{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T02:23:56Z","timestamp":1790475836285,"version":"4.1.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,2,24]],"date-time":"2023-02-24T00:00:00Z","timestamp":1677196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"German Ministry for Education and Research","award":["01IS18025A"],"award-info":[{"award-number":["01IS18025A"]}]},{"name":"German Ministry for Education and Research","award":["01IS18037A"],"award-info":[{"award-number":["01IS18037A"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Simulations of cancer evolution are highly useful to study the effects of selection and mutation rates on cellular fitness. However, most methods are either lattice-based and cannot simulate realistically sized tumours, or they omit spatial constraints and lack the clonal dynamics of real-world tumours.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Stochastic model of intra-tumour heterogeneity (SMITH) is an efficient and explainable model of cancer evolution that combines a branching process with a new confinement mechanism limiting clonal growth based on the size of the individual clones as well as the overall tumour population. We demonstrate how confinement is sufficient to induce the rich clonal dynamics observed in spatial models and cancer samples across tumour types, while allowing for a clear geometric interpretation and simulation of 1 billion cells within a few minutes on a desktop PC.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>SMITH is implemented in C# and freely available at https:\/\/bitbucket.org\/schwarzlab\/smith. For visualizations, we provide the accompanying Python package PyFish at https:\/\/bitbucket.org\/schwarzlab\/pyfish.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad102","type":"journal-article","created":{"date-parts":[[2023,2,24]],"date-time":"2023-02-24T14:29:38Z","timestamp":1677248978000},"source":"Crossref","is-referenced-by-count":18,"title":["SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7302-0147","authenticated-orcid":false,"given":"Adam","family":"Streck","sequence":"first","affiliation":[{"name":"Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology , Berlin, Germany"},{"name":"Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne , Cologne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom L","family":"Kaufmann","sequence":"additional","affiliation":[{"name":"BIFOLD\u2014Berlin Institute for the Foundations of Learning and Data , Berlin, Germany"},{"name":"Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne , Cologne, Germany"},{"name":"Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology , Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roland F","family":"Schwarz","sequence":"additional","affiliation":[{"name":"Institute for Computational Cancer Biology (ICCB), Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne , Cologne, Germany"},{"name":"BIFOLD\u2014Berlin Institute for the Foundations of Learning and Data , Berlin, Germany"},{"name":"Max Delbr\u00fcck Center for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology , Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,2,24]]},"reference":[{"key":"2023031318182027100_","doi-asserted-by":"crossref","first-page":"795","DOI":"10.1038\/s41586-022-05082-5","article-title":"Ordered and deterministic cancer genome evolution after p53 loss","volume":"608","author":"Baslan","year":"2022","journal-title":"Nature"},{"key":"2023031318182027100_","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/sysbio\/syu081","article-title":"Cancer evolution: mathematical models and computational inference","volume":"64","author":"Beerenwinkel","year":"2015","journal-title":"Syst. 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