{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:41:38Z","timestamp":1772138498235,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,8,30]],"date-time":"2022-08-30T00:00:00Z","timestamp":1661817600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"NIH\/NCI","award":["R01CA152063"],"award-info":[{"award-number":["R01CA152063"]}]},{"name":"NIH\/NCI","award":["1R01CA241554"],"award-info":[{"award-number":["1R01CA241554"]}]},{"DOI":"10.13039\/100004917","name":"CPRIT","doi-asserted-by":"publisher","award":["RP150445"],"award-info":[{"award-number":["RP150445"]}],"id":[{"id":"10.13039\/100004917","id-type":"DOI","asserted-by":"publisher"}]},{"name":"SU2C-CRUK Pediatric Cancer New Discoveries Challenge Team","award":["SU2C #RT6187"],"award-info":[{"award-number":["SU2C #RT6187"]}]},{"name":"NIH\/NIA","award":["F31AG072902"],"award-info":[{"award-number":["F31AG072902"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["GM139549"],"award-info":[{"award-number":["GM139549"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000005","name":"DOD","doi-asserted-by":"publisher","award":["CDMRP PR181598"],"award-info":[{"award-number":["CDMRP PR181598"]}],"id":[{"id":"10.13039\/100000005","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>R-loops are three-stranded nucleic acid structures formed from the hybridization of RNA and DNA. In 2012, Ginno et al. introduced the first R-loop mapping method. Since that time, dozens of R-loop mapping studies have been conducted, yielding hundreds of publicly available datasets. Current R-loop databases provide only limited access to these data. Moreover, no web tools for analyzing user-supplied R-loop datasets have yet been described. In our recent work, we reprocessed 810 R-loop mapping samples, building the largest R-loop data resource to date. We also defined R-loop consensus regions and developed a framework for R-loop data analysis. Now, we introduce RLBase, a user-friendly database that provides the capability to (i) explore hundreds of public R-loop mapping datasets, (ii) explore R-loop consensus regions, (iii) analyze user-supplied data and (iv) download standardized and reprocessed datasets. RLBase is directly accessible via the following URL: https:\/\/gccri.bishop-lab.uthscsa.edu\/shiny\/rlbase\/.<\/jats:p>","DOI":"10.1093\/nar\/gkac732","type":"journal-article","created":{"date-parts":[[2022,8,24]],"date-time":"2022-08-24T13:10:03Z","timestamp":1661346603000},"page":"D1129-D1137","source":"Crossref","is-referenced-by-count":12,"title":["Exploration and analysis of R-loop mapping data with\n                    <i>RLBase<\/i>"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3756-3918","authenticated-orcid":false,"given":"Henry E","family":"Miller","sequence":"first","affiliation":[{"name":"Department of Cell Systems and Anatomy, UT Health San Antonio , San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"},{"name":"Greehey Children\u2019s Cancer Research Institute, UT Health San Antonio ,\u00a0 San Antonio ,\u00a0 TX 78229 , USA"},{"name":"Bioinformatics Research Network , Atlanta , GA 30317 , USA"}]},{"given":"Daniel","family":"Montemayor","sequence":"additional","affiliation":[{"name":"Department of Medicine, UT Health San Antonio , San Antonio ,\u00a0 TX\u00a078229 ,\u00a0 USA"},{"name":"Center for Precision Medicine, UT Health San Antonio , San Antonio ,\u00a0 TX\u00a078229 ,\u00a0 USA"}]},{"given":"Janet","family":"Li","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Network , Atlanta , GA 30317 , USA"},{"name":"Bioinformatics Graduate Program, University of British Columbia ,\u00a0Vancouver,\u00a0 BC\u00a0V6T 1Z2 ,\u00a0 Canada"},{"name":"Canada's Michael Smith Genome Sciences Center, BC Cancer Research ,\u00a0Vancouver,\u00a0 BC V5Z 1L3 ,\u00a0 Canada"}]},{"given":"Simon\u00a0A","family":"Levy","sequence":"additional","affiliation":[{"name":"Department of Cell Systems and Anatomy, UT Health San Antonio , San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"},{"name":"Bioinformatics Research Network , Atlanta , GA 30317 , USA"},{"name":"Sam & Ann Barshop Institute for Longevity & Aging Studies , UT Health San Antonio, San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"},{"name":"Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases , UT Health San Antonio, San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"}]},{"given":"Roshan","family":"Pawar","sequence":"additional","affiliation":[{"name":"Bioinformatics Research Network , Atlanta , GA 30317 , USA"},{"name":"Faculty of Applied Science, University of British Columbia ,\u00a0 Vancouver, BC V6T 1Z2,\u00a0 Canada"}]},{"given":"Stella","family":"Hartono","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology , UC Davis, Davis ,\u00a0 CA 95616 ,\u00a0 USA"}]},{"given":"Kumar","family":"Sharma","sequence":"additional","affiliation":[{"name":"Department of Medicine, UT Health San Antonio , San Antonio ,\u00a0 TX\u00a078229 ,\u00a0 USA"},{"name":"Center for Precision Medicine, UT Health San Antonio , San Antonio ,\u00a0 TX\u00a078229 ,\u00a0 USA"}]},{"given":"Bess","family":"Frost","sequence":"additional","affiliation":[{"name":"Department of Cell Systems and Anatomy, UT Health San Antonio , San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"},{"name":"Sam & Ann Barshop Institute for Longevity & Aging Studies , UT Health San Antonio, San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"},{"name":"Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases , UT Health San Antonio, San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Chedin","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology , UC Davis, Davis ,\u00a0 CA 95616 ,\u00a0 USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5742-4387","authenticated-orcid":false,"given":"Alexander\u00a0J R","family":"Bishop","sequence":"additional","affiliation":[{"name":"Department of Cell Systems and Anatomy, UT Health San Antonio , San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"},{"name":"Greehey Children\u2019s Cancer Research Institute, UT Health San Antonio ,\u00a0 San Antonio ,\u00a0 TX 78229 , USA"},{"name":"May\u2019s Cancer Center, UT Health San Antonio , San Antonio ,\u00a0 TX 78229 ,\u00a0 USA"}]}],"member":"286","published-online":{"date-parts":[[2022,8,30]]},"reference":[{"key":"2023010804163318000_B1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1038\/s41580-019-0206-3","article-title":"Regulatory R-loops as facilitators of gene expression and genome stability","volume":"21","author":"Niehrs","year":"2020","journal-title":"Nat. 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