{"id":"https://openalex.org/W4283385398","doi":"https://doi.org/10.1371/journal.pcbi.1009294","title":"A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale","display_name":"A pipeline for the reconstruction and evaluation of context-specific human metabolic models at a large-scale","publication_year":2022,"publication_date":"2022-06-24","ids":{"openalex":"https://openalex.org/W4283385398","doi":"https://doi.org/10.1371/journal.pcbi.1009294","pmid":"https://pubmed.ncbi.nlm.nih.gov/35749559"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009294","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009294","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009294&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.1009294&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008693461","display_name":"V\u00edtor Vieira","orcid":"https://orcid.org/0000-0001-9604-9586"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"V\u00edtor Vieira","raw_affiliation_strings":["Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100785146","display_name":"Jorge Ferreira","orcid":"https://orcid.org/0000-0002-5132-1651"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Jorge Ferreira","raw_affiliation_strings":["Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal"],"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Miguel Rocha","raw_affiliation_strings":["Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal","LABBELS - Associate Laboratory, Braga/Guimar\u00e3es, Portugal"],"affiliations":[{"raw_affiliation_string":"Centre of Biological Engineering (CEB), Universidade do Minho, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]},{"raw_affiliation_string":"LABBELS - Associate Laboratory, Braga/Guimar\u00e3es, Portugal","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5040524717"],"corresponding_institution_ids":["https://openalex.org/I99682543"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.6466,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.83757715,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"18","issue":"6","first_page":"e1009294","last_page":"e1009294"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.996999979019165,"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":0.995199978351593,"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/computer-science","display_name":"Computer science","score":0.7038242816925049},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6154901385307312},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.587395429611206},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5737049579620361},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4351273775100708},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4254949688911438},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4083011746406555},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32300233840942383},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21205845475196838},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09799659252166748}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7038242816925049},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6154901385307312},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.587395429611206},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5737049579620361},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4351273775100708},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4254949688911438},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4083011746406555},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32300233840942383},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21205845475196838},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09799659252166748},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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":false},{"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":"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":"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":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009294","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009294","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009294&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:35749559","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35749559","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:repositorium.uminho.pt:1822/80434","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/80434","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1009294","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009294","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:e079cc99b9f349ba8073c78852e87e11","is_oa":true,"landing_page_url":"https://doaj.org/article/e079cc99b9f349ba8073c78852e87e11","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 6, p e1009294 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9278738","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9278738","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.1009294","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009294","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009294&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":[{"id":"https://openalex.org/G1203399442","display_name":null,"funder_award_id":"UIDB/04469/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G1690109813","display_name":null,"funder_award_id":"57/2016","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G3272457656","display_name":null,"funder_award_id":"UIDB/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G3284537356","display_name":null,"funder_award_id":"SFRH/B","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G3979008744","display_name":null,"funder_award_id":"SFRH/BD/118657/2016","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G3998201246","display_name":null,"funder_award_id":"Social","funder_id":"https://openalex.org/F4320338080","funder_display_name":"European Social Fund"},{"id":"https://openalex.org/G4009688636","display_name":null,"funder_award_id":"LA/P/0029/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4403996651","display_name":null,"funder_award_id":"UIDB/04469/2020 unit","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G5818630289","display_name":null,"funder_award_id":"SFRH/BD/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G6565430356","display_name":null,"funder_award_id":"UIDB/04469","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7049410507","display_name":null,"funder_award_id":"Portuguese Foundation for Science","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G724804869","display_name":null,"funder_award_id":"SFRH/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G8436637332","display_name":null,"funder_award_id":"LA/P/","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G943999617","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"},{"id":"https://openalex.org/F4320338080","display_name":"European Social Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283385398.pdf","grobid_xml":"https://content.openalex.org/works/W4283385398.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W1967717472","https://openalex.org/W2003517551","https://openalex.org/W2009282793","https://openalex.org/W2011880165","https://openalex.org/W2029403511","https://openalex.org/W2048214825","https://openalex.org/W2048465561","https://openalex.org/W2049792326","https://openalex.org/W2052025367","https://openalex.org/W2058568704","https://openalex.org/W2062573649","https://openalex.org/W2067094344","https://openalex.org/W2078355959","https://openalex.org/W2098824895","https://openalex.org/W2104108767","https://openalex.org/W2108195113","https://openalex.org/W2110723933","https://openalex.org/W2116694343","https://openalex.org/W2121404287","https://openalex.org/W2124653577","https://openalex.org/W2130364940","https://openalex.org/W2132218677","https://openalex.org/W2139070508","https://openalex.org/W2142500268","https://openalex.org/W2144589197","https://openalex.org/W2156409537","https://openalex.org/W2160541874","https://openalex.org/W2162790428","https://openalex.org/W2163841023","https://openalex.org/W2170564127","https://openalex.org/W2170974939","https://openalex.org/W2272140989","https://openalex.org/W2418056440","https://openalex.org/W2576681512","https://openalex.org/W2587946751","https://openalex.org/W2696298149","https://openalex.org/W2735132087","https://openalex.org/W2749689006","https://openalex.org/W2756562465","https://openalex.org/W2789128799","https://openalex.org/W2902335495","https://openalex.org/W2906906692","https://openalex.org/W2944727022","https://openalex.org/W2951171318","https://openalex.org/W2955088273","https://openalex.org/W2963932607","https://openalex.org/W2966282641","https://openalex.org/W2966546269","https://openalex.org/W2989881642","https://openalex.org/W3001475835","https://openalex.org/W3013554928","https://openalex.org/W3024148753","https://openalex.org/W3049657557","https://openalex.org/W3096568637","https://openalex.org/W3103526258","https://openalex.org/W3166449107"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380","https://openalex.org/W3193760048","https://openalex.org/W4285822516","https://openalex.org/W2505261959"],"abstract_inverted_index":{"Constraint-based":[0],"(CB)":[1],"metabolic":[2,265,273],"models":[3,74,186,203,214,266,281],"provide":[4],"a":[5,114],"mathematical":[6],"framework":[7],"and":[8,16,39,81,143,147,226],"scaffold":[9],"for":[10,51,90,177,193,283],"in":[11,124,152,198,242,252,264,292],"silico":[12],"cell":[13,180,195,237],"metabolism":[14,65,243],"analysis":[15],"manipulation.":[17],"In":[18,105],"the":[19,33,46,63,69,153,166,178,189,199,208,219,232,249],"past":[20],"decade,":[21],"significant":[22],"efforts":[23,135],"have":[24],"been":[25],"done":[26],"to":[27,206,245,270],"model":[28,53,145,192],"human":[29,76],"metabolism,":[30],"enabled":[31],"by":[32,112,133,222],"increased":[34],"availability":[35],"of":[36,48,66,71,75,101,120,139,234],"multi-omics":[37,163],"datasets":[38,164],"curated":[40],"genome-scale":[41],"reconstructions,":[42],"as":[43,45,204],"well":[44],"development":[47],"several":[49,67],"algorithms":[50,142],"context-specific":[52],"(CSM)":[54],"reconstruction.":[55],"Although":[56],"CSM":[57,116,141],"reconstruction":[58,117],"has":[59],"revealed":[60],"insights":[61],"on":[62,188,279],"deregulated":[64],"pathologies,":[68],"process":[70,92],"reconstructing":[72],"representative":[73],"tissues":[77],"still":[78,94],"lacks":[79],"benchmarks":[80],"appropriate":[82],"integrated":[83],"software":[84,98],"frameworks,":[85],"since":[86],"many":[87,250],"tools":[88],"required":[89],"this":[91,106,110],"are":[93,103],"disperse":[95],"across":[96],"various":[97],"platforms,":[99],"some":[100],"which":[102],"proprietary.":[104],"work,":[107],"we":[108,255],"address":[109],"challenge":[111],"assembling":[113],"scalable":[115],"pipeline":[118,159,259],"capable":[119],"integrating":[121],"transcriptomics":[122,262],"data":[123,263],"CB":[125,253],"models.":[126],"We":[127,182,229],"combined":[128],"omics":[129],"preprocessing":[130],"methods":[131],"inspired":[132],"previous":[134],"with":[136,162],"in-house":[137],"implementations":[138],"existing":[140],"new":[144],"refinement":[146],"validation":[148],"routines,":[149],"all":[150],"implemented":[151],"Troppo":[154],"Python-based":[155],"open-source":[156],"framework.":[157],"The":[158],"was":[160],"validated":[161],"from":[165],"Cancer":[167],"Cell":[168],"Line":[169],"Encyclopedia":[170],"(CCLE),":[171],"also":[172,230],"including":[173],"reference":[174,205,213],"fluxomics":[175,227],"measurements":[176],"MCF7":[179,202],"line.":[181],"reconstructed":[183],"over":[184],"6000":[185],"based":[187],"Human-GEM":[190],"template":[191,221],"733":[194],"lines":[196],"featured":[197],"CCLE,":[200],"using":[201,218,257],"find":[207],"best":[209],"parameter":[210],"combinations.":[211],"These":[212],"outperform":[215],"earlier":[216],"studies":[217],"same":[220],"comparing":[223],"gene":[224],"essentiality":[225],"experiments.":[228],"analysed":[231],"heterogeneity":[233],"breast":[235],"cancer":[236,246],"lines,":[238],"identifying":[239],"key":[240,272],"changes":[241],"related":[244],"aggressiveness.":[247],"Despite":[248],"challenges":[251],"modelling,":[254],"demonstrate":[256],"our":[258],"that":[260],"combining":[261],"can":[267],"be":[268],"used":[269],"investigate":[271],"shifts.":[274],"Significant":[275],"limitations":[276],"were":[277],"found":[278],"these":[280],"ability":[282],"reliable":[284],"quantitative":[285],"flux":[286],"prediction,":[287],"thus":[288],"motivating":[289],"further":[290],"work":[291],"genome-wide":[293],"phenotype":[294],"prediction.":[295]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
