{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,3]],"date-time":"2025-10-03T18:17:41Z","timestamp":1759515461270,"version":"3.37.3"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2021,4,26]],"date-time":"2021-04-26T00:00:00Z","timestamp":1619395200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100009164","name":"Moffitt Cancer Center","doi-asserted-by":"publisher","award":["NCI P30 CA076292"],"award-info":[{"award-number":["NCI P30 CA076292"]}],"id":[{"id":"10.13039\/100009164","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["T32 CA233399"],"award-info":[{"award-number":["T32 CA233399"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"James and Esther King Biomedical Research","award":["7JK02"],"award-info":[{"award-number":["7JK02"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,10,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The heterogeneous cell types of the tumor-immune microenvironment (TIME) play key roles in determining cancer progression, metastasis and response to treatment. We report the development of TIMEx, a novel TIME deconvolution method emphasizing on estimating infiltrating immune cells for bulk transcriptomics using pan-cancer single-cell RNA-seq signatures. We also implemented a comprehensive, user-friendly web-portal for users to evaluate TIMEx and other deconvolution methods with bulk transcriptomic profiles.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>TIMEx web-portal is freely accessible at http:\/\/timex.moffitt.org.<\/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\/btab244","type":"journal-article","created":{"date-parts":[[2021,4,14]],"date-time":"2021-04-14T00:22:13Z","timestamp":1618359733000},"page":"3681-3683","source":"Crossref","is-referenced-by-count":15,"title":["TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures"],"prefix":"10.1093","volume":"37","author":[{"given":"Mengyu","family":"Xie","sequence":"first","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Kyubum","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"John H","family":"Lockhart","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Scott D","family":"Cukras","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Rodrigo","family":"Carvajal","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Amer A","family":"Beg","sequence":"additional","affiliation":[{"name":"Department of Immunology H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Elsa R","family":"Flores","sequence":"additional","affiliation":[{"name":"Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8536-8941","authenticated-orcid":false,"given":"Mingxiang","family":"Teng","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"given":"Christine H","family":"Chung","sequence":"additional","affiliation":[{"name":"Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2955-8369","authenticated-orcid":false,"given":"Aik Choon","family":"Tan","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute , Tampa, FL 33612, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,4,26]]},"reference":[{"key":"2024041009364170000_btab244-B1","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/s13059-017-1349-1","article-title":"xCell: digitally portraying the tissue cellular heterogeneity landscape","volume":"18","author":"Aran","year":"2017","journal-title":"Genome Biol"},{"key":"2024041009364170000_btab244-B2","article-title":"Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression","volume":"17, 218","author":"Becht","year":"2016","journal-title":"Genome Biol.,"},{"key":"2024041009364170000_btab244-B3","doi-asserted-by":"crossref","first-page":"150051","DOI":"10.1038\/sdata.2015.51","article-title":"De novo transcriptome profiling of highly purified human lymphocytes primary cells","volume":"2","author":"Bonnal","year":"2015","journal-title":"Sci. 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