{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T07:56:16Z","timestamp":1768463776331,"version":"3.49.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2017,7,12]],"date-time":"2017-07-12T00:00:00Z","timestamp":1499817600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000861","name":"Burroughs Wellcome Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000861","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>A tumor arises from an evolutionary process that can be modeled as a phylogenetic tree. However, reconstructing this tree is challenging as most cancer sequencing uses bulk tumor tissue containing heterogeneous mixtures of cells.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce Probabilistic Algorithm for Somatic Tree Inference (PASTRI), a new algorithm for bulk-tumor sequencing data that clusters somatic mutations into clones and infers a phylogenetic tree that describes the evolutionary history of the tumor. PASTRI uses an importance sampling algorithm that combines a probabilistic model of DNA sequencing data with a enumeration algorithm based on the combinatorial constraints defined by the underlying phylogenetic tree. As a result, tree inference is fast, accurate and robust to noise. We demonstrate on simulated data that PASTRI outperforms other cancer phylogeny algorithms in terms of runtime and accuracy. On real data from a chronic lymphocytic leukemia (CLL) patient, we show that a simple linear phylogeny better explains the data the complex branching phylogeny that was previously reported. PASTRI provides a robust approach for phylogenetic tree inference from mixed samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>Software is available at compbio.cs.brown.edu\/software.<\/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\/btx270","type":"journal-article","created":{"date-parts":[[2017,5,4]],"date-time":"2017-05-04T11:10:22Z","timestamp":1493896222000},"page":"i152-i160","source":"Crossref","is-referenced-by-count":56,"title":["Tumor phylogeny inference using tree-constrained importance sampling"],"prefix":"10.1093","volume":"33","author":[{"given":"Gryte","family":"Satas","sequence":"first","affiliation":[{"name":"Department of Computer Science, Brown University, Providence, RI, USA"}]},{"given":"Benjamin J","family":"Raphael","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Princeton University, Princeton, NJ, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,7,12]]},"reference":[{"key":"2023051506470362900_btx270-B1","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s13059-015-0602-8","article-title":"PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors","volume":"16","author":"Deshwar","year":"2015","journal-title":"Genome Biol"},{"key":"2023051506470362900_btx270-B2","first-page":"83","volume-title":"International Conference on Research in Computational Molecular Biology","author":"Donmez","year":"2016"},{"key":"2023051506470362900_btx270-B3","doi-asserted-by":"crossref","first-page":"i62","DOI":"10.1093\/bioinformatics\/btv261","article-title":"Reconstruction of clonal trees and tumor composition from multi-sample sequencing data","volume":"31","author":"El-Kebir","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051506470362900_btx270-B4","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/j.cels.2016.07.004","article-title":"Inferring the mutational history of a tumor using multi-state perfect phylogeny mixtures","volume":"3","author":"El-Kebir","year":"2016","journal-title":"Cell Syst"},{"key":"2023051506470362900_btx270-B5","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1137\/0207024","article-title":"Finding all spanning trees of directed and undirected graphs","volume":"7","author":"Gabow","year":"1978","journal-title":"SIAM J. 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