{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:35Z","timestamp":1772138075074,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,6,13]],"date-time":"2025-06-13T00:00:00Z","timestamp":1749772800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Michael Smith Health Research BC scholar","award":["18245"],"award-info":[{"award-number":["18245"]}]},{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Cancer is driven by somatic mutations that result in the expansion of genomically distinct sub-populations of cells called clones. Identifying the clonal composition of tumours and understanding the evolutionary relationships between clones is a crucial task in cancer genomics. Bulk DNA sequencing is commonly used for studying the clonal composition of tumours, but it is challenging to infer the genetic relationship between different clones due to the mixture of different cell populations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we introduce a new probabilistic model called PhyClone that can infer clonal phylogenies from bulk-sequencing data. We demonstrate the performance of PhyClone on simulated and real-world datasets and show that it outperforms previous methods in terms of accuracy and sample scalability.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Source code is available on Github at: https:\/\/github.com\/Roth-Lab\/PhyClone under the GPL v3.0 license.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf344","type":"journal-article","created":{"date-parts":[[2025,6,12]],"date-time":"2025-06-12T07:46:59Z","timestamp":1749714419000},"source":"Crossref","is-referenced-by-count":0,"title":["PhyClone: accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-4005-4379","authenticated-orcid":false,"given":"Emilia","family":"Hurtado","sequence":"first","affiliation":[{"name":"Department of Molecular Oncology, BC Cancer Agency , 675 West 10th Avenue , Vancouver, BC, V5Z 1L3,","place":["Canada"]},{"name":"Graduate Bioinformatics Training Program, University of British Columbia , 315- 2185 East Mall , Vancouver, BC, V6T 1Z4,","place":["Canada"]}]},{"given":"Alexandre","family":"Bouchard-C\u00f4t\u00e9","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of British Columbia , 2207 Main Mall , Vancouver, BC, V6T 1Z4,","place":["Canada"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3422-8823","authenticated-orcid":false,"given":"Andrew","family":"Roth","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, BC Cancer Agency , 675 West 10th Avenue , Vancouver, BC, V5Z 1L3,","place":["Canada"]},{"name":"Department of Pathology and Laboratory Medicine, University of British Columbia , 2211 Wesbrook Mall , Vancouver, BC, V6T 1Z7,","place":["Canada"]},{"name":"Department of Computer Science, University of British Columbia , 2366 Main Mall, Vancouver, BC, V6T 1Z4,","place":["Canada"]}]}],"member":"286","published-online":{"date-parts":[[2025,6,13]]},"reference":[{"key":"2025072604012830400_btaf344-B1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/BFb0099421","volume-title":"\u00c9cole d\u2019\u00c9t\u00e9 de Probabilit\u00e9s de Saint-Flour XIII\u20141983","author":"Aldous","year":"1985"},{"key":"2025072604012830400_btaf344-B2","doi-asserted-by":"publisher","first-page":"269","DOI":"10.1111\/j.1467-9868.2009.00736.x","article-title":"Particle Markov chain Monte Carlo methods","volume":"72","author":"Andrieu","year":"2010","journal-title":"J R Stat Soc Ser B Stat 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