{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:39:39Z","timestamp":1740184779807,"version":"3.37.3"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2022,9,12]],"date-time":"2022-09-12T00:00:00Z","timestamp":1662940800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"German Science Foundation [DFG","award":["217328187","SFB 1074","450627322 (SFB 1506)"]},{"name":"German Federal Ministry of Education and Research (BMBF) e: MED confirm","award":["id 01ZX1708C"]},{"name":"TRANSCAN VI\u2014PMTR-pNET","award":["id 01KT1901B"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,31]]},"abstract":"Abstract<\/jats:title>Motivation<\/jats:title>Biological processes are complex systems with distinct behaviour. Despite the growing amount of available data, knowledge is sparse and often insufficient to investigate the complex regulatory behaviour of these systems. Moreover, different cellular phenotypes are possible under varying conditions. Mathematical models attempt to unravel these mechanisms by investigating the dynamics of regulatory networks. Therefore, a major challenge is to combine regulations and phenotypical information as well as the underlying mechanisms. To predict regulatory links in these models, we established an approach called CANTATA to support the integration of information into regulatory networks and retrieve potential underlying regulations. This is achieved by optimizing both static and dynamic properties of these networks.<\/jats:p><\/jats:sec>Results<\/jats:title>Initial results show that the algorithm predicts missing interactions by recapitulating the known phenotypes while preserving the original topology and optimizing the robustness of the model. The resulting models allow for hypothesizing about the biological impact of certain regulatory dependencies.<\/jats:p><\/jats:sec>Availability and implementation<\/jats:title>Source code of the application, example files and results are available at https:\/\/github.com\/sysbio-bioinf\/Cantata.<\/jats:p><\/jats:sec>Supplementary information<\/jats:title>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac623","type":"journal-article","created":{"date-parts":[[2022,9,10]],"date-time":"2022-09-10T00:38:12Z","timestamp":1662770292000},"page":"4893-4900","source":"Crossref","is-referenced-by-count":2,"title":["CANTATA\u2014<\/i>prediction of missing links in Boolean networks using genetic programming"],"prefix":"10.1093","volume":"38","author":[{"given":"Christoph","family":"M\u00fcssel","sequence":"first","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Ulm, Baden-Wuerttemberg 89081, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0780-5832","authenticated-orcid":false,"given":"Nensi","family":"Ikonomi","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Ulm, Baden-Wuerttemberg 89081, Germany"}]},{"given":"Silke D","family":"Werle","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Ulm, Baden-Wuerttemberg 89081, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6759-0509","authenticated-orcid":false,"given":"Felix M","family":"Weidner","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Ulm, Baden-Wuerttemberg 89081, Germany"}]},{"given":"Markus","family":"Maucher","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Ulm, Baden-Wuerttemberg 89081, Germany"}]},{"given":"Julian D","family":"Schwab","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Ulm, Baden-Wuerttemberg 89081, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4759-5254","authenticated-orcid":false,"given":"Hans A","family":"Kestler","sequence":"additional","affiliation":[{"name":"Institute of Medical Systems Biology, Ulm University , Ulm, Baden-Wuerttemberg 89081, Germany"}]}],"member":"286","published-online":{"date-parts":[[2022,9,12]]},"reference":[{"key":"2022103112484717400_btac623-B1","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1093\/bioinformatics\/16.8.727","article-title":"Inferring qualitative relations in genetic networks and metabolic pathways","volume":"16","author":"Akutsu","year":"2000","journal-title":"Bioinformatics"},{"key":"2022103112484717400_btac623-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/S0022-5193(03)00035-3","article-title":"The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster","volume":"223","author":"Albert","year":"2003","journal-title":"J. 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