{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T09:43:12Z","timestamp":1773826992349,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,10,23]],"date-time":"2023-10-23T00:00:00Z","timestamp":1698019200000},"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":["R01MH123177"],"award-info":[{"award-number":["R01MH123177"]}],"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":["R01AG078950"],"award-info":[{"award-number":["R01AG078950"]}],"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":["T32LM012424"],"award-info":[{"award-number":["T32LM012424"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Double-stranded RNAs (dsRNAs) are potent triggers of innate immune responses upon recognition by cytosolic dsRNA sensor proteins. Identification of endogenous dsRNAs helps to better understand the dsRNAome and its relevance to innate immunity related to human diseases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we report dsRID (double-stranded RNA identifier), a machine-learning-based method to predict dsRNA regions in silico, leveraging the power of long-read RNA-sequencing (RNA-seq) and molecular traits of dsRNAs. Using models trained with PacBio long-read RNA-seq data derived from Alzheimer\u2019s disease (AD) brain, we show that our approach is highly accurate in predicting dsRNA regions in multiple datasets. Applied to an AD cohort sequenced by the ENCODE consortium, we characterize the global dsRNA profile with potentially distinct expression patterns between AD and controls. Together, we show that dsRID provides an effective approach to capture global dsRNA profiles using long-read RNA-seq data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Software implementation of dsRID, and genomic coordinates of regions predicted by dsRID in all samples are available at the GitHub repository: https:\/\/github.com\/gxiaolab\/dsRID.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad649","type":"journal-article","created":{"date-parts":[[2023,10,23]],"date-time":"2023-10-23T17:56:26Z","timestamp":1698083786000},"source":"Crossref","is-referenced-by-count":4,"title":["dsRID: <i>in silico<\/i> identification of dsRNA regions using long-read RNA-seq data"],"prefix":"10.1093","volume":"39","author":[{"given":"Ryo","family":"Yamamoto","sequence":"first","affiliation":[{"name":"Bioinformatics Interdepartmental Program, University of California , Los Angeles, CA 90095-1570, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiheng","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology and Physiology, University of California , Los Angeles, CA 90095-7246, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mudra","family":"Choudhury","sequence":"additional","affiliation":[{"name":"Department of Integrative Biology and Physiology, University of California , Los Angeles, CA 90095-7246, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9362-8029","authenticated-orcid":false,"given":"Xinshu","family":"Xiao","sequence":"additional","affiliation":[{"name":"Bioinformatics Interdepartmental Program, University of California , Los Angeles, CA 90095-1570, United States"},{"name":"Department of Integrative Biology and Physiology, University of California , Los 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