{"id":"https://openalex.org/W4409252255","doi":"https://doi.org/10.1093/bioinformatics/btaf154","title":"Gradient matching accelerates mixed-effects inference for biochemical networks","display_name":"Gradient matching accelerates mixed-effects inference for biochemical networks","publication_year":2025,"publication_date":"2025-03-29","ids":{"openalex":"https://openalex.org/W4409252255","doi":"https://doi.org/10.1093/bioinformatics/btaf154","pmid":"https://pubmed.ncbi.nlm.nih.gov/40199819"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf154","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf154","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf154/62892646/btaf154.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/btaf154/62892646/btaf154.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001355279","display_name":"Yulan B. van Oppen","orcid":"https://orcid.org/0000-0001-8214-2907"},"institutions":[{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":true,"raw_author_name":"Yulan B van Oppen","raw_affiliation_strings":["Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG,","University of Groningen Groningen Biomolecular Sciences and Biotechnology Institute, , Nijenborgh 4, 9747 AG, Groningen, The"],"affiliations":[{"raw_affiliation_string":"Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG,","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"University of Groningen Groningen Biomolecular Sciences and Biotechnology Institute, , Nijenborgh 4, 9747 AG, Groningen, The","institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I169381384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003041168","display_name":"Andreas Milias\u2010Argeitis","orcid":"https://orcid.org/0000-0002-4291-4228"},"institutions":[{"id":"https://openalex.org/I1312106833","display_name":"Biotechnology Institute","ror":"https://ror.org/00s1jty20","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1312106833"]},{"id":"https://openalex.org/I169381384","display_name":"University of Groningen","ror":"https://ror.org/012p63287","country_code":"NL","type":"education","lineage":["https://openalex.org/I169381384"]}],"countries":["NL","US"],"is_corresponding":false,"raw_author_name":"Andreas Milias-Argeitis","raw_affiliation_strings":["Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG,","University of Groningen Groningen Biomolecular Sciences and Biotechnology Institute, , Nijenborgh 4, 9747 AG, Groningen, The"],"affiliations":[{"raw_affiliation_string":"Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Groningen 9747 AG,","institution_ids":["https://openalex.org/I169381384"]},{"raw_affiliation_string":"University of Groningen Groningen Biomolecular Sciences and Biotechnology Institute, , Nijenborgh 4, 9747 AG, Groningen, The","institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I169381384"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5001355279"],"corresponding_institution_ids":["https://openalex.org/I1312106833","https://openalex.org/I169381384"],"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":0.06092699,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9995999932289124,"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":0.9995999932289124,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9905999898910522,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9749000072479248,"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/computer-science","display_name":"Computer science","score":0.6581667065620422},{"id":"https://openalex.org/keywords/matching","display_name":"Matching (statistics)","score":0.6389870643615723},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6285890936851501},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.5024755001068115},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.5024731159210205},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.49220767617225647},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.45377829670906067},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.4526876211166382},{"id":"https://openalex.org/keywords/mathematical-optimization","display_name":"Mathematical optimization","score":0.4010118544101715},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22618886828422546},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2061976194381714},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.14487650990486145}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6581667065620422},{"id":"https://openalex.org/C165064840","wikidata":"https://www.wikidata.org/wiki/Q1321061","display_name":"Matching (statistics)","level":2,"score":0.6389870643615723},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6285890936851501},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5024755001068115},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.5024731159210205},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.49220767617225647},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.45377829670906067},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.4526876211166382},{"id":"https://openalex.org/C126255220","wikidata":"https://www.wikidata.org/wiki/Q141495","display_name":"Mathematical optimization","level":1,"score":0.4010118544101715},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22618886828422546},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2061976194381714},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.14487650990486145},{"id":"https://openalex.org/C149923435","wikidata":"https://www.wikidata.org/wiki/Q37732","display_name":"Demography","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","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":"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational 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},{"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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf154","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf154","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf154/62892646/btaf154.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:40199819","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40199819","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:pure.rug.nl:openaire_cris_publications/a925cce2-61aa-4de2-8b93-dea459e08e2a","is_oa":true,"landing_page_url":"https://research.rug.nl/en/publications/a925cce2-61aa-4de2-8b93-dea459e08e2a","pdf_url":"https://research.rug.nl/files/1448362818/btaf154.pdf","source":{"id":"https://openalex.org/S4306400420","display_name":"University of Groningen research database (University of Groningen / Centre for Information Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I169381384","host_organization_name":"University of Groningen","host_organization_lineage":["https://openalex.org/I169381384"],"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":"van Oppen, Y B & Milias-Argeitis, A 2025, 'Gradient matching accelerates mixed-effects inference for biochemical networks', Bioinformatics (Oxford, England), vol. 41, no. 4, btaf154. https://doi.org/10.1093/bioinformatics/btaf154","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:pubmedcentral.nih.gov:12034378","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12034378","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:pure.rug.nl:openaire/a925cce2-61aa-4de2-8b93-dea459e08e2a","is_oa":true,"landing_page_url":"https://hdl.handle.net/11370/a925cce2-61aa-4de2-8b93-dea459e08e2a","pdf_url":null,"source":{"id":"https://openalex.org/S4306400420","display_name":"University of Groningen research database (University of Groningen / Centre for Information Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I169381384","host_organization_name":"University of Groningen","host_organization_lineage":["https://openalex.org/I169381384"],"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":"van Oppen, Y B & Milias-Argeitis, A 2025, 'Gradient matching accelerates mixed-effects inference for biochemical networks', Bioinformatics (Oxford, England), vol. 41, no. 4, btaf154. https://doi.org/10.1093/bioinformatics/btaf154","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf154","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf154","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf154/62892646/btaf154.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":[],"awards":[{"id":"https://openalex.org/G3462424673","display_name":null,"funder_award_id":"VIDI_grant","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5327937453","display_name":null,"funder_award_id":"016.Vidi.189.116","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G629491556","display_name":null,"funder_award_id":"(NWO)","funder_id":"https://openalex.org/F4320321800","funder_display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321800","display_name":"Nederlandse Organisatie voor Wetenschappelijk Onderzoek","ror":"https://ror.org/04jsz6e67"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4409252255.pdf","grobid_xml":"https://content.openalex.org/works/W4409252255.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1575978816","https://openalex.org/W1645305843","https://openalex.org/W1973239973","https://openalex.org/W1985911638","https://openalex.org/W1997057704","https://openalex.org/W2004444246","https://openalex.org/W2020247204","https://openalex.org/W2044692345","https://openalex.org/W2051866702","https://openalex.org/W2061019845","https://openalex.org/W2063698062","https://openalex.org/W2111510713","https://openalex.org/W2114176419","https://openalex.org/W2114390747","https://openalex.org/W2114870653","https://openalex.org/W2122121413","https://openalex.org/W2127403997","https://openalex.org/W2141594707","https://openalex.org/W2155306598","https://openalex.org/W2159600872","https://openalex.org/W2179931687","https://openalex.org/W2187281001","https://openalex.org/W2188853907","https://openalex.org/W2211016425","https://openalex.org/W2262285937","https://openalex.org/W2309316521","https://openalex.org/W2497271017","https://openalex.org/W2529467471","https://openalex.org/W2579268339","https://openalex.org/W2768425954","https://openalex.org/W2949890765","https://openalex.org/W2986978594","https://openalex.org/W3006046957","https://openalex.org/W3026013299","https://openalex.org/W3029510707","https://openalex.org/W3188507076","https://openalex.org/W4200028525","https://openalex.org/W4211042066","https://openalex.org/W4213030992","https://openalex.org/W4285388094","https://openalex.org/W4292651708","https://openalex.org/W4382197066","https://openalex.org/W4383097042"],"related_works":["https://openalex.org/W2378076731","https://openalex.org/W4286888643","https://openalex.org/W3210795196","https://openalex.org/W2088988140","https://openalex.org/W3171015545","https://openalex.org/W2103019253","https://openalex.org/W2951529875","https://openalex.org/W2391453316","https://openalex.org/W2055243143","https://openalex.org/W4396648495"],"abstract_inverted_index":{"A":[0],"Matlab":[1],"implementation":[2],"of":[3],"GMGTS":[4],"is":[5],"provided":[6],"at":[7],"https://github.com/yulanvanoppen/GMGTS":[8],"(DOI:":[9],"http://doi.org/10.5281/zenodo.14884457).":[10]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
