{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T07:00:48Z","timestamp":1772521248672,"version":"3.50.1"},"reference-count":47,"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\/501100001711","name":"SNSF","doi-asserted-by":"publisher","award":["310030"],"award-info":[{"award-number":["310030"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"SNSF","doi-asserted-by":"publisher","award":["179518"],"award-info":[{"award-number":["179518"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020","award":["951970"],"award-info":[{"award-number":["951970"]}]}],"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>Understanding the genomic heterogeneity of tumors is an important task in computational oncology, especially in the context of finding personalized treatments based on the genetic profile of each patient\u2019s tumor. Tumor clustering that takes into account the temporal order of genetic events, as represented by tumor mutation trees, is a powerful approach for grouping together patients with genetically and evolutionarily similar tumors and can provide insights into discovering tumor subtypes, for more accurate clinical diagnosis and prognosis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we propose oncotree2vec, a method for clustering tumor mutation trees by learning vector representations of mutation trees that capture the different relationships between subclones in an unsupervised manner. Learning low-dimensional tree embeddings facilitates the visualization of relations between trees in large cohorts and can be used for downstream analyses, such as deep learning approaches for single-cell multi-omics data integration. We assessed the performance and the usefulness of our method in three simulation studies and on two real datasets: a cohort of 43 trees from six cancer types with different branching patterns corresponding to different modes of spatial tumor evolution and a cohort of 123 AML mutation trees.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/cbg-ethz\/oncotree2vec.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae214","type":"journal-article","created":{"date-parts":[[2024,6,28]],"date-time":"2024-06-28T09:27:27Z","timestamp":1719566847000},"page":"i180-i188","source":"Crossref","is-referenced-by-count":7,"title":["Oncotree2vec \u2014 a method for embedding and clustering of tumor mutation trees"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7719-5892","authenticated-orcid":false,"given":"Monica-Andreea","family":"Baciu-Dr\u0103gan","sequence":"first","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Z\u00fcrich , Schanzenstrasse 44 , Basel 4056, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Schanzenstrasse 44 , Basel 4056, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0573-6119","authenticated-orcid":false,"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Z\u00fcrich , Schanzenstrasse 44 , Basel 4056, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Schanzenstrasse 44 , Basel 4056, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2024,6,28]]},"reference":[{"key":"2024062809015995700_btae214-B1","doi-asserted-by":"crossref","first-page":"3240","DOI":"10.3390\/biomedicines10123240","article-title":"Evaluation and comparison of multi-omics data integration methods for subtyping of cutaneous melanoma","volume":"10","author":"Amaro","year":"2022","journal-title":"Biomedicines"},{"key":"2024062809015995700_btae214-B2","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1038\/s41592-019-0576-7","article-title":"Exploring single-cell data with deep multitasking neural networks","volume":"16","author":"Amodio","year":"2019","journal-title":"Nat Methods"},{"key":"2024062809015995700_btae214-B3","doi-asserted-by":"crossref","first-page":"e1\u201325","DOI":"10.1093\/sysbio\/syu081","article-title":"Cancer evolution: mathematical models and computational inference","volume":"64","author":"Beerenwinkel","year":"2015","journal-title":"Syst 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