{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T05:53:17Z","timestamp":1779169997476,"version":"3.51.4"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2019,2,7]],"date-time":"2019-02-07T00:00:00Z","timestamp":1549497600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"European Research Council Advanced","award":["EC-FP7-ERC-InMec 341131"],"award-info":[{"award-number":["EC-FP7-ERC-InMec 341131"]}]},{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","award":["AIRC 2013: IG-14216"],"award-info":[{"award-number":["AIRC 2013: IG-14216"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Acute myeloid leukemia (AML) is one of the most common hematological malignancies, characterized by high relapse and mortality rates. The inherent intra-tumor heterogeneity in AML is thought to play an important role in disease recurrence and resistance to chemotherapy. Although experimental protocols for cell proliferation studies are well established and widespread, they are not easily applicable to in\u00a0vivo contexts, and the analysis of related time-series data is often complex to achieve. To overcome these limitations, model-driven approaches can be exploited to investigate different aspects of cell population dynamics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this work, we present ProCell, a novel modeling and simulation framework to investigate cell proliferation dynamics that, differently from other approaches, takes into account the inherent stochasticity of cell division events. We apply ProCell to compare different models of cell proliferation in AML, notably leveraging experimental data derived from human xenografts in mice. ProCell is coupled with Fuzzy Self-Tuning Particle Swarm Optimization, a swarm-intelligence settings-free algorithm used to automatically infer the models parameterizations. Our results provide new insights on the intricate organization of AML cells with highly heterogeneous proliferative potential, highlighting the important role played by quiescent cells and proliferating cells characterized by different rates of division in the progression and evolution of the disease, thus hinting at the necessity to further characterize tumor cell subpopulations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code of ProCell and the experimental data used in this work are available under the GPL 2.0 license on GITHUB at the following URL: https:\/\/github.com\/aresio\/ProCell.<\/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\/btz063","type":"journal-article","created":{"date-parts":[[2019,2,6]],"date-time":"2019-02-06T20:14:20Z","timestamp":1549484060000},"page":"3378-3386","source":"Crossref","is-referenced-by-count":9,"title":["Modeling cell proliferation in human acute myeloid leukemia xenografts"],"prefix":"10.1093","volume":"35","author":[{"given":"Marco S","family":"Nobile","sequence":"first","affiliation":[{"name":"Department of Informatics, Systems and Communication, University of Milano-Bicocca , Milan, Italy"},{"name":"SYSBIO.IT Centre of Systems Biology , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thalia","family":"Vlachou","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simone","family":"Spolaor","sequence":"additional","affiliation":[{"name":"Department of Informatics, Systems and Communication, University of Milano-Bicocca , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela","family":"Bossi","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Cazzaniga","sequence":"additional","affiliation":[{"name":"SYSBIO.IT Centre of Systems Biology , Milan, Italy"},{"name":"Department of Human and Social Sciences, University of Bergamo , Bergamo, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luisa","family":"Lanfrancone","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Giancarlo","family":"Mauri","sequence":"additional","affiliation":[{"name":"Department of Informatics, Systems and Communication, University of Milano-Bicocca , Milan, Italy"},{"name":"SYSBIO.IT Centre of Systems Biology , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pier Giuseppe","family":"Pelicci","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , Milan, Italy"},{"name":"Department of Oncology and Hemato-Oncology, University of Milan , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daniela","family":"Besozzi","sequence":"additional","affiliation":[{"name":"Department of Informatics, Systems and Communication, University of Milano-Bicocca , Milan, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,2,7]]},"reference":[{"key":"2023013108061181500_btz063-B1","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1016\/j.cell.2016.10.022","article-title":"Hematopoietic stem cells count and remember self-renewal divisions","volume":"167","author":"Bernitz","year":"2016","journal-title":"Cell"},{"key":"2023013108061181500_btz063-B2","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/nm0797-730","article-title":"Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell","volume":"3","author":"Bonnet","year":"1997","journal-title":"Nat. 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