{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,31]],"date-time":"2026-03-31T09:27:43Z","timestamp":1774949263679,"version":"3.50.1"},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2021,3,15]],"date-time":"2021-03-15T00:00:00Z","timestamp":1615766400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 research and innovation programme","award":["667403"],"award-info":[{"award-number":["667403"]}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["292402"],"award-info":[{"award-number":["292402"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["325956"],"award-info":[{"award-number":["325956"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["314395"],"award-info":[{"award-number":["314395"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006306","name":"Sigrid Jus\u00e9lius Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006306","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Finnish Cancer Association"},{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"publisher","award":["322927"],"award-info":[{"award-number":["322927"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,9,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>A major challenge in analyzing cancer patient transcriptomes is that the tumors are inherently heterogeneous and evolving. We analyzed 214 bulk RNA samples of a longitudinal, prospective ovarian cancer cohort and found that the sample composition changes systematically due to chemotherapy and between the anatomical sites, preventing direct comparison of treatment-naive and treated samples.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>To overcome this, we developed PRISM, a latent statistical framework to simultaneously extract the sample composition and cell-type-specific whole-transcriptome profiles adapted to each individual sample. Our results indicate that the PRISM-derived composition-free transcriptomic profiles and signatures derived from them predict the patient response better than the composite raw bulk data. We validated our findings in independent ovarian cancer and melanoma cohorts, and verified that PRISM accurately estimates the composition and cell-type-specific expression through whole-genome sequencing and RNA in situ hybridization experiments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>https:\/\/bitbucket.org\/anthakki\/prism.<\/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\/btab178","type":"journal-article","created":{"date-parts":[[2021,3,11]],"date-time":"2021-03-11T20:11:15Z","timestamp":1615493475000},"page":"2882-2888","source":"Crossref","is-referenced-by-count":32,"title":["PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples"],"prefix":"10.1093","volume":"37","author":[{"given":"Antti","family":"H\u00e4kkinen","sequence":"first","affiliation":[{"name":"Research Programs Unit, Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , FI-00014 Helsinki, Finland"}]},{"given":"Kaiyang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Research Programs Unit, Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , FI-00014 Helsinki, Finland"}]},{"given":"Amjad","family":"Alkodsi","sequence":"additional","affiliation":[{"name":"Research Programs Unit, Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , FI-00014 Helsinki, Finland"}]},{"given":"Noora","family":"Andersson","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of 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Finland"}]},{"given":"Naziha","family":"Mansuri","sequence":"additional","affiliation":[{"name":"Research Center for Cancer, Infections and Immunity, Institute of Biomedicine, University of Turku , FI-20014 Turku, Finland"}]},{"given":"Kaisa","family":"Huhtinen","sequence":"additional","affiliation":[{"name":"Research Center for Cancer, Infections and Immunity, Institute of Biomedicine, University of Turku , FI-20014 Turku, Finland"}]},{"given":"Anna","family":"V\u00e4h\u00e4rautio","sequence":"additional","affiliation":[{"name":"Research Programs Unit, Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , FI-00014 Helsinki, Finland"}]},{"given":"Olli","family":"Carp\u00e9n","sequence":"additional","affiliation":[{"name":"Research Programs Unit, Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki , FI-00014 Helsinki, Finland"},{"name":"Department of Pathology, University of 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