{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T00:16:08Z","timestamp":1776471368541,"version":"3.51.2"},"reference-count":65,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T00:00:00Z","timestamp":1752537600000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003006","name":"ETH Zurich","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003006","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020 Research and Innovation Program","award":["951970"],"award-info":[{"award-number":["951970"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The complex dynamics of cancer evolution, driven by mutation and selection, underlies the molecular heterogeneity observed in tumors. The evolutionary histories of tumors of different patients can be encoded as mutation trees and reconstructed in high resolution from single-cell sequencing data, offering crucial insights for studying fitness effects of and epistasis among mutations. Existing models, however, either fail to separate mutation and selection or neglect the evolutionary histories encoded by the tumor phylogenetic trees.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce FiTree, a tree-structured multi-type branching process model with epistatic fitness parameterization and a Bayesian inference scheme to learn fitness landscapes from single-cell tumor mutation trees. Through simulations, we demonstrate that FiTree outperforms state-of-the-art methods in inferring the fitness landscape underlying tumor evolution. Applying FiTree to a single-cell acute myeloid leukemia dataset, we identify epistatic fitness effects consistent with known biological findings and quantify uncertainty in predicting future mutational events. The new model unifies probabilistic graphical models of cancer progression with population genetics, offering a principled framework for understanding tumor evolution and informing therapeutic strategies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The Python package FiTree and the analysis workflows are available at https:\/\/github.com\/cbg-ethz\/FiTree.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf193","type":"journal-article","created":{"date-parts":[[2025,7,15]],"date-time":"2025-07-15T13:02:07Z","timestamp":1752584527000},"page":"i160-i169","source":"Crossref","is-referenced-by-count":2,"title":["Bayesian inference of fitness landscapes via tree-structured branching processes"],"prefix":"10.1093","volume":"41","author":[{"given":"Xiang Ge","family":"Luo","sequence":"first","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4056,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Basel 4056,","place":["Switzerland"]}]},{"given":"Jack","family":"Kuipers","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4056,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Basel 4056,","place":["Switzerland"]}]},{"given":"Kevin","family":"Rupp","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4056,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Basel 4056,","place":["Switzerland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8027-9659","authenticated-orcid":false,"given":"Koichi","family":"Takahashi","sequence":"additional","affiliation":[{"name":"Department of Leukemia, The University of Texas MD Anderson Cancer Center , Houston, TX 77030,","place":["United States"]},{"name":"Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center , Houston, TX 77030,","place":["United States"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0573-6119","authenticated-orcid":false,"given":"Niko","family":"Beerenwinkel","sequence":"additional","affiliation":[{"name":"Department of Biosystems Science and Engineering, ETH Zurich , Basel 4056,","place":["Switzerland"]},{"name":"SIB Swiss Institute of Bioinformatics , Basel 4056,","place":["Switzerland"]}]}],"member":"286","published-online":{"date-parts":[[2025,7,15]]},"reference":[{"key":"2025071509020227000_btaf193-B1","doi-asserted-by":"crossref","first-page":"P08018","DOI":"10.1088\/1742-5468\/2011\/08\/P08018","article-title":"Exact solution of a two-type branching process: models of tumor progression","volume":"2011","author":"Antal","year":"2011","journal-title":"J Stat Mech: Theory 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