{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T22:09:22Z","timestamp":1761948562253,"version":"3.37.3"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,12,17]],"date-time":"2019-12-17T00:00:00Z","timestamp":1576540800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100003246","name":"Netherlands Organisation for Scientific Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003246","name":"NWO","doi-asserted-by":"publisher","award":["612.001.203","864.11.010"],"award-info":[{"award-number":["612.001.203","864.11.010"]}],"id":[{"id":"10.13039\/501100003246","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Genetic interaction (GI) patterns are characterized by the phenotypes of interacting single and double mutated gene pairs. Uncovering the regulatory mechanisms of GIs would provide a better understanding of their role in biological processes, diseases and drug response. Computational analyses can provide insights into the underpinning mechanisms of GIs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we present a framework for exhaustive modelling of GI patterns using Petri nets (PN). Four-node models were defined and generated on three levels with restrictions, to enable an exhaustive approach. Simulations suggest \u223c5 million models of GIs. Generalizing these we propose putative mechanisms for the GI patterns, inversion and suppression. We demonstrate that exhaustive PN modelling enables reasoning about mechanisms of GIs when only the phenotypes of gene pairs are known. The framework can be applied to other GI or genetic regulatory datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The framework is available at http:\/\/www.ibi.vu.nl\/programs\/ExhMod.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz917","type":"journal-article","created":{"date-parts":[[2019,12,13]],"date-time":"2019-12-13T20:11:16Z","timestamp":1576267876000},"page":"2142-2149","source":"Crossref","is-referenced-by-count":4,"title":["A framework for exhaustive modelling of genetic interaction patterns using Petri nets"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4818-2360","authenticated-orcid":false,"given":"Annika","family":"Jacobsen","sequence":"first","affiliation":[{"name":"Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam , 1081 HV Amsterdam, Netherlands"}]},{"given":"Olga","family":"Ivanova","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam , 1081 HV Amsterdam, Netherlands"}]},{"given":"Saman","family":"Amini","sequence":"additional","affiliation":[{"name":"Princess M\u00e1xima Center for Pediatric Oncology, 3584 CS Utrecht , Netherlands"},{"name":"Divison of Biomedical Genetics, Center for Molecular Medicine, University Medical Centre Utrecht , 3584 CX Utrecht, Netherlands"}]},{"given":"Jaap","family":"Heringa","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam , 1081 HV Amsterdam, Netherlands"}]},{"given":"Patrick","family":"Kemmeren","sequence":"additional","affiliation":[{"name":"Princess M\u00e1xima Center for Pediatric Oncology, 3584 CS Utrecht , Netherlands"},{"name":"Divison of Biomedical Genetics, Center for Molecular Medicine, University Medical Centre Utrecht , 3584 CX Utrecht, Netherlands"}]},{"given":"K Anton","family":"Feenstra","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam , 1081 HV Amsterdam, Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2019,12,17]]},"reference":[{"volume-title":"Verification, Model Checking, and Abstract Interpretation. 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