{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:48:30Z","timestamp":1778226510184,"version":"3.51.4"},"reference-count":204,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2022,6,7]],"date-time":"2022-06-07T00:00:00Z","timestamp":1654560000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100022657","name":"Faculty of Health Sciences, University of Macau","doi-asserted-by":"crossref","award":["MYRG2020-00213-FHS"],"award-info":[{"award-number":["MYRG2020-00213-FHS"]}],"id":[{"id":"10.13039\/501100022657","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62002212"],"award-info":[{"award-number":["62002212"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Li Ka Shing Foundation Cross-Disciplinary Research","award":["2020LKSFG07D"],"award-info":[{"award-number":["2020LKSFG07D"]}]},{"name":"Li Ka Shing Foundation Cross-Disciplinary Research","award":["2020LKSFG07A"],"award-info":[{"award-number":["2020LKSFG07A"]}]},{"name":"STU Scientific Research Foundation for Talents","award":["35941918"],"award-info":[{"award-number":["35941918"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,18]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>PIWI-interacting RNAs (piRNAs) are short 21\u201335 nucleotide molecules that comprise the largest class of non-coding RNAs and found in a large diversity of species including yeast, worms, flies, plants and mammals including humans. The most well-understood function of piRNAs is to monitor and protect the genome from transposons particularly in germline cells. Recent data suggest that piRNAs may have additional functions in somatic cells although they are expressed there in far lower abundance. Compared with microRNAs (miRNAs), piRNAs have more limited bioinformatics resources available. This review collates 39 piRNA specific and non-specific databases and bioinformatics resources, describes and compares their utility and attributes and provides an overview of their place in the field. In addition, we review 33 computational models based upon function: piRNA prediction, transposon element and mRNA-related piRNA prediction, cluster prediction, signature detection, target prediction and disease association. Based on the collection of databases and computational models, we identify trends and potential gaps in tool development. We further analyze the breadth and depth of piRNA data available in public sources, their contribution to specific human diseases, particularly in cancer and neurodegenerative conditions, and highlight a few specific piRNAs that appear to be associated with these diseases. This briefing presents the most recent and comprehensive mapping of piRNA bioinformatics resources including databases, models and tools for disease associations to date. Such a mapping should facilitate and stimulate further research on piRNAs.<\/jats:p>","DOI":"10.1093\/bib\/bbac217","type":"journal-article","created":{"date-parts":[[2022,6,6]],"date-time":"2022-06-06T20:59:47Z","timestamp":1654549187000},"source":"Crossref","is-referenced-by-count":13,"title":["PIWI-interacting RNAs in human diseases: databases and computational models"],"prefix":"10.1093","volume":"23","author":[{"given":"Tianjiao","family":"Zhang","sequence":"first","affiliation":[{"name":"Faculty of Health Sciences, University of Macau , Taipa, Macau S.A.R. 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6644-477X","authenticated-orcid":false,"given":"Liang","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, School of Engineering, Shantou University , Shantou, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rongzhen","family":"Li","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, University of Macau , Taipa, Macau S.A.R. 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ning","family":"Liu","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, University of Macau , Taipa, Macau S.A.R. 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaobing","family":"Huang","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, University of Macau , Taipa, Macau S.A.R. 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4566-9958","authenticated-orcid":false,"given":"Garry","family":"Wong","sequence":"additional","affiliation":[{"name":"Faculty of Health Sciences, University of Macau , Taipa, Macau S.A.R. 999078, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,6,7]]},"reference":[{"key":"2022071906085914300_ref1","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1146\/annurev-biochem-060614-034258","article-title":"PIWI-interacting RNA: its biogenesis and functions","volume":"84","author":"Iwasaki","year":"2015","journal-title":"Annu Rev Biochem"},{"key":"2022071906085914300_ref2","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1146\/annurev-genet-120417-031441","article-title":"piRNA-guided genome defense: from biogenesis to silencing","volume":"52","author":"Czech","year":"2018","journal-title":"Annu Rev Genet"},{"key":"2022071906085914300_ref3","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.bbagrm.2015.09.002","article-title":"piRNA biogenesis in the germline: from transcription of piRNA genomic sources to piRNA 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