{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,2]],"date-time":"2026-03-02T16:34:40Z","timestamp":1772469280973,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2020,5,19]],"date-time":"2020-05-19T00:00:00Z","timestamp":1589846400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Center for Cancer Evolution at Dana-Farber Cancer Insitute"},{"name":"Dana-Farber Cancer Institute Physical Science-Oncology Center"},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["U54CA193461"],"award-info":[{"award-number":["U54CA193461"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>ESTIpop is an R package designed to simulate and estimate parameters for continuous-time Markov branching processes with constant or time-dependent rates, a common model for asexually reproducing cell populations. Analytical approaches to parameter estimation quickly become intractable in complex branching processes. In ESTIpop, parameter estimation is based on a likelihood function with respect to a time series of cell counts, approximated by the Central Limit Theorem for multitype branching processes. Additionally, simulation in ESTIpop via approximation can be performed many times faster than exact simulation methods with similar results.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>ESTIpop is available as an R package on Github (https:\/\/github.com\/michorlab\/estipop).<\/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\/btaa526","type":"journal-article","created":{"date-parts":[[2020,5,14]],"date-time":"2020-05-14T22:25:55Z","timestamp":1589495155000},"page":"4372-4373","source":"Crossref","is-referenced-by-count":9,"title":["ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes"],"prefix":"10.1093","volume":"36","author":[{"given":"James P","family":"Roney","sequence":"first","affiliation":[{"name":"Harvard College, Cambridge MA 02138, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9062-5503","authenticated-orcid":false,"given":"Jeremy","family":"Ferlic","sequence":"additional","affiliation":[{"name":"Center for Cancer Evolution, Dana-Farber Cancer Institute Department of Data Sciences,"},{"name":"Harvard T. H. Chan School of Public Health Department of Biostatistics, , Boston, MA 02115, USA"}]},{"given":"Franziska","family":"Michor","sequence":"additional","affiliation":[{"name":"Center for Cancer Evolution, Dana-Farber Cancer Institute Department of Data Sciences,"},{"name":"Harvard T. H. Chan School of Public Health Department of Biostatistics, , Boston, MA 02115, USA"},{"name":"Harvard University Department of Stem Cell and Regenerative Biology, , Cambridge, MA 02138, USA"},{"name":"The Broad Institute of Harvard and MIT , Cambridge, MA 02139, USA"},{"name":"The Ludwig Center at Harvard , Boston, MA 02215, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5272-0187","authenticated-orcid":false,"given":"Thomas O","family":"McDonald","sequence":"additional","affiliation":[{"name":"Center for Cancer Evolution, Dana-Farber Cancer Institute Department of Data Sciences,"},{"name":"Harvard T. H. Chan School of Public Health Department of Biostatistics, , Boston, MA 02115, USA"},{"name":"Harvard University Department of Stem Cell and Regenerative Biology, , Cambridge, MA 02138, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,5,19]]},"reference":[{"key":"2023062312042023700_btaa526-B2","doi-asserted-by":"crossref","first-page":"e00747","DOI":"10.7554\/eLife.00747","article-title":"Evolutionary dynamics of cancer in response to targeted combination therapy","volume":"2","author":"Bozic","year":"2013","journal-title":"Elife"},{"key":"2023062312042023700_btaa526-B3","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/0304-4149(83)90048-0","article-title":"Inhomogenous Markov branching","volume":"14","author":"Cohn","year":"1981","journal-title":"Stoch. Proc. 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