{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,14]],"date-time":"2026-03-14T22:04:45Z","timestamp":1773525885957,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,10,5]],"date-time":"2020-10-05T00:00:00Z","timestamp":1601856000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japanese Society for the Promotion of Science","doi-asserted-by":"crossref","award":["B 15H04744"],"award-info":[{"award-number":["B 15H04744"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Specially Promoted Research","award":["16H06295"],"award-info":[{"award-number":["16H06295"]}]},{"DOI":"10.13039\/501100003382","name":"Core Research for Evolutional Science and Technology","doi-asserted-by":"publisher","award":["17 gm0410016h0006"],"award-info":[{"award-number":["17 gm0410016h0006"]}],"id":[{"id":"10.13039\/501100003382","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002241","name":"Japan Science and Technology Agency","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002241","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Leading Advanced Projects for medical innovation","award":["18 gm0010005h0001"],"award-info":[{"award-number":["18 gm0010005h0001"]}]},{"DOI":"10.13039\/100009619","name":"Japan\u2019s Agency for Medical Research and Development","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100009619","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,6,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>The possibility that RNA transcripts from clinical samples contain plenty of virus RNAs has not been pursued actively so far. We here developed a new tool for analyzing virus-transcribed mRNAs, not virus copy numbers, in the data of bulk and single-cell RNA-sequencing of human cells. Our pipeline, named VIRTUS (VIRal Transcript Usage Sensor), was able to detect 762 viruses including herpesviruses, retroviruses and even SARS-CoV-2 (COVID-19), and quantify their transcripts in the sequence data. This tool thus enabled simultaneously detecting infected cells, the composition of multiple viruses within the cell, and the endogenous host-gene expression profile of the cell. This bioinformatics method would be instrumental in addressing the possible effects of covertly infecting viruses on certain diseases and developing new treatments to target such viruses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>: VIRTUS is implemented using Common Workflow Language and Docker under a CC-NC license. VIRTUS is freely available at https:\/\/github.com\/yyoshiaki\/VIRTUS.<\/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\/btaa859","type":"journal-article","created":{"date-parts":[[2020,9,21]],"date-time":"2020-09-21T07:19:17Z","timestamp":1600672757000},"page":"1465-1467","source":"Crossref","is-referenced-by-count":26,"title":["VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9872-4909","authenticated-orcid":false,"given":"Yoshiaki","family":"Yasumizu","sequence":"first","affiliation":[{"name":"Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan"}]},{"given":"Atsushi","family":"Hara","sequence":"additional","affiliation":[{"name":"Nara Medical University Department of Immunology, , Kashihara, Nara 634-8521, Japan"}]},{"given":"Shimon","family":"Sakaguchi","sequence":"additional","affiliation":[{"name":"Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan"}]},{"given":"Naganari","family":"Ohkura","sequence":"additional","affiliation":[{"name":"Osaka University Department of Experimental Immunology, Immunology Frontier Research Center, , Osaka 565-0871, Japan"}]}],"member":"286","published-online":{"date-parts":[[2020,10,5]]},"reference":[{"key":"2023051709342412300_btaa859-B1","doi-asserted-by":"crossref","first-page":"816","DOI":"10.15252\/emmm.201607006","article-title":"Transcriptional response to hepatitis C virus infection and interferon-alpha treatment in the human liver","volume":"9","author":"Boldanova","year":"2017","journal-title":"EMBO Mol. 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