openalex.org/W2084477972","https://openalex.org/W2085993965","https://openalex.org/W2087563523","https://openalex.org/W2094928616","https://openalex.org/W2096245011","https://openalex.org/W2100084634","https://openalex.org/W2100818174","https://openalex.org/W2103017472","https://openalex.org/W2103950919","https://openalex.org/W2107459209","https://openalex.org/W2114124738","https://openalex.org/W2115020432","https://openalex.org/W2115559271","https://openalex.org/W2118053673","https://openalex.org/W2119215577","https://openalex.org/W2124737787","https://openalex.org/W2125122419","https://openalex.org/W2126175129","https://openalex.org/W2127257007","https://openalex.org/W2128601422","https://openalex.org/W2128746754","https://openalex.org/W2129462472","https://openalex.org/W2130364940","https://openalex.org/W2132092950","https://openalex.org/W2132754077","https://openalex.org/W2133298156","https://openalex.org/W2133313719","https://openalex.org/W2133452284","https://openalex.org/W2136951758","https://openalex.org/W2141360045","https://openalex.org/W2142527585","https://openalex.org/W2143861551","https://openalex.org/W2144589197","https://openalex.org/W2144656588","https://openalex.org/W2147472054","https://openalex.org/W2148485332","https://openalex.org/W2150908245","https://openalex.org/W2151450092","https://openalex.org/W2155331065","https://openalex.org/W2156522652","https://openalex.org/W2159299078","https://openalex.org/W2159614925","https://openalex.org/W2160572439","https://openalex.org/W2161033057","https://openalex.org/W2161656422","https://openalex.org/W2163240970","https://openalex.org/W2167493116","https://openalex.org/W2168465568","https://openalex.org/W2170298003","https://openalex.org/W2171911221","https://openalex.org/W2412612509","https://openalex.org/W4237293127","https://openalex.org/W4238101851","https://openalex.org/W4239621283","https://openalex.org/W6663544634"],"related_works":["https://openalex.org/W998956804","https://openalex.org/W3011687921","https://openalex.org/W1957676899","https://openalex.org/W2594864121","https://openalex.org/W2048385844","https://openalex.org/W2142946480","https://openalex.org/W2026200587","https://openalex.org/W2071690264","https://openalex.org/W2031294207","https://openalex.org/W4235339959"],"abstract_inverted_index":{"The":[0],"filamentous":[1],"fungus":[2],"Neurospora":[3,175],"crassa":[4],"played":[5],"a":[6,24,34,109,201],"central":[7],"role":[8],"in":[9,125,214],"the":[10,152,154,164,168,206,225],"development":[11],"of":[12,37,43,59,78,140,181,195,210],"twentieth-century":[13],"genetics,":[14],"biochemistry":[15],"and":[16,19,52,114,127,159,184,188,208,216],"molecular":[17],"biology,":[18],"continues":[20],"to":[21,150,166,229],"serve":[22],"as":[23],"model":[25,36,41,155,165,199],"organism":[26],"for":[27,97,205,235],"eukaryotic":[28],"biology.":[29],"Here,":[30],"we":[31,67,189,217],"have":[32],"reconstructed":[33],"genome-scale":[35,232],"its":[38],"metabolism.":[39],"This":[40],"consists":[42],"836":[44],"metabolic":[45,233],"genes,":[46],"257":[47],"pathways,":[48],"6":[49],"cellular":[50],"compartments,":[51],"is":[53],"supported":[54],"by":[55,176],"extensive":[56],"manual":[57,226],"curation":[58],"491":[60],"literature":[61],"citations.":[62],"To":[63],"aid":[64],"our":[65,196,220],"reconstruction,":[66],"developed":[68],"three":[69],"optimization-based":[70],"algorithms,":[71],"which":[72,91,104,121],"together":[73],"comprise":[74],"Fast":[75],"Automated":[76],"Reconstruction":[77],"Metabolism":[79],"(FARM).":[80],"These":[81],"algorithms":[82],"are:":[83],"LInear":[84],"MEtabolite":[85],"Dilution":[86],"Flux":[87],"Balance":[88],"Analysis":[89],"(limed-FBA),":[90],"predicts":[92],"flux":[93],"while":[94],"linearly":[95],"accounting":[96],"metabolite":[98],"dilution;":[99],"One-step":[100],"functional":[101],"Pruning":[102],"(OnePrune),":[103],"removes":[105],"blocked":[106],"reactions":[107],"with":[108],"single":[110],"compact":[111],"linear":[112],"program;":[113],"Consistent":[115],"Reproduction":[116],"Of":[117],"growth/no-growth":[118],"Phenotype":[119],"(CROP),":[120],"reconciles":[122],"differences":[123],"between":[124],"silico":[126],"experimental":[128,212],"gene":[129],"essentiality":[130],"faster":[131],"than":[132,142],"previous":[133],"approaches.":[134],"Against":[135],"an":[136],"independent":[137],"test":[138],"set":[139],"more":[141],"300":[143],"essential/non-essential":[144],"genes":[145,183],"that":[146,219],"were":[147],"not":[148],"used":[149,163],"train":[151],"model,":[153],"displays":[156],"93%":[157],"sensitivity":[158],"specificity.":[160],"We":[161],"also":[162],"simulate":[167],"biochemical":[169],"genetics":[170],"experiments":[171],"originally":[172],"performed":[173],"on":[174],"comprehensively":[177],"predicting":[178],"nutrient":[179],"rescue":[180],"essential":[182],"synthetic":[185],"lethal":[186],"interactions,":[187],"provide":[190],"detailed":[191],"pathway-based":[192],"mechanistic":[193],"explanations":[194],"predictions.":[197],"Our":[198],"provides":[200],"reliable":[202],"computational":[203],"framework":[204],"integration":[207],"interpretation":[209],"ongoing":[211],"efforts":[213],"Neurospora,":[215],"anticipate":[218],"methods":[221],"will":[222],"substantially":[223],"reduce":[224],"effort":[227],"required":[228],"develop":[230],"high-quality":[231],"models":[234],"other":[236],"organisms.":[237]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":7},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":7},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}