{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T03:30:02Z","timestamp":1762659002077},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2965,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: In genetics, many evolutionary pathways can be modeled by the ordered accumulation of permanent changes. Mixture models of mutagenetic trees have been used to describe disease progression in cancer and in HIV. In cancer, progression is modeled by the accumulation of chromosomal gains and losses in tumor cells; in HIV, the accumulation of drug resistance-associated mutations in the viral genome is known to be associated with disease progression. From such evolutionary models, genetic progression scores can be derived that assign measures for the disease state to single patients. Rtreemix is an R package for estimating mixture models of evolutionary pathways from observed cross-sectional data and for estimating associated genetic progression scores. The package also provides extended functionality for estimating confidence intervals for estimated model parameters and for evaluating the stability of the estimated evolutionary mixture models.<\/jats:p>\n               <jats:p>Availability: \u00a0Rtreemix is an R package that is freely available from the Bioconductor project at http:\/\/www.bioconductor.org and runs on Linux and Windows.<\/jats:p>\n               <jats:p>Contact: \u00a0jasmina@mpi-inf.mpg.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn410","type":"journal-article","created":{"date-parts":[[2008,8,22]],"date-time":"2008-08-22T00:33:56Z","timestamp":1219365236000},"page":"2391-2392","source":"Crossref","is-referenced-by-count":15,"title":["Rtreemix: an R package for estimating evolutionary pathways and genetic progression scores"],"prefix":"10.1093","volume":"24","author":[{"given":"Jasmina","family":"Bogojeska","sequence":"first","affiliation":[{"name":"1 Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbr\u00fccken and 2Fakult\u00e4t Statistik Technische Universit\u00e4t Dortmund, Vogelpothsweg 87, 44227 Dortmund, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Adrian","family":"Alexa","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbr\u00fccken and 2Fakult\u00e4t Statistik Technische Universit\u00e4t Dortmund, Vogelpothsweg 87, 44227 Dortmund, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andr\u00e9","family":"Altmann","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbr\u00fccken and 2Fakult\u00e4t Statistik Technische Universit\u00e4t Dortmund, Vogelpothsweg 87, 44227 Dortmund, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Lengauer","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbr\u00fccken and 2Fakult\u00e4t Statistik Technische Universit\u00e4t Dortmund, Vogelpothsweg 87, 44227 Dortmund, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00f6rg","family":"Rahnenf\u00fchrer","sequence":"additional","affiliation":[{"name":"1 Max Planck Institute for Informatics, Campus E1.4, 66123 Saarbr\u00fccken and 2Fakult\u00e4t Statistik Technische Universit\u00e4t Dortmund, Vogelpothsweg 87, 44227 Dortmund, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,8,20]]},"reference":[{"key":"2023020211255082600_B1","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":"2005","journal-title":"J. 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