{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T18:10:16Z","timestamp":1777486216465,"version":"3.51.4"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T00:00:00Z","timestamp":1719532800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Germany\u2019s Excellence Strategy","award":["EXC 2047\u2014390685813"],"award-info":[{"award-number":["EXC 2047\u2014390685813"]}]},{"name":"Germany\u2019s Excellence Strategy","award":["EXC 2151\u2014390873048"],"award-info":[{"award-number":["EXC 2151\u2014390873048"]}]},{"name":"Germany\u2019s Excellence Strategy","award":["432325352\u2014SFB 1454"],"award-info":[{"award-number":["432325352\u2014SFB 1454"]}]},{"name":"Germany\u2019s Excellence Strategy","award":["443187771"],"award-info":[{"award-number":["443187771"]}]},{"name":"German Federal Ministry of Education and Research"},{"DOI":"10.13039\/501100008131","name":"University of Bonn","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008131","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,6,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Quantitative dynamical models facilitate the understanding of biological processes and the prediction of their dynamics. The parameters of these models are commonly estimated from experimental data. Yet, experimental data generated from different techniques do not provide direct information about the state of the system but a nonlinear (monotonic) transformation of it. For such semi-quantitative data, when this transformation is unknown, it is not apparent how the model simulations and the experimental data can be compared.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose a versatile spline-based approach for the integration of a broad spectrum of semi-quantitative data into parameter estimation. We derive analytical formulas for the gradients of the hierarchical objective function and show that this substantially increases the estimation efficiency. Subsequently, we demonstrate that the method allows for the reliable discovery of unknown measurement transformations. Furthermore, we show that this approach can significantly improve the parameter inference based on semi-quantitative data in comparison to available methods.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Modelers can easily apply our method by using our implementation in the open-source Python Parameter EStimation TOolbox (pyPESTO) available at https:\/\/github.com\/ICB-DCM\/pyPESTO.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae210","type":"journal-article","created":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T09:36:06Z","timestamp":1719567366000},"page":"i558-i566","source":"Crossref","is-referenced-by-count":3,"title":["Efficient parameter estimation for ODE models of cellular processes using semi-quantitative data"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-1820-7375","authenticated-orcid":false,"given":"Domagoj","family":"Dore\u0161i\u0107","sequence":"first","affiliation":[{"name":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"},{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen \u2013 German Research Center for Environmental Health , 85764 Neuherberg, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9524-6633","authenticated-orcid":false,"given":"Stephan","family":"Grein","sequence":"additional","affiliation":[{"name":"Life and Medical Sciences (LIMES) Institute, University of Bonn , 53113 Bonn, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4935-3312","authenticated-orcid":false,"given":"Jan","family":"Hasenauer","sequence":"additional","affiliation":[{"name":"Life and 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