{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T15:17:47Z","timestamp":1772119067119,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Cancer development is driven by the accumulation of advantageous mutations and subsequent clonal expansion of cells harbouring these mutations, but the order in which mutations occur remains poorly understood. Advances in genome sequencing and the soon-arriving flood of cancer genome data produced by large cancer sequencing consortia hold the promise to elucidate cancer progression. However, new computational methods are needed to analyse these large datasets.<\/jats:p>\n               <jats:p>Results: We present a Bayesian inference scheme for Conjunctive Bayesian Networks, a probabilistic graphical model in which mutations accumulate according to partial order constraints and cancer genotypes are observed subject to measurement noise. We develop an efficient MCMC sampling scheme specifically designed to overcome local optima induced by dependency structures. We demonstrate the performance advantage of our sampler over traditional approaches on simulated data and show the advantages of adopting a Bayesian perspective when reanalyzing cancer datasets and comparing our results to previous maximum-likelihood-based approaches.<\/jats:p>\n               <jats:p>Availability: An R package including the sampler and examples is available at http:\/\/www.cbg.ethz.ch\/software\/bayes-cbn.<\/jats:p>\n               <jats:p>Contacts: \u00a0niko.beerenwinkel@bsse.ethz.ch<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts433","type":"journal-article","created":{"date-parts":[[2012,7,11]],"date-time":"2012-07-11T02:46:38Z","timestamp":1341974798000},"page":"2318-2324","source":"Crossref","is-referenced-by-count":24,"title":["Efficient sampling for Bayesian inference of conjunctive Bayesian networks"],"prefix":"10.1093","volume":"28","author":[{"given":"Thomas","family":"Sakoparnig","sequence":"first","affiliation":[{"name":"1,2 \u00a01Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel and 2SIB Swiss Institute of Bioinformatics, Supra-University, Basel, Switzerland"}]},{"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"1,2 \u00a01Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058 Basel and 2SIB Swiss Institute of Bioinformatics, Supra-University, Basel, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2012,7,10]]},"reference":[{"key":"2023012512590387200_bts433-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/biomet\/asp023","article-title":"Markov models for accumulating mutations","volume":"96","author":"Beerenwinkel","year":"2009","journal-title":"Biometrika"},{"key":"2023012512590387200_bts433-B2","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1089\/cmb.2005.12.584","article-title":"Learning multiple evolutionary pathways from cross-sectional data","volume":"12","author":"Beerenwinkel","year":"2004","journal-title":"J. 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