{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:29:18Z","timestamp":1787009358072,"version":"build-2736575974"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"D1","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Edmond J. Safra Center for Bioinformatics at Tel-Aviv University"},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["ERC-AdG 787514"],"award-info":[{"award-number":["ERC-AdG 787514"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We introduce ViroidDB, a value-added database that attempts to collect all known viroid and viroid-like circular RNA sequences into a single resource. Spanning about 10 000 unique sequences, ViroidDB includes viroids, retroviroid-like elements, small circular satellite RNAs, ribozyviruses, and retrozymes. Each sequence's secondary structure, ribozyme content, and cluster membership are predicted via a custom pipeline optimized for handling circular RNAs. The data can be explored via a purpose-built user interface that features visualizations, multiple sequence alignments, and a portal for downloading bulk data. Users can browse the data by sequence type, taxon, or typo-tolerant search of metadata fields. The database is freely accessible at https:\/\/viroids.org.<\/jats:p>","DOI":"10.1093\/nar\/gkab974","type":"journal-article","created":{"date-parts":[[2021,10,7]],"date-time":"2021-10-07T02:13:08Z","timestamp":1633572788000},"page":"D432-D438","source":"Crossref","is-referenced-by-count":25,"title":["ViroidDB: a database of viroids and viroid-like circular RNAs"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7133-8397","authenticated-orcid":false,"given":"Benjamin D","family":"Lee","sequence":"first","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD\u00a020894, USA"},{"name":"Nuffield Department of Medicine, University of Oxford, Oxford\u00a0OX1, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uri","family":"Neri","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv\u00a06997801, Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caleb J","family":"Oh","sequence":"additional","affiliation":[{"name":"Unaffiliated, Gambrills, MD\u00a021054, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter","family":"Simmonds","sequence":"additional","affiliation":[{"name":"Nuffield Department of Medicine, University of Oxford, Oxford\u00a0OX1, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3943-8299","authenticated-orcid":false,"given":"Eugene V","family":"Koonin","sequence":"additional","affiliation":[{"name":"National Center for Biotechnology Information, National Library of Medicine, National Institutes Health, Bethesda, MD\u00a020894, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,9]]},"reference":[{"key":"2022010507320327900_B1","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/0042-6822(71)90342-4","article-title":"Potato spindle tuber \u201cvirus\u201d","volume":"45","author":"Diener","year":"1971","journal-title":"Virology"},{"key":"2022010507320327900_B2","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/sj.embor.7400706","article-title":"Viroids: an Ariadne's thread into the RNA labyrinth","volume":"7","author":"Dar\u00f2s","year":"2006","journal-title":"EMBO Rep."},{"key":"2022010507320327900_B3","doi-asserted-by":"crossref","first-page":"450","DOI":"10.1126\/science.6197756","article-title":"A replication cycle for viroids and other small infectious RNA\u2019s","volume":"223","author":"Branch","year":"1984","journal-title":"Science"},{"key":"2022010507320327900_B4","doi-asserted-by":"crossref","first-page":"13805","DOI":"10.1073\/pnas.1206187109","article-title":"Viroid RNA redirects host DNA ligase 1 to act as an RNA ligase","volume":"109","author":"Nohales","year":"2012","journal-title":"Proc. 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