{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,10]],"date-time":"2026-09-10T22:48:13Z","timestamp":1789080493845,"version":"build-2803163510"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T00:00:00Z","timestamp":1667952000000},"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":["R15CA220059"],"award-info":[{"award-number":["R15CA220059"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB-2027611"],"award-info":[{"award-number":["MCB-2027611"]}],"id":[{"id":"10.13039\/100000001","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>tRNA-derived fragments (tRFs) are a class of emerging post-transcriptional regulators of gene expression likely binding to the transcripts of target genes. However, only a few tRFs targets have been experimentally validated, making it hard to extrapolate the functions or binding mechanisms of tRFs. The paucity of resources supporting the identification of the targets of tRFs creates a bottleneck in the fast-developing field. We have previously analyzed chimeric reads in crosslinked Argonaute1-RNA complexes to help infer the guide-target pairs and binding mechanisms of multiple tRFs based on experimental data in human HEK293 cells. To efficiently disseminate these results to the research community, we designed a web-based database tatDB (targets of tRFs DataBase) populated with close to 250 000 experimentally determined guide-target pairs with \u223c23 000 tRF isoforms. tatDB has a user-friendly interface with flexible query options\/filters allowing one to obtain comprehensive information on given tRFs (or targets). Modes of interactions are supported by secondary structures of potential guide-target hybrids and binding motifs, essential for understanding the targeting mechanisms of tRFs. Further, we illustrate the value of the database on an example of hypothesis-building for a tRFs potentially involved in the lifecycle of the SARS-CoV-2 virus. tatDB is freely accessible at https:\/\/grigoriev-lab.camden.rutgers.edu\/tatdb.<\/jats:p>","DOI":"10.1093\/nar\/gkac1018","type":"journal-article","created":{"date-parts":[[2022,11,7]],"date-time":"2022-11-07T16:46:15Z","timestamp":1667839575000},"page":"D297-D305","source":"Crossref","is-referenced-by-count":16,"title":["tatDB: a database of Ago1-mediated targets of transfer RNA fragments"],"prefix":"10.1093","volume":"51","author":[{"given":"Lingyu","family":"Guan","sequence":"first","affiliation":[{"name":"Department of Biology, Center for Computational and Integrative Biology, Rutgers University , Camden , NJ , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3227-532X","authenticated-orcid":false,"given":"Andrey","family":"Grigoriev","sequence":"additional","affiliation":[{"name":"Department of Biology, Center for Computational and Integrative Biology, Rutgers University , Camden , NJ , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,11,9]]},"reference":[{"key":"2023010804225085500_B1","doi-asserted-by":"crossref","first-page":"D93","DOI":"10.1093\/nar\/gkn787","article-title":"GtRNAdb: a database of transfer RNA genes detected in genomic sequence","volume":"37","author":"Chan","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023010804225085500_B2","doi-asserted-by":"crossref","first-page":"D159","DOI":"10.1093\/nar\/gkn772","article-title":"tRNAdb 2009: compilation of tRNA sequences and tRNA genes","volume":"37","author":"Juhling","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023010804225085500_B3","doi-asserted-by":"crossref","first-page":"114","DOI":"10.3389\/fgene.2014.00114","article-title":"tRNADB-CE: tRNA gene database well-timed in the era of big sequence data","volume":"5","author":"Abe","year":"2014","journal-title":"Front. 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