{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T23:09:49Z","timestamp":1773875389245,"version":"3.50.1"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2020,1,23]],"date-time":"2020-01-23T00:00:00Z","timestamp":1579737600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Singapore Ministry of Education\u2019s Tier 2 Grant","award":["MOE2019-T2-1-138"],"award-info":[{"award-number":["MOE2019-T2-1-138"]}]},{"name":"Singapore Ministry of Education\u2019s Tier 2 Grant","award":["T1-2016Apr-07"],"award-info":[{"award-number":["T1-2016Apr-07"]}]},{"name":"St. Baldrick\u2019s Foundation","award":["Duke-NUS-SBF\/2018\/0006"],"award-info":[{"award-number":["Duke-NUS-SBF\/2018\/0006"]}]},{"name":"Singapore Ministry of Health\u2019s National Medical Research Council"},{"DOI":"10.13039\/100007680","name":"NMRC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007680","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Open Fund Large Collaborative Grant","award":["NMRC\/OFLCG\/003\/2018"],"award-info":[{"award-number":["NMRC\/OFLCG\/003\/2018"]}]},{"DOI":"10.13039\/501100011744","name":"National University Health System","doi-asserted-by":"publisher","award":["NUHSRO\/2018\/091\/T1\/Seed-Nov\/01"],"award-info":[{"award-number":["NUHSRO\/2018\/091\/T1\/Seed-Nov\/01"]}],"id":[{"id":"10.13039\/501100011744","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Gradual population-level changes in tissues can be driven by stochastic plasticity, meaning rare stochastic transitions of single-cell phenotype. Quantifying the rates of these stochastic transitions requires time-intensive experiments, and analysis is generally confounded by simultaneous bidirectional transitions and asymmetric proliferation kinetics. To quantify cellular plasticity, we developed Transcompp (Transition Rate ANalysis of Single Cells to Observe and Measure Phenotypic Plasticity), a Markov modeling algorithm that uses optimization and resampling to compute best-fit rates and statistical intervals for stochastic cell-state transitions.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We applied Transcompp to time-series datasets in which purified subpopulations of stem-like or non-stem cancer cells were exposed to various cell culture environments, and allowed to re-equilibrate spontaneously over time. Results revealed that commonly used cell culture reagents hydrocortisone and cholera toxin shifted the cell population equilibrium toward stem-like or non-stem states, respectively, in the basal-like breast cancer cell line MCF10CA1a. In addition, applying Transcompp to patient-derived cells showed that transition rates computed from short-term experiments could predict long-term trajectories and equilibrium convergence of the cultured cell population.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Freely available for download at http:\/\/github.com\/nsuhasj\/Transcompp.<\/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\/btaa021","type":"journal-article","created":{"date-parts":[[2020,1,17]],"date-time":"2020-01-17T12:11:30Z","timestamp":1579263090000},"page":"2813-2820","source":"Crossref","is-referenced-by-count":11,"title":["<scp>Transcompp<\/scp>: understanding phenotypic plasticity by estimating Markov transition rates for cell state transitions"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1857-8789","authenticated-orcid":false,"given":"N Suhas","family":"Jagannathan","sequence":"first","affiliation":[{"name":"Cancer and Stem Cell Biology Programme , Centre for Computational Biology, Duke-NUS Medical School, 169857 Singapore"}]},{"given":"Mario O","family":"Ihsan","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , National University of Singapore, 117596 Singapore"},{"name":"NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore, 117456 Singapore"}]},{"given":"Xiao Xuan","family":"Kin","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , National University of Singapore, 117596 Singapore"}]},{"given":"Roy E","family":"Welsch","sequence":"additional","affiliation":[{"name":"Sloan School of Management and Center for Statistics and Data Science , Massachusetts Institute of Technology, Cambridge, MA 02142, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9442-9382","authenticated-orcid":false,"given":"Marie-V\u00e9ronique","family":"Cl\u00e9ment","sequence":"additional","affiliation":[{"name":"Department of Biochemistry , National University of Singapore, 117596 Singapore"},{"name":"NUS Graduate School for Integrative Sciences and Engineering , National University of Singapore, 117456 Singapore"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1301-7069","authenticated-orcid":false,"given":"Lisa","family":"Tucker-Kellogg","sequence":"additional","affiliation":[{"name":"Cancer and Stem Cell Biology Programme , Centre for Computational Biology, Duke-NUS Medical School, 169857 Singapore"}]}],"member":"286","published-online":{"date-parts":[[2020,1,23]]},"reference":[{"key":"2023020108352379300_btaa021-B1","doi-asserted-by":"crossref","first-page":"e32459","DOI":"10.1371\/journal.pone.0032459","article-title":"EGFR kinase promotes acquisition of stem cell-like properties: a potential therapeutic target in head and neck squamous cell carcinoma stem cells","volume":"7","author":"Abhold","year":"2012","journal-title":"PLoS One"},{"key":"2023020108352379300_btaa021-B2","doi-asserted-by":"crossref","first-page":"3983","DOI":"10.1073\/pnas.0530291100","article-title":"Prospective identification of tumorigenic breast cancer cells","volume":"100","author":"Al-Hajj","year":"2003","journal-title":"Proc. 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