{"id":"https://openalex.org/W4313455070","doi":"https://doi.org/10.1371/journal.pcbi.1010783","title":"Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks","display_name":"Efficient computation of adjoint sensitivities at steady-state in ODE models of biochemical reaction networks","publication_year":2023,"publication_date":"2023-01-03","ids":{"openalex":"https://openalex.org/W4313455070","doi":"https://doi.org/10.1371/journal.pcbi.1010783","pmid":"https://pubmed.ncbi.nlm.nih.gov/36595539"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1010783","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010783","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010783&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.1010783&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001044691","display_name":"Polina Lakrisenko","orcid":"https://orcid.org/0000-0002-7626-8420"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Polina Lakrisenko","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH), Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7626-8420","affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH), Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038659090","display_name":"Paul Stapor","orcid":"https://orcid.org/0000-0002-7567-3985"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Paul Stapor","raw_affiliation_strings":["Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH), Neuherberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Mathematics, Technische Universit\u00e4t M\u00fcnchen, Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH), Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048103149","display_name":"Stephan Grein","orcid":"https://orcid.org/0000-0001-9524-6633"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Stephan Grein","raw_affiliation_strings":["University of Bonn, Life and Medical Sciences Institute, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0001-9524-6633","affiliations":[{"raw_affiliation_string":"University of Bonn, Life and Medical Sciences Institute, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011716508","display_name":"\u0141ukasz Paszkowski","orcid":null},"institutions":[{"id":"https://openalex.org/I2799829267","display_name":"Simula Research Laboratory","ror":"https://ror.org/00vn06n10","country_code":"NO","type":"facility","lineage":["https://openalex.org/I2799829267"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"\u0141ukasz Paszkowski","raw_affiliation_strings":["Simula Research Laboratory, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Simula Research Laboratory, Oslo, Norway","institution_ids":["https://openalex.org/I2799829267"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029598458","display_name":"Dilan Pathirana","orcid":"https://orcid.org/0000-0001-7000-2659"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Dilan Pathirana","raw_affiliation_strings":["University of Bonn, Life and Medical Sciences Institute, Bonn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Bonn, Life and Medical Sciences Institute, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003197068","display_name":"Fabian Fr\u00f6hlich","orcid":"https://orcid.org/0000-0002-5360-4292"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fabian Fr\u00f6hlich","raw_affiliation_strings":["Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-5360-4292","affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013534678","display_name":"Glenn Terje Lines","orcid":"https://orcid.org/0000-0002-5512-8525"},"institutions":[{"id":"https://openalex.org/I2799829267","display_name":"Simula Research Laboratory","ror":"https://ror.org/00vn06n10","country_code":"NO","type":"facility","lineage":["https://openalex.org/I2799829267"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Glenn Terje Lines","raw_affiliation_strings":["Simula Research Laboratory, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Simula Research Laboratory, Oslo, Norway","institution_ids":["https://openalex.org/I2799829267"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014811978","display_name":"Daniel Weindl","orcid":"https://orcid.org/0000-0001-9963-6057"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Daniel Weindl","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH), Neuherberg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-9963-6057","affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH), Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063254041","display_name":"Jan Hasenauer","orcid":"https://orcid.org/0000-0002-4935-3312"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jan Hasenauer","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH), Neuherberg, Germany","University of Bonn, Life and Medical Sciences Institute, Bonn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH), Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"University of Bonn, Life and Medical Sciences Institute, Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001044691","https://openalex.org/A5003197068","https://openalex.org/A5011716508","https://openalex.org/A5013534678","https://openalex.org/A5014811978","https://openalex.org/A5029598458","https://openalex.org/A5038659090","https://openalex.org/A5048103149","https://openalex.org/A5063254041"],"corresponding_institution_ids":["https://openalex.org/I135140700","https://openalex.org/I136199984","https://openalex.org/I2799829267","https://openalex.org/I3018134672","https://openalex.org/I4210155419","https://openalex.org/I62916508"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.3515,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.79934737,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"19","issue":"1","first_page":"e1010783","last_page":"e1010783"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9976000189781189,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9908000230789185,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ode","display_name":"Ode","score":0.7230309247970581},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.6995354890823364},{"id":"https://openalex.org/keywords/ordinary-differential-equation","display_name":"Ordinary differential equation","score":0.6593912243843079},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6373680830001831},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6211300492286682},{"id":"https://openalex.org/keywords/adjoint-equation","display_name":"Adjoint equation","score":0.5652710795402527},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.5120935440063477},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4341018795967102},{"id":"https://openalex.org/keywords/steady-state","display_name":"Steady state (chemistry)","score":0.4312141239643097},{"id":"https://openalex.org/keywords/dynamical-systems-theory","display_name":"Dynamical systems theory","score":0.419749915599823},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.39389970898628235},{"id":"https://openalex.org/keywords/applied-mathematics","display_name":"Applied mathematics","score":0.3667908310890198},{"id":"https://openalex.org/keywords/differential-equation","display_name":"Differential equation","score":0.36429065465927124},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3340660631656647},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.28410017490386963},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.14846372604370117},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.10312047600746155},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.09532922506332397}],"concepts":[{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.7230309247970581},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.6995354890823364},{"id":"https://openalex.org/C51544822","wikidata":"https://www.wikidata.org/wiki/Q465274","display_name":"Ordinary differential equation","level":3,"score":0.6593912243843079},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6373680830001831},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6211300492286682},{"id":"https://openalex.org/C165551260","wikidata":"https://www.wikidata.org/wiki/Q4428962","display_name":"Adjoint equation","level":3,"score":0.5652710795402527},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.5120935440063477},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4341018795967102},{"id":"https://openalex.org/C8171440","wikidata":"https://www.wikidata.org/wiki/Q903414","display_name":"Steady state (chemistry)","level":2,"score":0.4312141239643097},{"id":"https://openalex.org/C79379906","wikidata":"https://www.wikidata.org/wiki/Q3174497","display_name":"Dynamical systems theory","level":2,"score":0.419749915599823},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.39389970898628235},{"id":"https://openalex.org/C28826006","wikidata":"https://www.wikidata.org/wiki/Q33521","display_name":"Applied mathematics","level":1,"score":0.3667908310890198},{"id":"https://openalex.org/C78045399","wikidata":"https://www.wikidata.org/wiki/Q11214","display_name":"Differential equation","level":2,"score":0.36429065465927124},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3340660631656647},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.28410017490386963},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.14846372604370117},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.10312047600746155},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.09532922506332397},{"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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"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":"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1010783","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010783","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010783&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:36595539","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36595539","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:pubmedcentral.nih.gov:9838866","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9838866","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9838866/pdf/pcbi.1010783.pdf","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1010783","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010783","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:154d58c3a25b4b748e7ec79817755d57","is_oa":true,"landing_page_url":"https://doaj.org/article/154d58c3a25b4b748e7ec79817755d57","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 19, Iss 1, p e1010783 (2023)","raw_type":"article"},{"id":"pmh:oai:opus-zb.helmholtz-muenchen.de:67115","is_oa":true,"landing_page_url":"https://push-zb.helmholtz-muenchen.de/frontdoor.php?source_opus=67115","pdf_url":null,"source":{"id":"https://openalex.org/S4377196115","display_name":"Site cant be reached","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput. Biol. 19:e1010783 (2023)","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:push-zb.helmholtz-munich.de:67115","is_oa":false,"landing_page_url":"https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=67115","pdf_url":null,"source":{"id":"https://openalex.org/S7407055352","display_name":"PuSH - Publication Server of Helmholtz Zentrum M\u00fcnchen","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput. Biol. 19:e1010783 (2023)","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1010783","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1010783","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010783&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/G1521016025","display_name":"EXC 2047: Hausdorff Center for Mathematics (HCM)","funder_award_id":"390685813","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G1894950364","display_name":"SFB 1454: Metaflammation und Zellul\u00e4re Programmierung","funder_award_id":"432325352","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2425020771","display_name":null,"funder_award_id":"EXC 2151 390685813","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4549622993","display_name":null,"funder_award_id":"EXC 2151","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G4787627496","display_name":null,"funder_award_id":"01ZX1916A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5612980095","display_name":null,"funder_award_id":"U54-CA225088","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6175022879","display_name":null,"funder_award_id":"LT000259/2019-L1","funder_id":"https://openalex.org/F4320320338","funder_display_name":"Human Frontier Science Program"},{"id":"https://openalex.org/G6238101420","display_name":null,"funder_award_id":"686282","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6354517727","display_name":null,"funder_award_id":"EXC 2047","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6672323505","display_name":"Generation of the CanPath prototype - a platform for predictive cancer pathway modeling","funder_award_id":"686282","funder_id":"https://openalex.org/F4320338482","funder_display_name":"H2020 LEIT Biotechnology"},{"id":"https://openalex.org/G7515004340","display_name":"Generation of the CanPath prototype - a platform for predictive cancer pathway modeling","funder_award_id":"686282","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G7795917239","display_name":null,"funder_award_id":"U54 CA225088","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8668678933","display_name":null,"funder_award_id":"EXC 2047 390873048","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8796401741","display_name":"EXC 2151: ImmunoSensation2  the immune sensory system","funder_award_id":"390873048","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G97110083","display_name":"AMICI  Skalierbare numerische Simulation und Sensitivit\u00e4tsanalyse dynamischer Systeme","funder_award_id":"443187771","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320338","display_name":"Human Frontier Science Program","ror":"https://ror.org/02ebx7v45"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320338482","display_name":"H2020 LEIT Biotechnology","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4313455070.pdf","grobid_xml":"https://content.openalex.org/works/W4313455070.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W400678491","https://openalex.org/W1579014599","https://openalex.org/W1964844730","https://openalex.org/W1974411859","https://openalex.org/W1981151876","https://openalex.org/W1989263028","https://openalex.org/W2011618311","https://openalex.org/W2045164356","https://openalex.org/W2102434872","https://openalex.org/W2107073512","https://openalex.org/W2123783513","https://openalex.org/W2143894094","https://openalex.org/W2166751342","https://openalex.org/W2270994990","https://openalex.org/W2389037713","https://openalex.org/W2512206536","https://openalex.org/W2825036749","https://openalex.org/W2902000707","https://openalex.org/W2949499968","https://openalex.org/W2950665010","https://openalex.org/W2952056515","https://openalex.org/W2964392985","https://openalex.org/W2997148015","https://openalex.org/W3011448036","https://openalex.org/W3014365047","https://openalex.org/W3024659207","https://openalex.org/W3039357575","https://openalex.org/W3105895642","https://openalex.org/W3112804643","https://openalex.org/W3125399711","https://openalex.org/W3134951790","https://openalex.org/W3142344196","https://openalex.org/W3164109950","https://openalex.org/W3204234525","https://openalex.org/W4225648581","https://openalex.org/W4280552812","https://openalex.org/W4283383602","https://openalex.org/W4283700072","https://openalex.org/W4285088295","https://openalex.org/W6796041746","https://openalex.org/W6893984457"],"related_works":["https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W2027972911","https://openalex.org/W2157978810","https://openalex.org/W4391547476","https://openalex.org/W2597809628"],"abstract_inverted_index":{"Dynamical":[0],"models":[1,23],"in":[2,16,161,164],"the":[3,59,101,115,129,153],"form":[4],"of":[5,7,21,62,114,122,128,138,145],"systems":[6,17],"ordinary":[8],"differential":[9],"equations":[10],"have":[11,28],"become":[12],"a":[13,90,112,120,136,143,158],"standard":[14],"tool":[15],"biology.":[18],"Many":[19],"parameters":[20],"such":[22,75],"are":[24,55,84],"usually":[25],"unknown":[26],"and":[27],"to":[29,39,119,147],"be":[30,40],"inferred":[31],"from":[32],"experimental":[33,102],"data.":[34],"Gradient-based":[35],"optimization":[36],"has":[37,69],"proven":[38],"effective":[41],"for":[42,51,57,72,81,94,166],"parameter":[43],"estimation.":[44],"However,":[45],"computing":[46,95],"gradients":[47],"becomes":[48],"increasingly":[49],"costly":[50],"larger":[52],"models,":[53,77,168],"which":[54,97],"required":[56],"capturing":[58],"complex":[60],"interactions":[61],"multiple":[63],"biochemical":[64],"pathways.":[65],"Adjoint":[66],"sensitivity":[67],"analysis":[68],"been":[70],"pivotal":[71],"working":[73],"with":[74],"large":[76],"but":[78],"methods":[79],"tailored":[80],"steady-state":[82,105],"data":[83,103],"currently":[85],"not":[86],"available.":[87],"We":[88],"propose":[89],"new":[91],"adjoint":[92],"method":[93,108,131],"gradients,":[96],"is":[98,109,172],"applicable":[99],"if":[100],"include":[104],"measurements.":[106],"The":[107,126],"based":[110],"on":[111],"reformulation":[113],"backward":[116],"integration":[117],"problem":[118],"system":[121],"linear":[123],"algebraic":[124],"equations.":[125],"evaluation":[127],"proposed":[130,154],"using":[132],"real-world":[133],"problems":[134],"shows":[135],"speedup":[137],"total":[139],"simulation":[140],"time":[141],"by":[142],"factor":[144],"up":[146],"4.4.":[148],"Our":[149],"results":[150],"demonstrate":[151],"that":[152],"approach":[155],"can":[156],"achieve":[157],"substantial":[159],"improvement":[160],"computation":[162],"time,":[163],"particular":[165],"large-scale":[167],"where":[169],"computational":[170],"efficiency":[171],"critical.":[173]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":2}],"updated_date":"2026-07-08T08:33:18.762332","created_date":"2025-10-10T00:00:00"}