{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T14:47:14Z","timestamp":1778770034155,"version":"3.51.4"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: We introduce TRanslational ONCOlogy (TRONCO), an open-source R package that implements the state-of-the-art algorithms for the inference of cancer progression models from (epi)genomic mutational profiles. TRONCO can be used to extract population-level models describing the trends of accumulation of alterations in a cohort of cross-sectional samples, e.g. retrieved from publicly available databases, and individual-level models that reveal the clonal evolutionary history in single cancer patients, when multiple samples, e.g. multiple biopsies or single-cell sequencing data, are available. The resulting models can provide key hints for uncovering the evolutionary trajectories of cancer, especially for precision medicine or personalized therapy.<\/jats:p>\n                  <jats:p>Availability and implementation: TRONCO is released under the GPL license, is hosted at http:\/\/bimib.disco.unimib.it\/ (Software section) and archived also at bioconductor.org.<\/jats:p>\n                  <jats:p>Contact: \u00a0tronco@disco.unimib.it<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw035","type":"journal-article","created":{"date-parts":[[2016,2,14]],"date-time":"2016-02-14T20:09:07Z","timestamp":1455480547000},"page":"1911-1913","source":"Crossref","is-referenced-by-count":39,"title":["TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data"],"prefix":"10.1093","volume":"32","author":[{"given":"Luca","family":"De Sano","sequence":"first","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giulio","family":"Caravagna","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"},{"name":"2 School of Informatics, University of Edinburgh, Edinburgh, UK,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniele","family":"Ramazzotti","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alex","family":"Graudenzi","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"},{"name":"3 Institute of Molecular Bioimaging and Physiology of the Italian National Research Council (IBFM-CNR), Milan, Italy,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giancarlo","family":"Mauri","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bud","family":"Mishra","sequence":"additional","affiliation":[{"name":"4 Courant Institute of Mathematical Sciences, New York University, New York, NY, USA and"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Antoniotti","sequence":"additional","affiliation":[{"name":"1 Department of Informatics, Systems and Communication, University of Milano-Bicocca,"},{"name":"5 Milan Center for Neuroscience, University of Milan-Bicocca, Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,2,9]]},"reference":[{"key":"2023020112320650700_btw035-B1","author":"Antoniotti","year":"2015"},{"key":"2023020112320650700_btw035-B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-015-0612-6","article-title":"Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations","volume":"16","author":"Babur","year":"2015","journal-title":"Genome Biol"},{"key":"2023020112320650700_btw035-B3","author":"Caravagna","year":"2015"},{"key":"2023020112320650700_btw035-B4","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","article-title":"The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data","volume":"2","author":"Cerami","year":"2012","journal-title":"Cancer Disc"},{"key":"2023020112320650700_btw035-B5","doi-asserted-by":"crossref","first-page":"1108","DOI":"10.1038\/nmeth.2651","article-title":"Network-based stratification of tumor mutations","volume":"10","author":"Hofree","year":"2013","journal-title":"Nat. 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