{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,18]],"date-time":"2026-07-18T09:23:06Z","timestamp":1784366586706,"version":"3.55.0"},"reference-count":32,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,4,5]],"date-time":"2025-04-05T00:00:00Z","timestamp":1743811200000},"content-version":"vor","delay-in-days":94,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Nih","award":["R01-GM132457"],"award-info":[{"award-number":["R01-GM132457"]}]},{"name":"Ministry of Education, Taiwan"},{"name":"Ministry of Science and Technology Council of Taiwan","award":["MOST 110-2221-E-006-198-MY3 MOST 112-2221-E-006-129-MY2 NSTC 111-2221-E-006-151-MY3 NSTC 113-2221-E-006-135-MY3"],"award-info":[{"award-number":["MOST 110-2221-E-006-198-MY3 MOST 112-2221-E-006-129-MY2 NSTC 111-2221-E-006-151-MY3 NSTC 113-2221-E-006-135-MY3"]}]},{"DOI":"10.13039\/501100007750","name":"National Cheng Kung University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007750","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Miin Wu School of Computing at National Cheng Kung University"},{"name":"Nih","award":["R01-GM132457"],"award-info":[{"award-number":["R01-GM132457"]}]},{"name":"Ministry of Education, Taiwan"},{"name":"Ministry of Science and Technology Council of Taiwan","award":["MOST 110-2221-E-006-198-MY3 MOST 112-2221-E-006-129-MY2 NSTC 111-2221-E-006-151-MY3 NSTC 113-2221-E-006-135-MY3"],"award-info":[{"award-number":["MOST 110-2221-E-006-198-MY3 MOST 112-2221-E-006-129-MY2 NSTC 111-2221-E-006-151-MY3 NSTC 113-2221-E-006-135-MY3"]}]},{"DOI":"10.13039\/501100007750","name":"National Cheng Kung University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007750","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Miin Wu School of Computing at National Cheng Kung University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,4,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>MicroRNAs (miRNAs) can target messenger RNAs to control their degradation or translation repression effects. Therefore, identifying the target and binding sites of different miRNAs is essential for understanding miRNA functions. To investigate these interactions, researchers have employed the cross-linking, ligation, and sequencing of hybrids (CLASH-seq) and similar CLASH-like approaches to generate chimeric reads formed by miRNAs and their targeting segments. These chimeric reads allow for the direct extraction of both the miRNA\u2013target gene pairs and their corresponding binding sites. Nevertheless, these studies lack user-friendly platforms for researchers to investigate these interactions efficiently, thus hindering scientists\u2019 ability to explore miRNA functions. To address this gap, we developed mirTarCLASH, a comprehensive database that deposits 502\u2009061\/322\u2009707\/224\u2009452 unique hybrid reads from human\/mouse\/worm miRNA chimeric read-based experiments. In mirTarCLASH, the chimera analysis algorithm ChiRA and two distinct binding site inference tools, RNAup and miRanda, were adopted to facilitate the exploration of miRNA\u2013target pairs derived from CLASH-like experiments. Compared with existing similar repositories, mirTarCLASH further enables several confidence evaluation filters with visualization functions for the extracted results. The results can be further refined based on the key properties of the miRNA targeting sites, including read depths, numbers of supporting algorithms, and cross-linking-induced mutations, to enhance confidence levels. In addition, these miRNA-binding sites are visually represented through an integrated transcript atlas. Finally, we demonstrated the biological applicability of mirTarCLASH via the well-characterized example interaction between cel-let-7-5p and lin-41 in Caenorhabditis elegans, showcasing the potential of mirTarCLASH to provide novel insights for subsequent experimental research designs. The constructed mirTarCLASH database is freely available at https:\/\/cosbi.ee.ncku.edu.tw\/MirTarClash.<\/jats:p>\n               <jats:p>Database URL: https:\/\/cosbi.ee.ncku.edu.tw\/MirTarClash<\/jats:p>","DOI":"10.1093\/database\/baaf023","type":"journal-article","created":{"date-parts":[[2025,3,13]],"date-time":"2025-03-13T16:23:36Z","timestamp":1741883016000},"source":"Crossref","is-referenced-by-count":4,"title":["mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments"],"prefix":"10.1093","volume":"2025","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9420-196X","authenticated-orcid":false,"given":"Tzu-Hsien","family":"Yang","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, National Cheng Kung University , No.1, University Road, Tainan 701,","place":["Taiwan"]},{"name":"Medical Device Innovation Center, National Cheng Kung University , No.1, University Road, Tainan 701,","place":["Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiang-Wei","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, National Cheng Kung University , No.1, University Road, Tainan 701,","place":["Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan-Han","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, National Cheng Kung University , No.1, University Road, Tainan 701,","place":["Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shang-Yi","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, National Cheng Kung University , No.1, University Road, Tainan 701,","place":["Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9919-9579","authenticated-orcid":false,"given":"Wei-Sheng","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering, National Cheng Kung University , No.1, University Road, Tainan 701,","place":["Taiwan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8154-906X","authenticated-orcid":false,"given":"Heng-Chi","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Molecular Genetics and Cell Biology, University of Chicago , 920 E. 58th Street, Suite 1106, Chicago, IL 60637,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,4,5]]},"reference":[{"key":"2025092510514301400_R1","first-page":"1","article-title":"The role of microRNAs in human 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