{"id":"https://openalex.org/W4220743479","doi":"https://doi.org/10.1371/journal.pcbi.1009341","title":"Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions","display_name":"Quantifying cumulative phenotypic and genomic evidence for procedural generation of metabolic network reconstructions","publication_year":2022,"publication_date":"2022-02-07","ids":{"openalex":"https://openalex.org/W4220743479","doi":"https://doi.org/10.1371/journal.pcbi.1009341","pmid":"https://pubmed.ncbi.nlm.nih.gov/35130271"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009341","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009341","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1009341","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037431205","display_name":"Thomas J. Moutinho","orcid":"https://orcid.org/0000-0002-8940-4970"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas J. Moutinho","raw_affiliation_strings":["University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008896114","display_name":"Benjamin C. Neubert","orcid":"https://orcid.org/0000-0002-3819-4803"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin C. Neubert","raw_affiliation_strings":["University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053077805","display_name":"Matthew L. Jenior","orcid":"https://orcid.org/0000-0003-1884-3543"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew L. Jenior","raw_affiliation_strings":["University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000119406","display_name":"Jason A. Papin","orcid":"https://orcid.org/0000-0002-2769-5805"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jason A. Papin","raw_affiliation_strings":["University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States of America"],"affiliations":[{"raw_affiliation_string":"University of Virginia, Department of Biomedical Engineering, Charlottesville, Virginia, United States of America","institution_ids":["https://openalex.org/I51556381"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5000119406"],"corresponding_institution_ids":["https://openalex.org/I51556381"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6076,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.63306958,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"18","issue":"2","first_page":"e1009341","last_page":"e1009341"},"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/T10171","display_name":"Biofuel production and bioconversion","score":0.9901999831199646,"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":0.9896000027656555,"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/annotation","display_name":"Annotation","score":0.7272462248802185},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6677881479263306},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.6449840664863586},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6274814009666443},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.6161638498306274},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.5609240531921387},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5277842879295349},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5140198469161987},{"id":"https://openalex.org/keywords/structuring","display_name":"Structuring","score":0.4790540933609009},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4656679630279541},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.4233614206314087},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30057492852211},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2949609160423279}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7272462248802185},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6677881479263306},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6449840664863586},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6274814009666443},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.6161638498306274},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.5609240531921387},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5277842879295349},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5140198469161987},{"id":"https://openalex.org/C2775945657","wikidata":"https://www.wikidata.org/wiki/Q381442","display_name":"Structuring","level":2,"score":0.4790540933609009},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4656679630279541},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.4233614206314087},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30057492852211},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2949609160423279},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C10138342","wikidata":"https://www.wikidata.org/wiki/Q43015","display_name":"Finance","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"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":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005798","descriptor_name":"Genes, Bacterial","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1009341","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009341","pdf_url":null,"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:35130271","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35130271","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:ebafa65a0cb7490a8e834ebe41b83a7c","is_oa":true,"landing_page_url":"https://doaj.org/article/ebafa65a0cb7490a8e834ebe41b83a7c","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 18, Iss 2, p e1009341 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8853471","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8853471","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.1009341","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009341","pdf_url":null,"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":[{"id":"https://openalex.org/G1433080148","display_name":null,"funder_award_id":"AT010253","funder_id":"https://openalex.org/F4320306080","funder_display_name":"Foundation for the National Institutes of Health"},{"id":"https://openalex.org/G5921281487","display_name":null,"funder_award_id":"number","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6894402473","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","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/F4320306080","display_name":"Foundation for the National Institutes of Health","ror":"https://ror.org/00k86s890"},{"id":"https://openalex.org/F4320310536","display_name":"University of Virginia","ror":"https://ror.org/0153tk833"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1551543102","https://openalex.org/W1895590483","https://openalex.org/W1986656046","https://openalex.org/W1991310235","https://openalex.org/W2012490955","https://openalex.org/W2016271868","https://openalex.org/W2032347305","https://openalex.org/W2033829415","https://openalex.org/W2045204781","https://openalex.org/W2075283200","https://openalex.org/W2078355959","https://openalex.org/W2084967844","https://openalex.org/W2085993965","https://openalex.org/W2105112252","https://openalex.org/W2115275873","https://openalex.org/W2128394626","https://openalex.org/W2129906961","https://openalex.org/W2139915240","https://openalex.org/W2160541874","https://openalex.org/W2166637863","https://openalex.org/W2232370058","https://openalex.org/W2559597060","https://openalex.org/W2560707317","https://openalex.org/W2604346094","https://openalex.org/W2605504874","https://openalex.org/W2764202526","https://openalex.org/W2797443945","https://openalex.org/W2904207487","https://openalex.org/W2949418748","https://openalex.org/W2950900779","https://openalex.org/W2987028578","https://openalex.org/W3002175424","https://openalex.org/W3016499228","https://openalex.org/W3083321322","https://openalex.org/W3090689814","https://openalex.org/W3118382168","https://openalex.org/W3161293250","https://openalex.org/W4240404008"],"related_works":["https://openalex.org/W4394443292","https://openalex.org/W4251394462","https://openalex.org/W1580673008","https://openalex.org/W1510936208","https://openalex.org/W2486167009","https://openalex.org/W1595575899","https://openalex.org/W2361861616","https://openalex.org/W756498608","https://openalex.org/W2350653470","https://openalex.org/W2061627113"],"abstract_inverted_index":{"Genome-scale":[0],"metabolic":[1,20,31,152,230,288],"network":[2],"reconstructions":[3],"(GENREs)":[4],"are":[5],"valuable":[6],"tools":[7],"for":[8,62,91,101,128,136,162,166,178,191,225,283],"understanding":[9],"microbial":[10],"metabolism.":[11],"The":[12,33,173],"process":[13],"of":[14,96,175,182,208,220,229,256,287],"automatically":[15,65],"generating":[16,236,263],"GENREs":[17,97,157],"includes":[18],"identifying":[19],"reactions":[21,41,64,193],"supported":[22],"by":[23,235,262,290],"sufficient":[24],"genomic":[25],"evidence":[26,74,78,135,165,190],"to":[27,44,98,204,214,245,258],"generate":[28],"a":[29,80,89,121,126,159,260],"draft":[30,34,68],"network.":[32,172],"GENRE":[35,142],"is":[36,72,88,202],"then":[37],"gapfilled":[38],"with":[39,51,112,158],"additional":[40],"in":[42,67,79,93,103,170,198,217,295],"order":[43],"recapitulate":[45],"specific":[46],"growth":[47],"phenotypes":[48],"as":[49],"indicated":[50],"associated":[52,111],"experimental":[53,209],"data.":[54,297],"Previous":[55],"methods":[56],"have":[57],"implemented":[58],"absolute":[59],"mapping":[60],"thresholds":[61],"the":[63,94,163,171,179,206,218,221,226,246,254,284],"included":[66,169],"GENREs;":[69],"however,":[70],"there":[71],"growing":[73],"that":[75,124,194,274],"integrating":[76],"annotation":[77,211],"continuous":[81],"form":[82],"can":[83],"improve":[84],"model":[85,241,261,269],"accuracy.":[86],"There":[87],"need":[90],"flexibility":[92],"structure":[95],"better":[99],"account":[100],"uncertainty":[102,292],"biological":[104,296],"data,":[105],"unknown":[106],"regulatory":[107],"mechanisms,":[108],"and":[109,133,210,213,242,293],"context-specificity":[110],"data":[113,184,273],"inputs.":[114],"To":[115],"address":[116,280],"this":[117],"issue,":[118],"we":[119,252,275],"present":[120],"novel":[122,271],"method":[123,278],"provides":[125],"framework":[127],"quantifying":[129],"combined":[130],"genomic,":[131],"biochemical,":[132],"phenotypic":[134,272],"each":[137,167],"biochemical":[138,192],"reaction":[139,149,168],"during":[140],"automated":[141],"construction.":[143],"Our":[144],"method,":[145],"Constraint-based":[146],"Analysis":[147],"Yielding":[148],"Usage":[150],"across":[151],"Networks":[153],"(CANYUNs),":[154],"generates":[155],"accurate":[156],"quantitative":[160],"metric":[161],"cumulative":[164],"structuring":[174],"CANYUNs":[176,201,234,257,268],"allows":[177],"simultaneous":[180],"integration":[181],"three":[183],"inputs":[185],"while":[186],"maintaining":[187],"all":[188],"supporting":[189],"may":[195,279],"be":[196],"active":[197],"an":[199,237,264],"organism.":[200],"designed":[203],"maximize":[205],"utility":[207],"datasets":[212,223],"ultimately":[215],"assist":[216],"curation":[219],"reference":[222],"used":[224],"automatic":[227],"construction":[228,286],"networks.":[231],"We":[232],"validated":[233],"E.":[238,265],"coli":[239,266],"K-12":[240],"compared":[243],"it":[244],"manually":[247],"curated":[248],"reconstruction":[249],"iML1515.":[250],"Finally,":[251],"demonstrated":[253],"use":[255],"build":[259],"Nissle":[267],"using":[270],"collected.":[276],"This":[277],"key":[281],"challenges":[282],"procedural":[285],"networks":[289],"leveraging":[291],"redundancy":[294]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
