{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T22:28:20Z","timestamp":1768429700648,"version":"3.49.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,2,26]],"date-time":"2024-02-26T00:00:00Z","timestamp":1708905600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HL111362"],"award-info":[{"award-number":["HL111362"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["CA271891"],"award-info":[{"award-number":["CA271891"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["MH110504"],"award-info":[{"award-number":["MH110504"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["NS123719"],"award-info":[{"award-number":["NS123719"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of Defence","award":["BC171885P1"],"award-info":[{"award-number":["BC171885P1"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Complex tissues are dynamic ecosystems consisting of molecularly distinct yet interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell type compositions and cell-specific expressions. With few exceptions, most existing deconvolution tools exploit supervised approaches requiring various types of references that may be unreliable or even unavailable for specific tissue microenvironments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We previously developed a fully unsupervised deconvolution method\u2014Convex Analysis of Mixtures (CAM), that enables estimation of cell type composition and expression from bulk tissues. We now introduce CAM3.0 tool that improves this framework with three new and highly efficient algorithms, namely, radius-fixed clustering to identify reliable markers, linear programming to detect an initial scatter simplex, and a smart floating search for the optimum latent variable model. The comparative experimental results obtained from both realistic simulations and case studies show that the CAM3.0 tool can help biologists more accurately identify known or novel cell markers, determine cell proportions, and estimate cell-specific expressions, complementing the existing tools particularly when study- or datatype-specific references are unreliable or unavailable.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The open-source R Scripts of CAM3.0 is freely available at https:\/\/github.com\/ChiungTingWu\/CAM3\/(https:\/\/github.com\/Bioconductor\/Contributions\/issues\/3205). A user\u2019s guide and a vignette are provided.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae107","type":"journal-article","created":{"date-parts":[[2024,2,25]],"date-time":"2024-02-25T13:39:32Z","timestamp":1708868372000},"source":"Crossref","is-referenced-by-count":3,"title":["CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0493-2812","authenticated-orcid":false,"given":"Chiung-Ting","family":"Wu","sequence":"first","affiliation":[{"name":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dongping","family":"Du","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lulu","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University , Arlington, VA 22203, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9979-3295","authenticated-orcid":false,"given":"Rujia","family":"Dai","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, SUNY Upstate Medical University , Syracuse, NY 13210, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5986-4415","authenticated-orcid":false,"given":"Chunyu","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, SUNY Upstate Medical University , Syracuse, NY 13210, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6743-7413","authenticated-orcid":false,"given":"Guoqiang","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Automation, Tsinghua University , Beijing 100084, P. 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