{"id":"https://openalex.org/W3125963348","doi":"https://doi.org/10.1371/journal.pcbi.1007694","title":"Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions","display_name":"Physicochemical and metabolic constraints for thermodynamics-based stoichiometric modelling under mesophilic growth conditions","publication_year":2021,"publication_date":"2021-01-25","ids":{"openalex":"https://openalex.org/W3125963348","doi":"https://doi.org/10.1371/journal.pcbi.1007694","mag":"3125963348","pmid":"https://pubmed.ncbi.nlm.nih.gov/33493151"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007694","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007694","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007694&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.1007694&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004197895","display_name":"Claudio Tomi-Andrino","orcid":"https://orcid.org/0000-0002-3611-2130"},"institutions":[{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]},{"id":"https://openalex.org/I2799693246","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982","country_code":"GB","type":"government","lineage":["https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Claudio Tomi-Andrino","raw_affiliation_strings":["Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom","Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom","Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-3611-2130","affiliations":[{"raw_affiliation_string":"Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I142263535"]},{"raw_affiliation_string":"Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I2799693246","https://openalex.org/I142263535"]},{"raw_affiliation_string":"Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I2799693246","https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056482122","display_name":"Rupert Norman","orcid":"https://orcid.org/0000-0003-4772-3698"},"institutions":[{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]},{"id":"https://openalex.org/I2799693246","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982","country_code":"GB","type":"government","lineage":["https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rupert Norman","raw_affiliation_strings":["Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0003-4772-3698","affiliations":[{"raw_affiliation_string":"Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I2799693246","https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081500764","display_name":"Thomas Millat","orcid":"https://orcid.org/0000-0002-5023-4142"},"institutions":[{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]},{"id":"https://openalex.org/I2799693246","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982","country_code":"GB","type":"government","lineage":["https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Thomas Millat","raw_affiliation_strings":["Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-5023-4142","affiliations":[{"raw_affiliation_string":"Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I2799693246","https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048440222","display_name":"Philippe Soucaille","orcid":"https://orcid.org/0000-0002-1724-7136"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I205747304","display_name":"Institut National Polytechnique de Toulouse","ror":"https://ror.org/033p9g875","country_code":"FR","type":"education","lineage":["https://openalex.org/I205747304"]},{"id":"https://openalex.org/I2799693246","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982","country_code":"GB","type":"government","lineage":["https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["FR","GB"],"is_corresponding":false,"raw_author_name":"Philippe Soucaille","raw_affiliation_strings":["CNRS, UMR5504, Toulouse, France","INRA, UMR792, Toulouse, France","INSA, UPS, INP, Toulouse Biotechnology Institute, (TBI), Universit\u00e9 de Toulouse, Toulouse, France","Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CNRS, UMR5504, Toulouse, France","institution_ids":["https://openalex.org/I1294671590"]},{"raw_affiliation_string":"INRA, UMR792, Toulouse, France","institution_ids":[]},{"raw_affiliation_string":"INSA, UPS, INP, Toulouse Biotechnology Institute, (TBI), Universit\u00e9 de Toulouse, Toulouse, France","institution_ids":["https://openalex.org/I205747304","https://openalex.org/I17866349","https://openalex.org/I134560555"]},{"raw_affiliation_string":"Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I2799693246","https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032485641","display_name":"Klaus Winzer","orcid":"https://orcid.org/0000-0002-3956-8096"},"institutions":[{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]},{"id":"https://openalex.org/I2799693246","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982","country_code":"GB","type":"government","lineage":["https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Klaus Winzer","raw_affiliation_strings":["Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, BioDiscovery Institute, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I2799693246","https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056321186","display_name":"David A. Barrett","orcid":"https://orcid.org/0000-0001-6900-9474"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David A. Barrett","raw_affiliation_strings":["Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I142263535"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010038899","display_name":"John R. King","orcid":"https://orcid.org/0000-0002-6228-8375"},"institutions":[{"id":"https://openalex.org/I1299528221","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842","country_code":"GB","type":"government","lineage":["https://openalex.org/I1299528221","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]},{"id":"https://openalex.org/I2799693246","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982","country_code":"GB","type":"government","lineage":["https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John King","raw_affiliation_strings":["Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-6228-8375","affiliations":[{"raw_affiliation_string":"Nottingham BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Mathematical Sciences, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I1299528221","https://openalex.org/I2799693246","https://openalex.org/I142263535"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100454672","display_name":"Dong\u2010Hyun Kim","orcid":"https://orcid.org/0000-0002-3689-2130"},"institutions":[{"id":"https://openalex.org/I142263535","display_name":"University of Nottingham","ror":"https://ror.org/01ee9ar58","country_code":"GB","type":"education","lineage":["https://openalex.org/I142263535"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Dong-Hyun Kim","raw_affiliation_strings":["Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom"],"raw_orcid":"https://orcid.org/0000-0002-3689-2130","affiliations":[{"raw_affiliation_string":"Centre for Analytical Bioscience, Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, United Kingdom","institution_ids":["https://openalex.org/I142263535"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100454672"],"corresponding_institution_ids":["https://openalex.org/I142263535"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.3965,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.56796313,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"17","issue":"1","first_page":"e1007694","last_page":"e1007694"},"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":0.9958999752998352,"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/T10791","display_name":"Advanced Control Systems Optimization","score":0.9815999865531921,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems 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/flux-balance-analysis","display_name":"Flux balance analysis","score":0.8096574544906616},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.7183662056922913},{"id":"https://openalex.org/keywords/metabolic-engineering","display_name":"Metabolic engineering","score":0.7001525163650513},{"id":"https://openalex.org/keywords/metabolic-flux-analysis","display_name":"Metabolic flux analysis","score":0.6684162616729736},{"id":"https://openalex.org/keywords/metabolomics","display_name":"Metabolomics","score":0.6181572675704956},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.585889458656311},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.5726830959320068},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.49942731857299805},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4738733470439911},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.4718984067440033},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.40465861558914185},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3721523880958557},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.33345744013786316},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24085566401481628},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22284480929374695},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.13671034574508667},{"id":"https://openalex.org/keywords/metabolism","display_name":"Metabolism","score":0.1136842668056488},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.10421490669250488}],"concepts":[{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.8096574544906616},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.7183662056922913},{"id":"https://openalex.org/C6350086","wikidata":"https://www.wikidata.org/wiki/Q6822347","display_name":"Metabolic engineering","level":3,"score":0.7001525163650513},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.6684162616729736},{"id":"https://openalex.org/C21565614","wikidata":"https://www.wikidata.org/wiki/Q12149006","display_name":"Metabolomics","level":2,"score":0.6181572675704956},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.585889458656311},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.5726830959320068},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.49942731857299805},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4738733470439911},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.4718984067440033},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.40465861558914185},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3721523880958557},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.33345744013786316},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24085566401481628},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22284480929374695},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.13671034574508667},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.1136842668056488},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.10421490669250488},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"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":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002247","descriptor_name":"Carbon Isotopes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060847","descriptor_name":"Metabolic Engineering","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D064688","descriptor_name":"Metabolic Flux Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007694","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007694","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007694&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:33493151","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33493151","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-03162419v1","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-03162419","pdf_url":null,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology, 2021, 17 (1), &#x27E8;10.1371/journal.pcbi.1007694&#x27E9;","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7861524","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7861524","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:0122054efe1e4c55af55f94128895a9f","is_oa":true,"landing_page_url":"https://doaj.org/article/0122054efe1e4c55af55f94128895a9f","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 17, Iss 1, p e1007694 (2021)","raw_type":"article"},{"id":"pmh:oai:nottingham-repository.worktribe.com:5275831","is_oa":true,"landing_page_url":"https://nottingham-repository.worktribe.com/output/5275831","pdf_url":null,"source":{"id":"https://openalex.org/S4306402483","display_name":"Repository@Nottingham (University of Nottingham)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I142263535","host_organization_name":"University of Nottingham","host_organization_lineage":["https://openalex.org/I142263535"],"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":"Journal Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007694","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007694","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007694&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/G3559947993","display_name":null,"funder_award_id":"BB/L013940/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G3642178571","display_name":"SBRC NOTTINGHAM: Sustainable Routes to Platform Chemicals","funder_award_id":"BB/L013940/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G5621553766","display_name":null,"funder_award_id":"BB/L013940/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W3125963348.pdf"},"referenced_works_count":77,"referenced_works":["https://openalex.org/W399385914","https://openalex.org/W1156627145","https://openalex.org/W1854214752","https://openalex.org/W1944909517","https://openalex.org/W1963489914","https://openalex.org/W1968101639","https://openalex.org/W1972990890","https://openalex.org/W1978907149","https://openalex.org/W1981096637","https://openalex.org/W1981100467","https://openalex.org/W1982403564","https://openalex.org/W1983202741","https://openalex.org/W1984378303","https://openalex.org/W1991509434","https://openalex.org/W2005270533","https://openalex.org/W2007820233","https://openalex.org/W2008875008","https://openalex.org/W2010451964","https://openalex.org/W2016514521","https://openalex.org/W2025325354","https://openalex.org/W2030933109","https://openalex.org/W2034518398","https://openalex.org/W2036318837","https://openalex.org/W2037911829","https://openalex.org/W2042067428","https://openalex.org/W2046546139","https://openalex.org/W2048601646","https://openalex.org/W2049196570","https://openalex.org/W2056756011","https://openalex.org/W2057685234","https://openalex.org/W2068044722","https://openalex.org/W2070787626","https://openalex.org/W2078355959","https://openalex.org/W2091282042","https://openalex.org/W2092504964","https://openalex.org/W2103795997","https://openalex.org/W2107409961","https://openalex.org/W2111421616","https://openalex.org/W2111905282","https://openalex.org/W2114775507","https://openalex.org/W2116976883","https://openalex.org/W2117270601","https://openalex.org/W2119719542","https://openalex.org/W2123875295","https://openalex.org/W2124737787","https://openalex.org/W2126175129","https://openalex.org/W2133505559","https://openalex.org/W2135394763","https://openalex.org/W2141776893","https://openalex.org/W2147472054","https://openalex.org/W2155537325","https://openalex.org/W2156528225","https://openalex.org/W2156850933","https://openalex.org/W2157125182","https://openalex.org/W2160259320","https://openalex.org/W2160317546","https://openalex.org/W2346094579","https://openalex.org/W2554210752","https://openalex.org/W2580762423","https://openalex.org/W2737068766","https://openalex.org/W2737993744","https://openalex.org/W2763457230","https://openalex.org/W2766164287","https://openalex.org/W2787179672","https://openalex.org/W2794432101","https://openalex.org/W2810239425","https://openalex.org/W2846896496","https://openalex.org/W2889493410","https://openalex.org/W2902733144","https://openalex.org/W2931682998","https://openalex.org/W2950093550","https://openalex.org/W2950547188","https://openalex.org/W2951700574","https://openalex.org/W2963227893","https://openalex.org/W2970801850","https://openalex.org/W6928862005","https://openalex.org/W6966414819"],"related_works":["https://openalex.org/W2046546139","https://openalex.org/W1992844569","https://openalex.org/W1999460937","https://openalex.org/W2113329733","https://openalex.org/W1918238777","https://openalex.org/W2341681417","https://openalex.org/W1984242440","https://openalex.org/W4285237197","https://openalex.org/W1983989854","https://openalex.org/W2613838074"],"abstract_inverted_index":{"Metabolic":[0],"engineering":[1,24],"in":[2,91,151,204],"the":[3,9,20,56,65,102,112,131,134,140,152,161,169,194,200,205],"post-genomic":[4],"era":[5],"is":[6,80,221],"characterised":[7],"by":[8,19],"development":[10],"of":[11,22,58,68,77,88,111,123,133,147,164],"new":[12],"methods":[13,79,93,220],"for":[14,101,167,202],"metabolomics":[15,61],"and":[16,26,44,60,75,99,158],"fluxomics,":[17],"supported":[18],"integration":[21],"genetic":[23],"tools":[25],"mathematical":[27],"modelling.":[28],"Particularly,":[29],"constraint-based":[30],"stoichiometric":[31],"models":[32],"have":[33,54],"been":[34],"widely":[35],"studied:":[36],"(i)":[37],"flux":[38,47,148],"balance":[39],"analysis":[40,48,87,146],"(FBA)":[41],"(in":[42,50],"silico),":[43],"(ii)":[45],"metabolic":[46],"(MFA)":[49],"vivo).":[51],"Recent":[52],"studies":[53],"enabled":[55],"incorporation":[57],"thermodynamics":[59],"data":[62,97,129],"to":[63,138,182,191],"improve":[64],"predictive":[66],"capabilities":[67,163],"these":[69,78],"approaches.":[70],"However,":[71],"an":[72],"in-depth":[73],"comparison":[74,216],"evaluation":[76],"lacking.":[81],"This":[82],"study":[83,198],"presents":[84],"a":[85,108,120,174,214],"thorough":[86,215],"two":[89],"different":[90],"silico":[92],"tested":[94],"against":[95,127],"experimental":[96,128],"(metabolomics":[98],"13C-MFA)":[100],"mesophile":[103],"Escherichia":[104],"coli.":[105],"In":[106,172],"particular,":[107],"modified":[109],"version":[110],"recently":[113],"published":[114],"matTFA":[115],"toolbox":[116],"was":[117,180],"created,":[118],"providing":[119],"broader":[121],"range":[122],"physicochemical":[124,136],"parameters.":[125],"Validating":[126],"allowed":[130],"determination":[132],"best":[135],"parameters":[137],"perform":[139],"TFA":[141,159],"(Thermodynamics-based":[142],"Flux":[143],"Analysis).":[144],"An":[145],"pattern":[149],"changes":[150],"central":[153],"carbon":[154],"metabolism":[155],"between":[156],"13C-MFA":[157],"highlighted":[160],"limited":[162],"both":[165],"approaches":[166,209],"elucidating":[168],"anaplerotic":[170],"fluxes.":[171],"addition,":[173],"method":[175],"based":[176],"on":[177],"centrality":[178],"measures":[179],"suggested":[181],"identify":[183],"important":[184],"metabolites":[185],"that":[186],"(if":[187],"quantified)":[188],"would":[189],"allow":[190],"further":[192],"constrain":[193],"TFA.":[195],"Finally,":[196],"this":[197],"emphasised":[199],"need":[201],"standardisation":[203],"fluxomics":[206],"community:":[207],"novel":[208],"are":[210],"frequently":[211],"released":[212],"but":[213],"with":[217],"currently":[218],"accepted":[219],"not":[222],"always":[223],"performed.":[224]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
