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Methods to detect selection at the level of modules, as opposed to genes or nucleotides, are relatively underdeveloped.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here we present CanSRMaPP (Cancer Selection Recovery by Maximum Posterior Probability), a Bayesian model of the cancer genome that infers mutational selection on single genes and multi-genic modules while simultaneously modeling background events. Applying CanSRMaPP to lung adenocarcinoma genomes, we identify positive selection on 63 modules, yielding a model that parsimoniously explains the observed pattern of genetic alterations observed in new cancer cohorts. We further show that CanSRMaPP is adaptable to more tumor types and to alternative module definitions. We show that these modules serve as an effective scaffold for translating the cancer genome to molecular states, with prediction of cancer biomarker status as demonstration.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>CanSRMaPP is freely available on GitHub.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag668","type":"journal-article","created":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T04:42:29Z","timestamp":1789015349000},"source":"Crossref","is-referenced-by-count":0,"title":["Identifying multigenic modules under selection in the tumor genome"],"prefix":"10.1093","volume":"42","author":[{"given":"Marcus R","family":"Kelly","sequence":"first","affiliation":[{"name":"School of Medicine, University of California San Diego , La Jolla, CA,","place":["United States"]},{"name":"Moores Cancer Center, UC San Diego , La Jolla, CA,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bur\u00e7ak","family":"Otlu","sequence":"additional","affiliation":[{"name":"Moores Cancer Center, UC San Diego , La Jolla, CA,","place":["United States"]},{"name":"Department of Cellular and Molecular Medicine, UC San Diego , La Jolla, CA,","place":["United States"]},{"name":"Department of Health Informatics, Graduate School of Informatics, Middle East Technical University , Ankara 06800,","place":["Turkey"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8363-4882","authenticated-orcid":false,"given":"Roded","family":"Sharan","sequence":"additional","affiliation":[{"name":"Blavatnik School of Computer Science and AI, Tel Aviv University , Tel Aviv 6997801,","place":["Israel"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1708-8454","authenticated-orcid":false,"given":"Trey","family":"Ideker","sequence":"additional","affiliation":[{"name":"School of Medicine, University of California San Diego , La Jolla, CA,","place":["United States"]},{"name":"Moores Cancer Center, UC San Diego , La Jolla, CA,","place":["United States"]},{"name":"Department of Bioengineering, UC San Diego , La Jolla, CA,","place":["United States"]},{"name":"University of Oxford Big Data Institute, , Oxford OX26BD,","place":["United Kingdom"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"2026092610363324200_btag668-B1","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1038\/s41586-020-1943-3","article-title":"The repertoire of mutational signatures in human cancer","volume":"578","author":"Alexandrov","year":"2020","journal-title":"Nature"},{"key":"2026092610363324200_btag668-B2","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1080\/19336950.2019.1666455","article-title":"Voltage gated sodium channels in cancer and their potential mechanisms of action","volume":"13","author":"Angus","year":"2019","journal-title":"Channels (Austin)"},{"key":"2026092610363324200_btag668-B3","doi-asserted-by":"crossref","DOI":"10.1145\/3620665.3640366","article-title":"PyTorch 2: faster machine learning through dynamic python bytecode transformation and graph compilation","author":"Ansel","year":"2024"},{"key":"2026092610363324200_btag668-B4","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1016\/j.canlet.2018.01.046","article-title":"BAFfling pathologies: alterations of BAF complexes in cancer","volume":"419","author":"Arnaud","year":"2018","journal-title":"Cancer Lett"},{"key":"2026092610363324200_btag668-B5","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology. 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