{"id":"https://openalex.org/W4410106391","doi":"https://doi.org/10.1093/bioinformatics/btaf287","title":"Algebraic differentiation for fast sensitivity analysis of optimal flux modes in metabolic models","display_name":"Algebraic differentiation for fast sensitivity analysis of optimal flux modes in metabolic models","publication_year":2025,"publication_date":"2025-05-06","ids":{"openalex":"https://openalex.org/W4410106391","doi":"https://doi.org/10.1093/bioinformatics/btaf287","pmid":"https://pubmed.ncbi.nlm.nih.gov/40327453"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf287","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf287/63069969/btaf287.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf287/63069969/btaf287.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Hester Chapman","orcid":"https://orcid.org/0009-0004-5697-5592"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Hester Chapman","raw_affiliation_strings":["Institute of Quantitative and Theoretical Biology, Heinrich Heine University , D\u00fcsseldorf 40255,","Heinrich Heine University Institute of Quantitative and Theoretical Biology, , 40255 D\u00fcsseldorf,"],"affiliations":[{"raw_affiliation_string":"Institute of Quantitative and Theoretical Biology, Heinrich Heine University , D\u00fcsseldorf 40255,","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Heinrich Heine University Institute of Quantitative and Theoretical Biology, , 40255 D\u00fcsseldorf,","institution_ids":["https://openalex.org/I44260953"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081106885","display_name":"Miroslav Kratochv\u00edl","orcid":"https://orcid.org/0000-0001-7356-4075"},"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":"Miroslav Kratochv\u00edl","raw_affiliation_strings":["Luxembourg Centre of Systems Biomedicine, University of Luxembourg , Esch-sur-Alzette L-4367,","University of Luxembourg Luxembourg Centre of Systems Biomedicine, , Belval Campus, 6 avenue du Swing, Belvaux, L-4367, Esch-sur-Alzette,"],"affiliations":[{"raw_affiliation_string":"Luxembourg Centre of Systems Biomedicine, University of Luxembourg , Esch-sur-Alzette L-4367,","institution_ids":["https://openalex.org/I186903577"]},{"raw_affiliation_string":"University of Luxembourg Luxembourg Centre of Systems Biomedicine, , Belval Campus, 6 avenue du Swing, Belvaux, L-4367, Esch-sur-Alzette,","institution_ids":["https://openalex.org/I186903577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026460206","display_name":"Oliver Ebenh\u00f6h","orcid":"https://orcid.org/0000-0002-7229-7398"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Oliver Ebenh\u00f6h","raw_affiliation_strings":["Institute of Quantitative and Theoretical Biology, Heinrich Heine University , D\u00fcsseldorf 40255,","Heinrich Heine University Institute of Quantitative and Theoretical Biology, , 40255 D\u00fcsseldorf,"],"affiliations":[{"raw_affiliation_string":"Institute of Quantitative and Theoretical Biology, Heinrich Heine University , D\u00fcsseldorf 40255,","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Heinrich Heine University Institute of Quantitative and Theoretical Biology, , 40255 D\u00fcsseldorf,","institution_ids":["https://openalex.org/I44260953"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015224862","display_name":"St. Elmo Wilken","orcid":"https://orcid.org/0000-0002-4113-2590"},"institutions":[{"id":"https://openalex.org/I44260953","display_name":"Heinrich Heine University D\u00fcsseldorf","ror":"https://ror.org/024z2rq82","country_code":"DE","type":"education","lineage":["https://openalex.org/I44260953"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"St Elmo Wilken","raw_affiliation_strings":["Institute of Quantitative and Theoretical Biology, Heinrich Heine University , D\u00fcsseldorf 40255,","Heinrich Heine University Institute of Quantitative and Theoretical Biology, , 40255 D\u00fcsseldorf,"],"affiliations":[{"raw_affiliation_string":"Institute of Quantitative and Theoretical Biology, Heinrich Heine University , D\u00fcsseldorf 40255,","institution_ids":["https://openalex.org/I44260953"]},{"raw_affiliation_string":"Heinrich Heine University Institute of Quantitative and Theoretical Biology, , 40255 D\u00fcsseldorf,","institution_ids":["https://openalex.org/I44260953"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I44260953"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08427474,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"6","first_page":null,"last_page":null},"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/T10404","display_name":"Enzyme Catalysis and Immobilization","score":0.9968000054359436,"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":0.9943000078201294,"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/sensitivity","display_name":"Sensitivity (control systems)","score":0.8274209499359131},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6385804414749146},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6250767707824707},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.6152682304382324},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5937061309814453},{"id":"https://openalex.org/keywords/automatic-differentiation","display_name":"Automatic differentiation","score":0.575772762298584},{"id":"https://openalex.org/keywords/metabolic-flux-analysis","display_name":"Metabolic flux analysis","score":0.5644016265869141},{"id":"https://openalex.org/keywords/flux","display_name":"Flux (metallurgy)","score":0.5610337257385254},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4987461566925049},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.43542179465293884},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4329372048377991},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4327344298362732},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3014723062515259},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.21435943245887756},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09915286302566528},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.0901026725769043}],"concepts":[{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.8274209499359131},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6385804414749146},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6250767707824707},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.6152682304382324},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5937061309814453},{"id":"https://openalex.org/C133512626","wikidata":"https://www.wikidata.org/wiki/Q787371","display_name":"Automatic differentiation","level":3,"score":0.575772762298584},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.5644016265869141},{"id":"https://openalex.org/C68709404","wikidata":"https://www.wikidata.org/wiki/Q1134475","display_name":"Flux (metallurgy)","level":2,"score":0.5610337257385254},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4987461566925049},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.43542179465293884},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4329372048377991},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4327344298362732},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3014723062515259},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.21435943245887756},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09915286302566528},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0901026725769043},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"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":"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":"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":"D000465","descriptor_name":"Algorithms","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":"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":"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":"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":"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":"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf287","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf287/63069969/btaf287.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40327453","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40327453","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:orbilu.uni.lu:10993/65074","is_oa":true,"landing_page_url":"https://orbilu.uni.lu/handle/10993/65074","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Bioinformatics (2025-05-06)","raw_type":"peer reviewed"},{"id":"pmh:oai:europepmc.org:10946725","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12133274","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:10.1093/bioinformatics/btaf287","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf287","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf287/63069969/btaf287.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"display_name":"Responsible consumption and production","id":"https://metadata.un.org/sdg/12"}],"awards":[{"id":"https://openalex.org/G1037239894","display_name":"Innvative approaches to identification  of metabolic Targets for antimicrobials","funder_award_id":"956154","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2642650165","display_name":null,"funder_award_id":"EXC-2048","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2958780423","display_name":null,"funder_award_id":"EXC-2048/1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7021525608","display_name":null,"funder_award_id":"390686111","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7231943246","display_name":null,"funder_award_id":"Horizon 2020 Programme","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G762232396","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7735813670","display_name":null,"funder_award_id":"2048/1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8318064016","display_name":null,"funder_award_id":"Horizon","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8697265622","display_name":"HPC/Exascale Centre of Excellence in Personalised Medicine - PerMedCoE","funder_award_id":"951773","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8826631963","display_name":null,"funder_award_id":"Horizon 2020 Program","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320323939","display_name":"Copenhagen Graduate School for Nanoscience and Nanotechnology","ror":"https://ror.org/035b05819"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410106391.pdf","grobid_xml":"https://content.openalex.org/works/W4410106391.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1621975707","https://openalex.org/W1965909561","https://openalex.org/W1967434028","https://openalex.org/W1969622794","https://openalex.org/W1972486342","https://openalex.org/W1985517408","https://openalex.org/W1996700024","https://openalex.org/W1996791690","https://openalex.org/W2020836755","https://openalex.org/W2033557504","https://openalex.org/W2062245653","https://openalex.org/W2067268731","https://openalex.org/W2076573047","https://openalex.org/W2078355959","https://openalex.org/W2127589936","https://openalex.org/W2142750990","https://openalex.org/W2157457604","https://openalex.org/W2157589025","https://openalex.org/W2191824721","https://openalex.org/W2401624724","https://openalex.org/W2416065856","https://openalex.org/W2468889898","https://openalex.org/W2592233514","https://openalex.org/W2606897259","https://openalex.org/W2743063996","https://openalex.org/W2764202526","https://openalex.org/W2789128799","https://openalex.org/W2902098281","https://openalex.org/W2922405027","https://openalex.org/W2972255548","https://openalex.org/W3017898716","https://openalex.org/W3082397379","https://openalex.org/W3088424108","https://openalex.org/W3153936674","https://openalex.org/W4200538989","https://openalex.org/W4283032119","https://openalex.org/W4297878114","https://openalex.org/W4384023735","https://openalex.org/W4404129141","https://openalex.org/W4404458588","https://openalex.org/W4404509609","https://openalex.org/W4407284042","https://openalex.org/W6684563919"],"related_works":["https://openalex.org/W2912883929","https://openalex.org/W2245096339","https://openalex.org/W2345428922","https://openalex.org/W3037347004","https://openalex.org/W2420406980","https://openalex.org/W2006196154","https://openalex.org/W1865446941","https://openalex.org/W2026690417","https://openalex.org/W4200244030","https://openalex.org/W1984004049"],"abstract_inverted_index":{"Software":[0],"introduced":[1],"here":[2],"is":[3,30],"available":[4,31],"as":[5,35],"open-source":[6],"Julia":[7],"packages":[8],"DifferentiableMetabolism.jl":[9],"(https://github.com/stelmo/DifferentiableMetabolism.jl)":[10],"and":[11,22,34],"ElementaryFluxModes.jl":[12],"(https://github.com/HettieC/ElementaryFluxModes.jl),":[13],"which":[14],"both":[15],"work":[16],"on":[17],"all":[18,28],"major":[19],"operating":[20],"systems":[21],"computer":[23],"architectures.":[24],"Code":[25],"to":[26],"reproduce":[27],"results":[29],"from":[32,38],"https://github.com/HettieC/DifferentiableOFMPaper,":[33],"an":[36],"archive":[37],"https://doi.org/10.5281/zenodo.15183208.":[39]},"counts_by_year":[],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}