{"id":"https://openalex.org/W2247374442","doi":"https://doi.org/10.1093/bib/bbv100","title":"Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond","display_name":"Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond","publication_year":2015,"publication_date":"2015-11-28","ids":{"openalex":"https://openalex.org/W2247374442","doi":"https://doi.org/10.1093/bib/bbv100","mag":"2247374442","pmid":"https://pubmed.ncbi.nlm.nih.gov/26615025"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv100","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv100","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/1060/8280351/bbv100.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/17/6/1060/8280351/bbv100.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5012349487","display_name":"Thomas Pfau","orcid":"https://orcid.org/0000-0001-5048-2923"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Thomas Pfau","raw_affiliation_strings":["University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >","institution_ids":["https://openalex.org/I186903577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022936776","display_name":"Maria Pires Pacheco","orcid":"https://orcid.org/0000-0001-7956-8093"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Maria Pires Pacheco","raw_affiliation_strings":["University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >","institution_ids":["https://openalex.org/I186903577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050871083","display_name":"Thomas Sauter","orcid":"https://orcid.org/0000-0001-8225-2954"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["LU"],"is_corresponding":true,"raw_author_name":"Thomas Sauter","raw_affiliation_strings":["Corresponding author: Thomas Sauter, Life Sciences Research Unit, University of Luxembourg, Campus Limpertsberg, 162a avenue de la Fa\u00efencerie, L-1511 Luxembourg, Luxembourg","University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Corresponding author: Thomas Sauter, Life Sciences Research Unit, University of Luxembourg, Campus Limpertsberg, 162a avenue de la Fa\u00efencerie, L-1511 Luxembourg, Luxembourg","institution_ids":["https://openalex.org/I186903577"]},{"raw_affiliation_string":"University of Luxembourg > Faculty of Science, Technology and Communication (FSTC) > Life Science Research Unit >","institution_ids":["https://openalex.org/I186903577"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5050871083"],"corresponding_institution_ids":["https://openalex.org/I186903577"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":{"value":3885,"currency":"USD","value_usd":3885},"fwci":1.6649,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.84136278,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":98},"biblio":{"volume":"17","issue":"6","first_page":"bbv100","last_page":"bbv100"},"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":0.9965000152587891,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9919000267982483,"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/metabolic-network","display_name":"Metabolic network","score":0.6509361267089844},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6347947120666504},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.6248556971549988},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5733182430267334},{"id":"https://openalex.org/keywords/unification","display_name":"Unification","score":0.5040735006332397},{"id":"https://openalex.org/keywords/organism","display_name":"Organism","score":0.49436020851135254},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4718104600906372},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4135139286518097},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38226914405822754},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31830573081970215},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23605689406394958}],"concepts":[{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6509361267089844},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6347947120666504},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.6248556971549988},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5733182430267334},{"id":"https://openalex.org/C96146094","wikidata":"https://www.wikidata.org/wiki/Q609057","display_name":"Unification","level":2,"score":0.5040735006332397},{"id":"https://openalex.org/C137858568","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Organism","level":2,"score":0.49436020851135254},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4718104600906372},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4135139286518097},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38226914405822754},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31830573081970215},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23605689406394958},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","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":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bib/bbv100","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv100","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/1060/8280351/bbv100.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26615025","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26615025","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:orbilu.uni.lu:10993/22766","is_oa":true,"landing_page_url":"https://orbilu.uni.lu/handle/10993/22766","pdf_url":"https://orbilu.uni.lu/bitstream/10993/22766/1/Pfau_et_al.pdf","source":{"id":"https://openalex.org/S4306401815","display_name":"Open Repository and Bibliography (University of Luxembourg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I186903577","host_organization_name":"University of Luxembourg","host_organization_lineage":["https://openalex.org/I186903577"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics (2015)","raw_type":"http://purl.org/coar/resource_type/c_6501"},{"id":"pmh:oai:europepmc.org:4088880","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5142010","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:open-archive.highwire.org:bib:17/6/1060","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/6/1060","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv100","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv100","pdf_url":"https://academic.oup.com/bib/article-pdf/17/6/1060/8280351/bbv100.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2247374442.pdf"},"referenced_works_count":140,"referenced_works":["https://openalex.org/W1529170481","https://openalex.org/W1559311404","https://openalex.org/W1601495365","https://openalex.org/W1913751664","https://openalex.org/W1964362163","https://openalex.org/W1969067437","https://openalex.org/W1971278266","https://openalex.org/W1972863608","https://openalex.org/W1974426660","https://openalex.org/W1976288529","https://openalex.org/W1979294707","https://openalex.org/W1979770972","https://openalex.org/W1985738984","https://openalex.org/W1988482582","https://openalex.org/W1999938932","https://openalex.org/W2001786365","https://openalex.org/W2004548026","https://openalex.org/W2004659174","https://openalex.org/W2009282793","https://openalex.org/W2011307711","https://openalex.org/W2011920499","https://openalex.org/W2012284471","https://openalex.org/W2020561965","https://openalex.org/W2020916135","https://openalex.org/W2021808692","https://openalex.org/W2023506303","https://openalex.org/W2024036230","https://openalex.org/W2036652670","https://openalex.org/W2038617558","https://openalex.org/W2042012882","https://openalex.org/W2046527060","https://openalex.org/W2047017978","https://openalex.org/W2047632644","https://openalex.org/W2047817180","https://openalex.org/W2048073138","https://openalex.org/W2048214825","https://openalex.org/W2048464962","https://openalex.org/W2049715920","https://openalex.org/W2050002679","https://openalex.org/W2050222746","https://openalex.org/W2054719673","https://openalex.org/W2057752933","https://openalex.org/W2058650387","https://openalex.org/W2059546521","https://openalex.org/W2059761552","https://openalex.org/W2059803317","https://openalex.org/W2060797027","https://openalex.org/W2061636126","https://openalex.org/W2067094344","https://openalex.org/W2069356347","https://openalex.org/W2070001149","https://openalex.org/W2071746055","https://openalex.org/W2077149408","https://openalex.org/W2079531107","https://openalex.org/W2080944633","https://openalex.org/W2085945924","https://openalex.org/W2085966233","https://openalex.org/W2085993965","https://openalex.org/W2087461579","https://openalex.org/W2087558745","https://openalex.org/W2088217817","https://openalex.org/W2092170757","https://openalex.org/W2096097217","https://openalex.org/W2096245011","https://openalex.org/W2096465161","https://openalex.org/W2098337987","https://openalex.org/W2100084634","https://openalex.org/W2101501829","https://openalex.org/W2102789902","https://openalex.org/W2103017472","https://openalex.org/W2103950919","https://openalex.org/W2103986409","https://openalex.org/W2104108767","https://openalex.org/W2104224685","https://openalex.org/W2107580398","https://openalex.org/W2107881499","https://openalex.org/W2108024305","https://openalex.org/W2109615707","https://openalex.org/W2110868158","https://openalex.org/W2111796963","https://openalex.org/W2111973517","https://openalex.org/W2114034054","https://openalex.org/W2117474489","https://openalex.org/W2124737787","https://openalex.org/W2127316014","https://openalex.org/W2128572161","https://openalex.org/W2128601422","https://openalex.org/W2130479394","https://openalex.org/W2131581981","https://openalex.org/W2131848047","https://openalex.org/W2132218677","https://openalex.org/W2133556195","https://openalex.org/W2134394193","https://openalex.org/W2137575744","https://openalex.org/W2138413337","https://openalex.org/W2140611297","https://openalex.org/W2141458291","https://openalex.org/W2141885858","https://openalex.org/W2142314840","https://openalex.org/W2144589197","https://openalex.org/W2146980885","https://openalex.org/W2147472054","https://openalex.org/W2150315679","https://openalex.org/W2150908245","https://openalex.org/W2154969423","https://openalex.org/W2156476088","https://openalex.org/W2157221164","https://openalex.org/W2158637000","https://openalex.org/W2159184004","https://openalex.org/W2159482845","https://openalex.org/W2160541874","https://openalex.org/W2160620582","https://openalex.org/W2160810865","https://openalex.org/W2161062388","https://openalex.org/W2162666840","https://openalex.org/W2163841023","https://openalex.org/W2164111097","https://openalex.org/W2165373392","https://openalex.org/W2167539386","https://openalex.org/W2168465568","https://openalex.org/W2170427655","https://openalex.org/W2170806980","https://openalex.org/W2170974939","https://openalex.org/W2171777347","https://openalex.org/W2183271564","https://openalex.org/W2247766769","https://openalex.org/W2605068739","https://openalex.org/W2885727518","https://openalex.org/W3042475334","https://openalex.org/W3104005457","https://openalex.org/W4210290733","https://openalex.org/W4210323379","https://openalex.org/W4210531204","https://openalex.org/W4213060373","https://openalex.org/W4230346224","https://openalex.org/W4230770774","https://openalex.org/W4241391257","https://openalex.org/W4248681633","https://openalex.org/W4294216483","https://openalex.org/W6631777726"],"related_works":["https://openalex.org/W1999460937","https://openalex.org/W2083413061","https://openalex.org/W1984242440","https://openalex.org/W2341681417","https://openalex.org/W2113329733","https://openalex.org/W1983989854","https://openalex.org/W2070388085","https://openalex.org/W2886446279","https://openalex.org/W832244386","https://openalex.org/W2047334633"],"abstract_inverted_index":{"Genome-scale":[0],"metabolic":[1,12,139,225],"network":[2],"reconstructions":[3,19,65,231],"provide":[4],"a":[5,35,51,69,116],"basis":[6],"for":[7,21,31,79,83,101],"the":[8,11,32,40,48,73,76,113,135,153,209,224],"investigation":[9],"of":[10,14,34,42,50,61,72,75,81,88,94,99,115,138,152,155,177,211,223],"properties":[13],"an":[15],"organism.":[16],"There":[17],"are":[18,218,232],"available":[20,77,167],"multiple":[22],"organisms,":[23],"from":[24,119,143,186,195,208],"prokaryotes":[25],"to":[26,46,112,133,146,173,228],"higher":[27],"organisms":[28],"and":[29,66,90,179,220],"methods":[30],"analysis":[33,45],"reconstruction.":[36],"One":[37],"example":[38],"is":[39],"use":[41,210],"flux":[43],"balance":[44],"improve":[47,134],"yields":[49],"target":[52],"chemical,":[53],"which":[54],"has":[55],"been":[56],"applied":[57],"successfully.":[58],"However,":[59],"comparison":[60],"results":[62],"between":[63],"existing":[64],"models":[67,140],"presents":[68],"challenge":[70],"because":[71],"heterogeneity":[74],"reconstructions,":[78],"example,":[80],"standards":[82],"presenting":[84],"gene-protein-reaction":[85,144],"associations,":[86,148],"nomenclature":[87],"metabolites":[89],"reactions":[91,106],"or":[92,104],"selection":[93],"protonation":[95,202],"states.":[96,203],"The":[97],"lack":[98],"comparability":[100],"gene":[102,158],"identifiers":[103],"model-specific":[105],"without":[107],"annotated":[108],"evidence":[109],"often":[110],"leads":[111],"creation":[114],"new":[117],"model":[118,230],"scratch,":[120],"as":[121],"data":[122],"cannot":[123],"be":[124,171],"properly":[125],"matched":[126],"otherwise.":[127],"In":[128,204],"this":[129,163,175],"contribution,":[130],"we":[131,165,190],"propose":[132],"predictive":[136],"power":[137],"by":[141],"switching":[142],"associations":[145],"transcript-isoform-reaction":[147],"thus":[149],"taking":[150],"advantage":[151],"improvement":[154],"precision":[156],"in":[157,201],"expression":[159],"measurements.":[160],"To":[161],"achieve":[162],"precision,":[164],"discuss":[166],"databases":[168],"that":[169,183,193],"can":[170,184],"used":[172],"retrieve":[174],"type":[176],"information":[178],"point":[180],"at":[181],"issues":[182,192],"arise":[185,194],"their":[187],"neglect.":[188],"Further,":[189],"stress":[191],"non-standardized":[196],"building":[197],"pipelines,":[198],"like":[199],"inconsistencies":[200],"addition,":[205],"problems":[206],"arising":[207],"non-specific":[212],"cofactors,":[213],"e.g.":[214],"artificial":[215],"futile":[216],"cycles,":[217],"discussed,":[219],"finally":[221],"efforts":[222],"modelling":[226],"community":[227],"unify":[229],"highlighted.":[233]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":4},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":4},{"year":2016,"cited_by_count":3}],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2025-10-10T00:00:00"}
