{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T18:20:58Z","timestamp":1773339658930,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,2,25]],"date-time":"2025-02-25T00:00:00Z","timestamp":1740441600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation program","award":["965193"],"award-info":[{"award-number":["965193"]}]},{"name":"European Union\u2019s Horizon 2020 research and innovation program","award":["847912"],"award-info":[{"award-number":["847912"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Spatial and temporal intra-tumor heterogeneity drives tumor evolution and therapy resistance. Existing visualization tools often fail to capture both dimensions simultaneously. To address this, we developed Jellyfish, a tool that integrates phylogenetic and sample trees into a single plot, providing a holistic view of tumor evolution and capturing both spatial and temporal evolution. Available as a JavaScript library and R package, Jellyfish generates interactive visualizations from tumor phylogeny and clonal composition data. We demonstrate its ability to visualize complex subclonal dynamics using data from ovarian high-grade serous carcinoma.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Jellyfish is freely available with MIT license at https:\/\/github.com\/HautaniemiLab\/jellyfish (JavaScript library) and https:\/\/github.com\/HautaniemiLab\/jellyfisher (R package).<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf091","type":"journal-article","created":{"date-parts":[[2025,2,25]],"date-time":"2025-02-25T18:12:31Z","timestamp":1740507151000},"source":"Crossref","is-referenced-by-count":2,"title":["Jellyfish: integrative visualization of spatio-temporal tumor evolution and clonal dynamics"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4163-4945","authenticated-orcid":false,"given":"Kari","family":"Lavikka","sequence":"first","affiliation":[{"name":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","place":["Finland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8851-4265","authenticated-orcid":false,"given":"Altti Ilari","family":"Maarala","sequence":"additional","affiliation":[{"name":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","place":["Finland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1063-2736","authenticated-orcid":false,"given":"Jaana","family":"Oikkonen","sequence":"additional","affiliation":[{"name":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","place":["Finland"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7749-2694","authenticated-orcid":false,"given":"Sampsa","family":"Hautaniemi","sequence":"additional","affiliation":[{"name":"Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , Helsinki 00014,","place":["Finland"]}]}],"member":"286","published-online":{"date-parts":[[2025,2,25]]},"reference":[{"key":"2025031206274279400_btaf091-B1","doi-asserted-by":"publisher","first-page":"21","DOI":"10.1002\/path.4230","article-title":"Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling","volume":"231","author":"Bashashati","year":"2013","journal-title":"J Pathol"},{"key":"2025031206274279400_btaf091-B2","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1038\/nrclinonc.2017.166","article-title":"Tumour heterogeneity and resistance to cancer 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