{"id":"https://openalex.org/W4388982138","doi":"https://doi.org/10.1093/bioinformatics/btad711","title":"pyPESTO: a modular and scalable tool for parameter estimation for dynamic models","display_name":"pyPESTO: a modular and scalable tool for parameter estimation for dynamic models","publication_year":2023,"publication_date":"2023-11-01","ids":{"openalex":"https://openalex.org/W4388982138","doi":"https://doi.org/10.1093/bioinformatics/btad711","pmid":"https://pubmed.ncbi.nlm.nih.gov/37995297"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad711","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad711","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad711/53703014/btad711.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/btad711/53703014/btad711.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082656548","display_name":"Yannik Sch\u00e4lte","orcid":"https://orcid.org/0000-0003-1293-820X"},"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"]},{"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":"Yannik Sch\u00e4lte","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 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":false,"raw_author_name":"Fabian Fr\u00f6hlich","raw_affiliation_strings":["Department of Systems Biology, Harvard Medical School , Boston, MA 02115, United States"],"affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School , Boston, MA 02115, United States","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000915010","display_name":"Paul Jonas Jost","orcid":"https://orcid.org/0000-0001-7613-6244"},"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":false,"raw_author_name":"Paul J Jost","raw_affiliation_strings":["Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038339360","display_name":"Jakob Vanhoefer","orcid":"https://orcid.org/0000-0002-3451-1701"},"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":false,"raw_author_name":"Jakob Vanhoefer","raw_affiliation_strings":["Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"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":false,"raw_author_name":"Dilan Pathirana","raw_affiliation_strings":["Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"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":false,"raw_author_name":"Paul Stapor","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","Department of Mathematics, Technical University of Munich , 85748 Garching, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","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":false,"raw_author_name":"Polina Lakrisenko","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","School of Life Sciences, Technical University of Munich , 85354 Freising, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"School of Life Sciences, Technical University of Munich , 85354 Freising, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101939585","display_name":"Dantong Wang","orcid":"https://orcid.org/0000-0002-3277-5033"},"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":false,"raw_author_name":"Dantong Wang","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","Department of Mathematics, Technical University of Munich , 85748 Garching, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025694782","display_name":"Elba Raim\u00fandez","orcid":"https://orcid.org/0000-0002-2790-6668"},"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"]},{"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":false,"raw_author_name":"Elba Raim\u00fandez","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021665404","display_name":"Simon Merkt","orcid":"https://orcid.org/0000-0002-8017-4494"},"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":false,"raw_author_name":"Simon Merkt","raw_affiliation_strings":["Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085002161","display_name":"Leonard Schmiester","orcid":"https://orcid.org/0000-0001-7946-3232"},"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":false,"raw_author_name":"Leonard Schmiester","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","Department of Mathematics, Technical University of Munich , 85748 Garching, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016122054","display_name":"Philipp St\u00e4dter","orcid":"https://orcid.org/0000-0002-4586-6604"},"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/I4210162077","display_name":"Leibniz-Institut f\u00fcr Naturstoff-Forschung und Infektionsbiologie e. V. - Hans-Kn\u00f6ll-Institut (HKI)","ror":"https://ror.org/055s37c97","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210162077"]},{"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":false,"raw_author_name":"Philipp St\u00e4dter","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","Leibniz Institute for Natural Product Research and Infection Biology , 07745 Jena, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Leibniz Institute for Natural Product Research and Infection Biology , 07745 Jena, Germany","institution_ids":["https://openalex.org/I4210162077"]}]},{"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":false,"raw_author_name":"Stephan Grein","raw_affiliation_strings":["Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026146978","display_name":"Erika Dudkin","orcid":"https://orcid.org/0000-0002-9649-0029"},"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":false,"raw_author_name":"Erika Dudkin","raw_affiliation_strings":["Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072886358","display_name":"Domagoj Dore\u0161i\u0107","orcid":"https://orcid.org/0009-0007-1820-7375"},"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":false,"raw_author_name":"Domagoj Doresic","raw_affiliation_strings":["Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]},{"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":false,"raw_author_name":"Daniel Weindl","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 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"]},{"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":false,"raw_author_name":"Jan Hasenauer","raw_affiliation_strings":["Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"],"affiliations":[{"raw_affiliation_string":"Computational Health Center, Helmholtz Zentrum M\u00fcnchen Deutsches Forschungszentrum f\u00fcr Gesundheit und Umwelt (GmbH) , 85764 Neuherberg, Germany","institution_ids":["https://openalex.org/I3018134672"]},{"raw_affiliation_string":"Department of Mathematics, Technical University of Munich , 85748 Garching, Germany","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany","institution_ids":["https://openalex.org/I135140700"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":17,"corresponding_author_ids":["https://openalex.org/A5082656548"],"corresponding_institution_ids":["https://openalex.org/I135140700","https://openalex.org/I3018134672","https://openalex.org/I62916508"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.5651,"has_fulltext":true,"cited_by_count":50,"citation_normalized_percentile":{"value":0.97910289,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"39","issue":"11","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":0.9997000098228455,"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":0.9997000098228455,"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":0.9936000108718872,"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/T10928","display_name":"Probabilistic and Robust Engineering Design","score":0.9873999953269958,"subfield":{"id":"https://openalex.org/subfields/1804","display_name":"Statistics, Probability and Uncertainty"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8135681748390198},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7854143381118774},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.758634090423584},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7378591895103455},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.6484096050262451},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6391386389732361},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6005359292030334},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.5120790600776672},{"id":"https://openalex.org/keywords/estimation-theory","display_name":"Estimation theory","score":0.4905199408531189},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.48625648021698},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.4791623651981354},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.46153318881988525},{"id":"https://openalex.org/keywords/usable","display_name":"USable","score":0.43607598543167114},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4290737509727478},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2872048318386078},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1660245656967163},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.16273224353790283}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8135681748390198},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7854143381118774},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.758634090423584},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7378591895103455},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6484096050262451},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6391386389732361},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6005359292030334},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.5120790600776672},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.4905199408531189},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.48625648021698},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.4791623651981354},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.46153318881988525},{"id":"https://openalex.org/C2780615836","wikidata":"https://www.wikidata.org/wiki/Q2471869","display_name":"USable","level":2,"score":0.43607598543167114},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4290737509727478},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2872048318386078},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1660245656967163},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.16273224353790283},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035501","descriptor_name":"Uncertainty","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad711","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad711","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad711/53703014/btad711.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:37995297","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37995297","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:pubmedcentral.nih.gov:10689677","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10689677","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10689677/pdf/btad711.pdf","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:push-zb.helmholtz-munich.de:68911","is_oa":true,"landing_page_url":"https://push-zb.helmholtz-munich.de/frontdoor.php?source_opus=68911","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics 39:btad711 (2023)","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad711","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad711","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad711/53703014/btad711.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/G1521016025","display_name":null,"funder_award_id":"390685813","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G185132324","display_name":null,"funder_award_id":"EXC 2047/1 390685813","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G1894950364","display_name":null,"funder_award_id":"432325352","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2270087404","display_name":null,"funder_award_id":"TRR333","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G352791218","display_name":null,"funder_award_id":"(BMBF)","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"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/G5683662034","display_name":null,"funder_award_id":"450149205","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5950108395","display_name":null,"funder_award_id":"TRR33","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6007275143","display_name":null,"funder_award_id":"EXC 215","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6052429835","display_name":null,"funder_award_id":"(DFG)","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6257653221","display_name":null,"funder_award_id":"2047/1 390685813","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/G6743243744","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6955755495","display_name":null,"funder_award_id":"Germany","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7225624288","display_name":null,"funder_award_id":"This work was","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7469274427","display_name":null,"funder_award_id":"SFB 145","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7984835289","display_name":null,"funder_award_id":"90685813","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8330397625","display_name":null,"funder_award_id":"Funding","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8413167928","display_name":null,"funder_award_id":"Excellence Strategy","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8429607460","display_name":null,"funder_award_id":"SFB 1454","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8796401741","display_name":null,"funder_award_id":"390873048","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G97110083","display_name":null,"funder_award_id":"443187771","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320310697","display_name":"Joachim Herz Stiftung","ror":"https://ror.org/01j8qgg43"},{"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/F4320324900","display_name":"Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn","ror":"https://ror.org/041nas322"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388982138.pdf"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1512208174","https://openalex.org/W1773696741","https://openalex.org/W1830738118","https://openalex.org/W1978486653","https://openalex.org/W2041215343","https://openalex.org/W2063397409","https://openalex.org/W2102434872","https://openalex.org/W2102653059","https://openalex.org/W2115252128","https://openalex.org/W2123871098","https://openalex.org/W2168648059","https://openalex.org/W2217402295","https://openalex.org/W2619381903","https://openalex.org/W2708632824","https://openalex.org/W2765845615","https://openalex.org/W2783515600","https://openalex.org/W2931388211","https://openalex.org/W2964392985","https://openalex.org/W3003257820","https://openalex.org/W3014365047","https://openalex.org/W3024659207","https://openalex.org/W3044040797","https://openalex.org/W3102014803","https://openalex.org/W3103145119","https://openalex.org/W3142344196","https://openalex.org/W4285088295","https://openalex.org/W4386373863","https://openalex.org/W6677618333","https://openalex.org/W6770353520"],"related_works":["https://openalex.org/W2132241624","https://openalex.org/W4311683883","https://openalex.org/W4212902261","https://openalex.org/W4400311305","https://openalex.org/W2790811106","https://openalex.org/W4385413248","https://openalex.org/W2789551765","https://openalex.org/W3097598351","https://openalex.org/W3170192653","https://openalex.org/W4287775886"],"abstract_inverted_index":{"pyPESTO":[0],"is":[1],"implemented":[2],"in":[3],"Python,":[4],"open-source":[5],"under":[6],"a":[7],"3-Clause":[8],"BSD":[9],"license.":[10],"Code":[11],"and":[12],"documentation":[13],"are":[14],"available":[15],"on":[16],"GitHub":[17],"(https://github.com/icb-dcm/pypesto).":[18]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":25},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":2}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
