{"id":"https://openalex.org/W4415125877","doi":"https://doi.org/10.1371/journal.pcbi.1013564","title":"A compact model of Escherichia coli core and biosynthetic metabolism","display_name":"A compact model of Escherichia coli core and biosynthetic metabolism","publication_year":2025,"publication_date":"2025-10-13","ids":{"openalex":"https://openalex.org/W4415125877","doi":"https://doi.org/10.1371/journal.pcbi.1013564","pmid":"https://pubmed.ncbi.nlm.nih.gov/41082574"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013564","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013564","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.1013564","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087312496","display_name":"M. Corrao","orcid":"https://orcid.org/0009-0000-2113-5703"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I4210146410","display_name":"Science Oxford","ror":"https://ror.org/04j8yhy50","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210146410"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Marco Corrao","raw_affiliation_strings":["Department of Engineering Science, University of Oxford, Oxford, United Kingdom"],"raw_orcid":"https://orcid.org/0009-0000-2113-5703","affiliations":[{"raw_affiliation_string":"Department of Engineering Science, University of Oxford, Oxford, United Kingdom","institution_ids":["https://openalex.org/I4210146410","https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068997962","display_name":"Hai He","orcid":"https://orcid.org/0000-0003-1223-2813"},"institutions":[{"id":"https://openalex.org/I4210166203","display_name":"Max Planck Institute for Terrestrial Microbiology","ror":"https://ror.org/05r7n9c40","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210166203"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Hai He","raw_affiliation_strings":["Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1223-2813","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany","institution_ids":["https://openalex.org/I4210166203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046914403","display_name":"Wolfram Liebermeister","orcid":"https://orcid.org/0000-0002-2568-2381"},"institutions":[{"id":"https://openalex.org/I277688954","display_name":"Universit\u00e9 Paris-Saclay","ror":"https://ror.org/03xjwb503","country_code":"FR","type":"education","lineage":["https://openalex.org/I277688954"]},{"id":"https://openalex.org/I4210088668","display_name":"Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement","ror":"https://ror.org/003vg9w96","country_code":"FR","type":"government","lineage":["https://openalex.org/I4210088668"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Wolfram Liebermeister","raw_affiliation_strings":["Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France","institution_ids":["https://openalex.org/I277688954","https://openalex.org/I4210088668"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021074279","display_name":"\u0395lad Noor","orcid":"https://orcid.org/0000-0001-8776-4799"},"institutions":[{"id":"https://openalex.org/I53964585","display_name":"Weizmann Institute of Science","ror":"https://ror.org/0316ej306","country_code":"IL","type":"education","lineage":["https://openalex.org/I53964585"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Elad Noor","raw_affiliation_strings":["Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel"],"raw_orcid":"https://orcid.org/0000-0001-8776-4799","affiliations":[{"raw_affiliation_string":"Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel","institution_ids":["https://openalex.org/I53964585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044028530","display_name":"Arren Bar\u2010Even","orcid":"https://orcid.org/0000-0002-1039-4328"},"institutions":[{"id":"https://openalex.org/I4210105972","display_name":"Max Planck Institute of Molecular Plant Physiology","ror":"https://ror.org/01fbde567","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210105972"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Arren Bar-Even","raw_affiliation_strings":["Group of Systems and Synthetic Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Group of Systems and Synthetic Metabolism, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany","institution_ids":["https://openalex.org/I4210105972"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5021074279","https://openalex.org/A5044028530","https://openalex.org/A5046914403","https://openalex.org/A5068997962","https://openalex.org/A5087312496"],"corresponding_institution_ids":["https://openalex.org/I277688954","https://openalex.org/I40120149","https://openalex.org/I4210088668","https://openalex.org/I4210105972","https://openalex.org/I4210146410","https://openalex.org/I4210166203","https://openalex.org/I53964585"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.5259,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.8375297,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"21","issue":"10","first_page":"e1013564","last_page":"e1013564"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9940999746322632,"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":0.9904999732971191,"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/metabolic-network","display_name":"Metabolic network","score":0.7609000205993652},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.6363000273704529},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.6233000159263611},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.6057999730110168},{"id":"https://openalex.org/keywords/metabolic-pathway","display_name":"Metabolic pathway","score":0.5521000027656555},{"id":"https://openalex.org/keywords/metabolic-flux-analysis","display_name":"Metabolic flux analysis","score":0.48730000853538513},{"id":"https://openalex.org/keywords/metabolic-engineering","display_name":"Metabolic engineering","score":0.4691999852657318},{"id":"https://openalex.org/keywords/escherichia-coli-proteins","display_name":"Escherichia coli Proteins","score":0.44190001487731934},{"id":"https://openalex.org/keywords/energy-metabolism","display_name":"Energy metabolism","score":0.4194999933242798}],"concepts":[{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.7609000205993652},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.6363000273704529},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.6233000159263611},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.6057999730110168},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.5521000027656555},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5220999717712402},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.48730000853538513},{"id":"https://openalex.org/C6350086","wikidata":"https://www.wikidata.org/wiki/Q6822347","display_name":"Metabolic engineering","level":3,"score":0.4691999852657318},{"id":"https://openalex.org/C2908821069","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli Proteins","level":4,"score":0.44190001487731934},{"id":"https://openalex.org/C2986317502","wikidata":"https://www.wikidata.org/wiki/Q570714","display_name":"Energy metabolism","level":2,"score":0.4194999933242798},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.41839998960494995},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.41600000858306885},{"id":"https://openalex.org/C2778012447","wikidata":"https://www.wikidata.org/wiki/Q1034415","display_name":"Scope (computer science)","level":2,"score":0.4009000062942505},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3984000086784363},{"id":"https://openalex.org/C2994212657","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Cellular metabolism","level":3,"score":0.38760000467300415},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3637999892234802},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.36309999227523804},{"id":"https://openalex.org/C553450214","wikidata":"https://www.wikidata.org/wiki/Q851162","display_name":"Biosynthesis","level":3,"score":0.35929998755455017},{"id":"https://openalex.org/C101014631","wikidata":"https://www.wikidata.org/wiki/Q4889568","display_name":"Microbial metabolism","level":3,"score":0.35670000314712524},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3555999994277954},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.334199994802475},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.32850000262260437},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.32829999923706055},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.3138999938964844},{"id":"https://openalex.org/C2988540567","wikidata":"https://www.wikidata.org/wiki/Q12070446","display_name":"Model system","level":2,"score":0.30559998750686646},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.304500013589859},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.2996000051498413},{"id":"https://openalex.org/C2780366209","wikidata":"https://www.wikidata.org/wiki/Q5170200","display_name":"Core model","level":2,"score":0.2865000069141388},{"id":"https://openalex.org/C2777423268","wikidata":"https://www.wikidata.org/wiki/Q3663116","display_name":"Energy balance","level":2,"score":0.26930001378059387},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.2635999917984009},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.26030001044273376},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2551000118255615},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.2524999976158142},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.2508000135421753}],"mesh":[{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053898","descriptor_name":"Biosynthetic Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1013564","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013564","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:41082574","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41082574","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:HAL:hal-05056734v2","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-05056734","pdf_url":"https://hal.inrae.fr/hal-05056734/document","source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"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 Computational Biology, 2025, 21 (10), pp.e1013564. &#x27E8;10.1371/journal.pcbi.1013564&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:be8d5a986d2949489e805406c0c3fd97","is_oa":true,"landing_page_url":"https://doaj.org/article/be8d5a986d2949489e805406c0c3fd97","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 10, p e1013564 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11341829","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12533975","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013564","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013564","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/G2928068030","display_name":"The Oxford Interdisciplinary Bioscience Doctoral Training Partnership","funder_award_id":"BB/T008784/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1587777700","https://openalex.org/W1665355332","https://openalex.org/W1862094217","https://openalex.org/W1984936164","https://openalex.org/W1997733142","https://openalex.org/W2022374283","https://openalex.org/W2039230661","https://openalex.org/W2040774388","https://openalex.org/W2041918033","https://openalex.org/W2048465561","https://openalex.org/W2101981035","https://openalex.org/W2107409961","https://openalex.org/W2110355460","https://openalex.org/W2122638857","https://openalex.org/W2124737787","https://openalex.org/W2132022337","https://openalex.org/W2140937954","https://openalex.org/W2170427655","https://openalex.org/W2176595367","https://openalex.org/W2191824721","https://openalex.org/W2312280072","https://openalex.org/W2559588208","https://openalex.org/W2560707317","https://openalex.org/W2566157169","https://openalex.org/W2743063996","https://openalex.org/W2749464300","https://openalex.org/W2764202526","https://openalex.org/W2786627077","https://openalex.org/W2804515387","https://openalex.org/W2842089854","https://openalex.org/W2903357856","https://openalex.org/W2915782277","https://openalex.org/W2952015518","https://openalex.org/W2966850388","https://openalex.org/W2988505142","https://openalex.org/W3003224093","https://openalex.org/W3012335944","https://openalex.org/W3082397379","https://openalex.org/W3087744872","https://openalex.org/W3095049046","https://openalex.org/W3102587633","https://openalex.org/W3115294611","https://openalex.org/W3138245369","https://openalex.org/W3207760869","https://openalex.org/W3216494066","https://openalex.org/W4245225949","https://openalex.org/W4281675111","https://openalex.org/W4283032119","https://openalex.org/W4286698076","https://openalex.org/W4384023735","https://openalex.org/W4386319785","https://openalex.org/W4387965228","https://openalex.org/W4404022106","https://openalex.org/W4413055782"],"related_works":[],"abstract_inverted_index":{"Metabolic":[0],"models":[1,24,36],"condense":[2],"biochemical":[3],"knowledge":[4],"about":[5],"organisms":[6],"in":[7,63,197,213],"a":[8,64,69,116,137,156,236],"structured":[9],"and":[10,31,42,44,81,94,98,101,123,146,155,172,177,183,203,210,225],"standardised":[11],"way.":[12],"As":[13],"large-scale":[14],"network":[15,167,209],"reconstructions":[16],"are":[17,25,49,90],"readily":[18],"available":[19],"for":[20,126,161,241],"many":[21],"organisms,":[22],"genome-scale":[23,143,201],"being":[26],"widely":[27],"used":[28],"among":[29],"modellers":[30],"engineers.":[32],"However,":[33],"these":[34,109],"large":[35],"can":[37],"be":[38],"difficult":[39],"to":[40,51,77,92,103,199,234],"analyse":[41],"visualise,":[43],"occasionally":[45],"generate":[46],"predictions":[47],"that":[48],"hard":[50],"interpret":[52],"or":[53],"even":[54],"biologically":[55],"unrealistic.":[56],"Of":[57],"the":[58,73,96,127,140,165,181,186,192,205,208,232],"thousands":[59],"of":[60,121,139,152,158,185,194,207],"enzymatic":[61],"reactions":[62],"typical":[65],"bacterial":[66],"metabolism,":[67],"only":[68],"few":[70],"hundred":[71],"form":[72],"metabolic":[74,105,111,159,239],"pathways":[75,85],"essential":[76],"produce":[78],"energy":[79,102,122],"carriers":[80],"biosynthetic":[82],"precursors.":[83],"These":[84],"carry":[86],"relatively":[87],"high":[88],"flux,":[89],"central":[91,110],"maintaining":[93],"reproducing":[95],"cell,":[97],"provide":[99],"precursors":[100],"engineered":[104],"pathways.":[106],"Focusing":[107],"on":[108],"subsystems,":[112],"we":[113,190],"present":[114],"iCH360,":[115],"manually":[117],"curated":[118],"medium-scale":[119,238],"model":[120,135,196,230,240],"biosynthesis":[124],"metabolism":[125],"well-studied":[128],"bacterium":[129],"Escherichia":[130],"coli":[131],"K-12":[132],"MG1655.":[133],"The":[134],"is":[136],"sub-network":[138],"most":[141],"recent":[142],"reconstruction,":[144],"iML1515,":[145],"comes":[147],"with":[148,168],"an":[149],"updated":[150],"layer":[151],"database":[153],"annotations":[154],"range":[157],"maps":[160],"visualisation.":[162],"We":[163],"enriched":[164],"stoichiometric":[166],"extensive":[169],"biological":[170],"information":[171],"quantitative":[173],"data,":[174],"including":[175,216],"thermodynamic":[176,226],"kinetic":[178],"constants,":[179],"enhancing":[180],"scope":[182],"applicability":[184],"model.":[187],"In":[188],"addition,":[189],"assess":[191],"properties":[193],"this":[195,229],"comparison":[198],"its":[200],"parent":[202],"demonstrate":[204],"use":[206],"supporting":[211],"data":[212],"various":[214],"scenarios,":[215],"enzyme-constrained":[217],"flux":[218,222],"balance":[219],"analysis,":[220,224],"elementary":[221],"mode":[223],"analysis.":[227],"Overall,":[228],"holds":[231],"potential":[233],"become":[235],"reference":[237],"E.":[242],"coli.":[243]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-10-10T00:00:00"}
