{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T16:20:24Z","timestamp":1759335624782,"version":"3.41.2"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,4,13]],"date-time":"2024-04-13T00:00:00Z","timestamp":1712966400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Neoantigen vaccines make use of tumor-specific mutations to enable the patient\u2019s immune system to recognize and eliminate cancer. Selecting vaccine elements, however, is a complex task which needs to take into account not only the underlying antigen presentation pathway but also tumor heterogeneity.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present NeoAgDT, a two-step approach consisting of: (i) simulating individual cancer cells to create a digital twin of the patient\u2019s tumor cell population and (ii) optimizing the vaccine composition by integer linear programming based on this digital twin. NeoAgDT shows improved selection of experimentally validated neoantigens over ranking-based approaches in a study of seven patients.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The NeoAgDT code is published on Github: https:\/\/github.com\/nec-research\/neoagdt.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae205","type":"journal-article","created":{"date-parts":[[2024,4,13]],"date-time":"2024-04-13T23:02:57Z","timestamp":1713049377000},"source":"Crossref","is-referenced-by-count":3,"title":["NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6008-0220","authenticated-orcid":false,"given":"Anja","family":"M\u00f6sch","sequence":"first","affiliation":[{"name":"Biomedical AI Group, NEC Laboratories Europe GmbH , Heidelberg 69115, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8888-133X","authenticated-orcid":false,"given":"Filippo","family":"Grazioli","sequence":"additional","affiliation":[{"name":"Biomedical AI Group, NEC Laboratories Europe GmbH , Heidelberg 69115, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2646-3674","authenticated-orcid":false,"given":"Pierre","family":"Machart","sequence":"additional","affiliation":[{"name":"Biomedical AI Group, NEC Laboratories Europe GmbH , Heidelberg 69115, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7027-3157","authenticated-orcid":false,"given":"Brandon","family":"Malone","sequence":"additional","affiliation":[{"name":"Biomedical AI Group, NEC Laboratories Europe GmbH , Heidelberg 69115, 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