{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:30:01Z","timestamp":1783488601605,"version":"3.55.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,4,24]],"date-time":"2023-04-24T00:00:00Z","timestamp":1682294400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ELIXIR-GR: The Greek Research Infrastructure for Data Management and Analysis in Life Sciences","award":["MIS-5002780"],"award-info":[{"award-number":["MIS-5002780"]}]},{"name":"Competitiveness, Entrepreneurship and Innovation","award":["NSRF 2014\u20132020"],"award-info":[{"award-number":["NSRF 2014\u20132020"]}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013209","name":"Hellenic Foundation for Research and Innovation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013209","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>DIANA-microT-CDS is a state-of-the-art miRNA target prediction algorithm catering the scientific community since 2009. It is one of the first algorithms to predict miRNA binding sites in both the 3\u2032 Untranslated Region (3\u2032-UTR) and the coding sequence (CDS) of transcripts, with increased performance. Its current version, DIANA-microT 2023 (www.microrna.gr\/microt_webserver\/), brings forward a significantly updated set of interactions. DIANA-microT-CDS has been executed utilizing annotation information from Ensembl v102, miRBase 22.1 and, for the first time, MirGeneDB 2.1, yielding more than 83 million interactions in human, mouse, rat, chicken, fly and worm species. Additionally, this version delivers predicted interactions of miRNAs encoded from 20 viruses against host transcripts from human, mouse and chicken species. Numerous resources have been interconnected into DIANA-microT, including DIANA-TarBase, plasmiR, HMDD, UCSC, dbSNP, ClinVar, as well as miRNA\/gene abundance values for 369 distinct cell-lines\/tissues. The server interface has been redesigned allowing users to use smart filtering options, identify abundance patterns of interest, pinpoint known SNPs residing on binding sites and obtain miRNA-disease information. The contents of DIANA-microT webserver are freely accessible and can also be locally downloaded without any login requirements.<\/jats:p>","DOI":"10.1093\/nar\/gkad283","type":"journal-article","created":{"date-parts":[[2023,4,24]],"date-time":"2023-04-24T18:10:28Z","timestamp":1682359828000},"page":"W148-W153","source":"Crossref","is-referenced-by-count":107,"title":["DIANA-microT 2023: including predicted targets of virally encoded miRNAs"],"prefix":"10.1093","volume":"51","author":[{"given":"Spyros","family":"Tastsoglou","sequence":"first","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly , Lamia \u00a035131, Greece"},{"name":"Hellenic Pasteur Institute , Athens \u00a011521, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Athanasios","family":"Alexiou","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly , Lamia \u00a035131, Greece"},{"name":"Hellenic Pasteur Institute , Athens \u00a011521, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimitra","family":"Karagkouni","sequence":"additional","affiliation":[{"name":"Department of Pathology, Beth Israel Deaconess Medical Center , Boston, MA, USA"},{"name":"Harvard Medical School , Boston, MA, USA"},{"name":"Broad Institute of MIT and Harvard , Cambridge, MA, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giorgos","family":"Skoufos","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly , Lamia \u00a035131, Greece"},{"name":"Hellenic Pasteur Institute , Athens \u00a011521, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elissavet","family":"Zacharopoulou","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly , Lamia \u00a035131, Greece"},{"name":"Hellenic Pasteur Institute , Athens \u00a011521, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1414-5668","authenticated-orcid":false,"given":"Artemis G","family":"Hatzigeorgiou","sequence":"additional","affiliation":[{"name":"DIANA-Lab, Department of Computer Science and Biomedical Informatics, Univ. of Thessaly , Lamia \u00a035131, Greece"},{"name":"Hellenic Pasteur Institute , Athens \u00a011521, Greece"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,4,24]]},"reference":[{"key":"2023070504594997200_B1","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.cell.2018.03.006","article-title":"Metazoan micrornas","volume":"173","author":"Bartel","year":"2018","journal-title":"Cell"},{"key":"2023070504594997200_B2","doi-asserted-by":"crossref","first-page":"1124","DOI":"10.1038\/nature07299","article-title":"MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation","volume":"455","author":"Tay","year":"2008","journal-title":"Nature"},{"key":"2023070504594997200_B3","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1016\/j.cell.2011.09.028","article-title":"A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA","volume":"147","author":"Cesana","year":"2011","journal-title":"Cell"},{"key":"2023070504594997200_B4","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/978-981-13-1426-1_6","article-title":"Circular RNAs act as miRNA sponges","volume":"1087","author":"Panda","year":"2018","journal-title":"Adv. Exp. Med. Biol."},{"key":"2023070504594997200_B5","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1126\/science.1096781","article-title":"Identification of virus-encoded microRNAs","volume":"304","author":"Pfeffer","year":"2004","journal-title":"Science"},{"key":"2023070504594997200_B6","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1038\/nmeth746","article-title":"Identification of microRNAs of the herpesvirus family","volume":"2","author":"Pfeffer","year":"2005","journal-title":"Nat. Methods"},{"key":"2023070504594997200_B7","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1261\/rna.2326106","article-title":"A combined computational and microarray-based approach identifies novel microRNAs encoded by human gamma-herpesviruses","volume":"12","author":"Grundhoff","year":"2006","journal-title":"RNA"},{"key":"2023070504594997200_B8","doi-asserted-by":"crossref","first-page":"3333","DOI":"10.1128\/JVI.01689-08","article-title":"Identification of novel Epstein-Barr virus microRNA genes from nasopharyngeal carcinomas","volume":"83","author":"Zhu","year":"2009","journal-title":"J. Virol."},{"key":"2023070504594997200_B9","doi-asserted-by":"crossref","first-page":"D155","DOI":"10.1093\/nar\/gky1141","article-title":"miRBase: from microRNA sequences to function","volume":"47","author":"Kozomara","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B10","doi-asserted-by":"crossref","first-page":"3079","DOI":"10.3389\/fimmu.2019.03079","article-title":"The interplay between viral-derived miRNAs and host immunity during infection","volume":"10","author":"Mishra","year":"2020","journal-title":"Front. Immunol."},{"key":"2023070504594997200_B11","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1016\/j.chom.2008.05.002","article-title":"Viral and cellular microRNAs as determinants of viral pathogenesis and immunity","volume":"3","author":"Gottwein","year":"2008","journal-title":"Cell Host Microbe"},{"key":"2023070504594997200_B12","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/j.chom.2010.03.008","article-title":"Systematic analysis of viral and cellular microRNA targets in cells latently infected with human \u03b3-herpesviruses by RISC immunoprecipitation assay","volume":"7","author":"D\u00f6lken","year":"2010","journal-title":"Cell Host Microbe"},{"key":"2023070504594997200_B13","doi-asserted-by":"crossref","first-page":"D239","DOI":"10.1093\/nar\/gkx1141","article-title":"DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA\u2013gene interactions","volume":"46","author":"Karagkouni","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B14","doi-asserted-by":"crossref","first-page":"D222","DOI":"10.1093\/nar\/gkab1079","article-title":"miRTarBase update 2022: an informative resource for experimentally validated miRNA\u2013target interactions","volume":"50","author":"Huang","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B15","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gkab1101","article-title":"MirGeneDB 2.1: toward a complete sampling of all major animal phyla","volume":"50","author":"Fromm","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B16","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/nmeth954","article-title":"A guide through present computational approaches for the identification of mammalian microRNA targets","volume":"3","author":"Sethupathy","year":"2006","journal-title":"Nat. Methods"},{"key":"2023070504594997200_B17","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1101\/gad.1184704","article-title":"A combined computational-experimental approach predicts human microRNA targets","volume":"18","author":"Kiriakidou","year":"2004","journal-title":"Genes Dev."},{"key":"2023070504594997200_B18","doi-asserted-by":"crossref","first-page":"e05005","DOI":"10.7554\/eLife.05005","article-title":"Predicting effective microRNA target sites in mammalian mRNAs","volume":"4","author":"Agarwal","year":"2015","journal-title":"Elife"},{"key":"2023070504594997200_B19","doi-asserted-by":"crossref","first-page":"eaav1741","DOI":"10.1126\/science.aav1741","article-title":"The biochemical basis of microRNA targeting efficacy","volume":"366","author":"McGeary","year":"2019","journal-title":"Science"},{"key":"2023070504594997200_B20","doi-asserted-by":"crossref","first-page":"906","DOI":"10.1101\/gr.166702.113","article-title":"Widespread context dependency of microRNA-mediated regulation","volume":"24","author":"Erhard","year":"2014","journal-title":"Genome Res."},{"key":"2023070504594997200_B21","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1093\/bioinformatics\/bts043","article-title":"Functional microRNA targets in protein coding sequences","volume":"28","author":"Reczko","year":"2012","journal-title":"Bioinformatics"},{"key":"2023070504594997200_B22","doi-asserted-by":"crossref","first-page":"W169","DOI":"10.1093\/nar\/gkt393","article-title":"DIANA-microT web server v5. 0: service integration into miRNA functional analysis workflows","volume":"41","author":"Paraskevopoulou","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B23","doi-asserted-by":"crossref","first-page":"W460","DOI":"10.1093\/nar\/gkv403","article-title":"DIANA-miRPath v3. 0: deciphering microRNA function with experimental support","volume":"43","author":"Vlachos","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B24","doi-asserted-by":"crossref","first-page":"W128","DOI":"10.1093\/nar\/gkw455","article-title":"DIANA-mirExTra v2. 0: uncovering microRNAs and transcription factors with crucial roles in NGS expression data","volume":"44","author":"Vlachos","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B25","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B26","doi-asserted-by":"crossref","first-page":"D835","DOI":"10.1093\/nar\/gkz972","article-title":"ClinVar: improvements to accessing data","volume":"48","author":"Landrum","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B27","doi-asserted-by":"crossref","first-page":"D1055","DOI":"10.1093\/nar\/gkab733","article-title":"DIANA-miTED: a microRNA tissue expression database","volume":"50","author":"Kavakiotis","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B28","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1126\/science.1262110","article-title":"The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans","volume":"348","author":"Consortium","year":"2015","journal-title":"Science"},{"key":"2023070504594997200_B29","first-page":"A68","article-title":"The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge","volume":"19","author":"Tomczak","year":"2015","journal-title":"Contemp Oncol"},{"key":"2023070504594997200_B30","doi-asserted-by":"crossref","first-page":"170185","DOI":"10.1038\/sdata.2017.185","article-title":"An RNA-seq atlas of gene expression in mouse and rat normal tissues","volume":"4","author":"S\u00f6llner","year":"2017","journal-title":"Sci Data"},{"key":"2023070504594997200_B31","doi-asserted-by":"crossref","first-page":"D1013","DOI":"10.1093\/nar\/gky1010","article-title":"HMDD v3. 0: a database for experimentally supported human microRNA\u2013disease associations","volume":"47","author":"Huang","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B32","doi-asserted-by":"crossref","first-page":"3680","DOI":"10.3390\/cancers13153680","article-title":"Plasmir: a manual collection of circulating micrornas of prognostic and diagnostic value","volume":"13","author":"Tastsoglou","year":"2021","journal-title":"Cancers"},{"key":"2023070504594997200_B33","doi-asserted-by":"crossref","first-page":"D884","DOI":"10.1093\/nar\/gkaa942","article-title":"Ensembl 2021","volume":"49","author":"Howe","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B34","doi-asserted-by":"crossref","first-page":"D1115","DOI":"10.1093\/nar\/gkab959","article-title":"The UCSC genome browser database: 2022 update","volume":"50","author":"Lee","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B35","doi-asserted-by":"crossref","first-page":"W135","DOI":"10.1093\/nar\/gkh449","article-title":"S fold web server for statistical folding and rational design of nucleic acids","volume":"32","author":"Ding","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023070504594997200_B36","doi-asserted-by":"crossref","first-page":"2204","DOI":"10.1093\/bioinformatics\/btq351","article-title":"BigWig and BigBed: enabling browsing of large distributed datasets","volume":"26","author":"Kent","year":"2010","journal-title":"Bioinformatics"},{"key":"2023070504594997200_B37","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1093\/bib\/bbs038","article-title":"The UCSC genome browser and associated tools","volume":"14","author":"Kuhn","year":"2013","journal-title":"Briefings Bioinf."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W148\/50736663\/gkad283.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/51\/W1\/W148\/50736663\/gkad283.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,5]],"date-time":"2023-07-05T10:17:14Z","timestamp":1688552234000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/51\/W1\/W148\/7137452"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,4,24]]},"references-count":37,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2023,4,24]]},"published-print":{"date-parts":[[2023,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkad283","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,5]]},"published":{"date-parts":[[2023,4,24]]}}}