{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T20:10:45Z","timestamp":1762459845898,"version":"3.37.3"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,3,14]],"date-time":"2020-03-14T00:00:00Z","timestamp":1584144000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"JST CREST","award":["14531766"],"award-info":[{"award-number":["14531766"]}]},{"DOI":"10.13039\/501100001700","name":"MEXT","doi-asserted-by":"publisher","award":["15K06916"],"award-info":[{"award-number":["15K06916"]}],"id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009619","name":"AMED","doi-asserted-by":"publisher","award":["16ck0106013h0003","19cm0106536h0002"],"award-info":[{"award-number":["16ck0106013h0003","19cm0106536h0002"]}],"id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The flood of recent cancer genomic data requires a coherent model that can sort out the findings to systematically explain clonal evolution and the resultant intra-tumor heterogeneity (ITH). Here, we present a new mathematical model designed to computationally simulate the evolution of cancer cells. The model connects the well-known hallmarks of cancer with the specific mutational states of tumor-related genes. The cell behavior phenotypes are stochastically determined, and the hallmarks probabilistically interfere with the phenotypic probabilities. In turn, the hallmark variables depend on the mutational states of tumor-related genes. Thus, our software can deepen our understanding of cancer-cell evolution and generation of ITH.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The open-source code is available in the repository https:\/\/github.com\/nagornovys\/Cancer_cell_evolution.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>mamkato@ncc.go.jp<\/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\/btaa182","type":"journal-article","created":{"date-parts":[[2020,3,11]],"date-time":"2020-03-11T12:40:01Z","timestamp":1583930401000},"page":"3597-3599","source":"Crossref","is-referenced-by-count":8,"title":["tugHall: a simulator of cancer-cell evolution based on the hallmarks of cancer and tumor-related genes"],"prefix":"10.1093","volume":"36","author":[{"given":"Iurii S","family":"Nagornov","sequence":"first","affiliation":[{"name":"Department of Bioinformatics , Research Institute, National Cancer Center Japan, Tokyo 104-0045, Japan"}]},{"given":"Mamoru","family":"Kato","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics , Research Institute, National Cancer Center Japan, Tokyo 104-0045, Japan"}]}],"member":"286","published-online":{"date-parts":[[2020,3,14]]},"reference":[{"key":"2023062312022171900_btaa182-B1","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1162\/artl.2006.12.4.617","article-title":"Simulating the hallmarks of cancer","volume":"12","author":"Abbott","year":"2006","journal-title":"Artif. 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