{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T21:36:44Z","timestamp":1775338604677,"version":"3.50.1"},"reference-count":84,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2019,10,10]],"date-time":"2019-10-10T00:00:00Z","timestamp":1570665600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004359","name":"Swedish Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006095","name":"Southern and Eastern Norway Regional Health Authority","doi-asserted-by":"publisher","award":["2014041"],"award-info":[{"award-number":["2014041"]}],"id":[{"id":"10.13039\/501100006095","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006095","name":"Southern and Eastern Norway Regional Health Authority","doi-asserted-by":"publisher","award":["2018014"],"award-info":[{"award-number":["2018014"]}],"id":[{"id":"10.13039\/501100006095","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["18-15-00098"],"award-info":[{"award-number":["18-15-00098"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000837","name":"University of Nottingham","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005416","name":"Norwegian Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100005416","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NASA-Ames"},{"DOI":"10.13039\/100008299","name":"Dartmouth College","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008299","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Small non-coding RNAs have gained substantial attention due to their roles in animal development and human disorders. Among them, microRNAs are special because individual gene sequences are conserved across the animal kingdom. In addition, unique and mechanistically well understood features can clearly distinguish bona fide miRNAs from the myriad other small RNAs generated by cells. However, making this distinction is not a common practice and, thus, not surprisingly, the heterogeneous quality of available miRNA complements has become a major concern in microRNA research. We addressed this by extensively expanding our curated microRNA gene database -\u00a0MirGeneDB -\u00a0to 45 organisms, encompassing a wide phylogenetic swath of animal evolution. By consistently annotating and naming 10,899 microRNA genes in these organisms, we show that previous microRNA annotations contained not only many false positives, but surprisingly lacked &amp;gt;2000 bona fide microRNAs. Indeed, curated microRNA complements of closely related organisms are very similar and can be used to reconstruct ancestral miRNA repertoires. MirGeneDB represents a robust platform for microRNA-based research, providing deeper and more significant insights into the biology and evolution of miRNAs as well as biomedical and biomarker research. MirGeneDB is publicly and freely available at http:\/\/mirgenedb.org\/.<\/jats:p>","DOI":"10.1093\/nar\/gkz885","type":"journal-article","created":{"date-parts":[[2019,10,1]],"date-time":"2019-10-01T15:26:54Z","timestamp":1569943614000},"page":"D132-D141","source":"Crossref","is-referenced-by-count":242,"title":["MirGeneDB 2.0: the metazoan microRNA complement"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0352-3037","authenticated-orcid":false,"given":"Bastian","family":"Fromm","sequence":"first","affiliation":[{"name":"Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden"},{"name":"Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"}]},{"given":"Diana","family":"Domanska","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway"},{"name":"Department of Pathology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway"}]},{"given":"Eirik","family":"H\u00f8ye","sequence":"additional","affiliation":[{"name":"Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"},{"name":"Institute of Clinical Medicine, University of Oslo, Oslo, Norway"}]},{"given":"Vladimir","family":"Ovchinnikov","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Faculty of Health and Life Sciences, University of Nottingham, UK"},{"name":"Department of Human and Animal Genetics, The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation"}]},{"given":"Wenjing","family":"Kang","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden"}]},{"given":"Ernesto","family":"Aparicio-Puerta","sequence":"additional","affiliation":[{"name":"Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain"}]},{"given":"Morten","family":"Johansen","sequence":"additional","affiliation":[{"name":"Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway"}]},{"given":"Kjersti","family":"Flatmark","sequence":"additional","affiliation":[{"name":"Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"},{"name":"Institute of Clinical Medicine, University of Oslo, Oslo, Norway"},{"name":"Department of Gastroenterological Surgery, The Norwegian Radium Hospital, Oslo University Hospital, Nydalen, Oslo, Norway"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5127-5459","authenticated-orcid":false,"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[{"name":"Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway"},{"name":"Department of Cancer Genetics, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital Radiumhospitalet, Oslo, Norway"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9103-1077","authenticated-orcid":false,"given":"Eivind","family":"Hovig","sequence":"additional","affiliation":[{"name":"Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway"},{"name":"Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2248-3114","authenticated-orcid":false,"given":"Michael","family":"Hackenberg","sequence":"additional","affiliation":[{"name":"Department of Genetics, Faculty of Sciences, University of Granada, Granada, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6577-4363","authenticated-orcid":false,"given":"Marc R","family":"Friedl\u00e4nder","sequence":"additional","affiliation":[{"name":"Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden"}]},{"given":"Kevin J","family":"Peterson","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, Dartmouth College, Hanover, NH, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,10,10]]},"reference":[{"key":"2020010521380690100_B1","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/nrm2124","article-title":"Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs","volume":"8","author":"Matera","year":"2007","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2020010521380690100_B2","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1126\/science.286.5441.950","article-title":"A species of small antisense RNA in posttranscriptional gene silencing in plants","volume":"286","author":"Hamilton","year":"1999","journal-title":"Science"},{"key":"2020010521380690100_B3","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1126\/science.1130164","article-title":"Characterization of the piRNA complex from rat testes","volume":"313","author":"Lau","year":"2006","journal-title":"Science"},{"key":"2020010521380690100_B4","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/0092-8674(93)90529-Y","article-title":"The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14","volume":"75","author":"Lee","year":"1993","journal-title":"Cell"},{"key":"2020010521380690100_B5","doi-asserted-by":"crossref","first-page":"853","DOI":"10.1126\/science.1064921","article-title":"Identification of novel genes coding for small expressed RNAs","volume":"294","author":"Lagos-Quintana","year":"2001","journal-title":"Science"},{"key":"2020010521380690100_B6","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1126\/science.1065062","article-title":"An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans","volume":"294","author":"Lau","year":"2001","journal-title":"Science"},{"key":"2020010521380690100_B7","doi-asserted-by":"crossref","first-page":"862","DOI":"10.1126\/science.1065329","article-title":"An extensive class of small RNAs in Caenorhabditis elegans","volume":"294","author":"Lee","year":"2001","journal-title":"Science"},{"key":"2020010521380690100_B8","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1016\/j.cell.2015.02.053","article-title":"Endogenous tRNA-Derived fragments suppress breast cancer progression via YBX1 Displacement","volume":"161","author":"Goodarzi","year":"2015","journal-title":"Cell"},{"key":"2020010521380690100_B9","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1261\/rna.049098.114","article-title":"A deeply conserved, noncanonical miRNA hosted by ribosomal DNA","volume":"21","author":"Chak","year":"2015","journal-title":"RNA"},{"key":"2020010521380690100_B10","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1038\/35002607","article-title":"The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans","volume":"403","author":"Reinhart","year":"2000","journal-title":"Nature"},{"key":"2020010521380690100_B11","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1111\/j.1525-142X.2008.00302.x","article-title":"The deep evolution of metazoan microRNAs","volume":"11","author":"Wheeler","year":"2009","journal-title":"Evol. Dev."},{"key":"2020010521380690100_B12","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1002\/jez.b.21118","article-title":"The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint","volume":"306","author":"Sempere","year":"2006","journal-title":"J. Exp. Zool. B. Mol. Dev. Evol."},{"key":"2020010521380690100_B13","doi-asserted-by":"crossref","first-page":"3339","DOI":"10.1093\/nar\/gks1474","article-title":"Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues","volume":"41","author":"Castellano","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B14","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1101\/gad.1884710","article-title":"Mammalian microRNAs: experimental evaluation of novel and previously annotated genes","volume":"24","author":"Chiang","year":"2010","journal-title":"Genes Dev."},{"key":"2020010521380690100_B15","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/s11103-011-9829-2","article-title":"Conservation and divergence in plant microRNAs","volume":"80","author":"Jones-Rhoades","year":"2012","journal-title":"Plant Mol. Biol."},{"key":"2020010521380690100_B16","doi-asserted-by":"crossref","first-page":"5162","DOI":"10.1038\/s41598-017-05070-0","article-title":"Bias in recent miRBase annotations potentially associated with RNA quality issues","volume":"7","author":"Ludwig","year":"2017","journal-title":"Sci. Rep."},{"key":"2020010521380690100_B17","first-page":"1","volume-title":"MicroRNA or Not MicroRNA? Advances in Bioinformatics and Computational Biology","author":"Langenberger","year":"2011"},{"key":"2020010521380690100_B18","doi-asserted-by":"crossref","first-page":"249","DOI":"10.4161\/rna.19230","article-title":"Are all the miRBase-registered microRNAs true? A structure- and expression-based re-examination in plants","volume":"9","author":"Meng","year":"2012","journal-title":"RNA Biol."},{"key":"2020010521380690100_B19","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1002\/bies.201200055","article-title":"Do miRNAs have a deep evolutionary history","volume":"34","author":"Tarver","year":"2012","journal-title":"Bioessays"},{"key":"2020010521380690100_B20","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.tplants.2013.11.008","article-title":"Evolutionary history of plant microRNAs","volume":"19","author":"Taylor","year":"2014","journal-title":"Trends Plant Sci."},{"key":"2020010521380690100_B21","doi-asserted-by":"crossref","first-page":"25","DOI":"10.3389\/fgene.2011.00025","article-title":"Systematic curation of miRBase annotation using integrated small RNA High-Throughput sequencing data for C. elegans and Drosophila","volume":"2","author":"Wang","year":"2011","journal-title":"Front. Genet."},{"key":"2020010521380690100_B22","first-page":"272","article-title":"Revisiting criteria for plant MicroRNA Annotation in the era of Big Data","volume":"30","author":"Axtell","year":"2018","journal-title":"Plant Cell. Am. Soc Plant Biol."},{"key":"2020010521380690100_B23","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1146\/annurev-genet-120213-092023","article-title":"A uniform system for the annotation of vertebrate microRNA Genes and the evolution of the human microRNAome","volume":"49","author":"Fromm","year":"2015","journal-title":"Annu. Rev. Genet."},{"key":"2020010521380690100_B24","doi-asserted-by":"crossref","first-page":"E1106","DOI":"10.1073\/pnas.1420955112","article-title":"Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs","volume":"112","author":"Londin","year":"2015","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020010521380690100_B25","doi-asserted-by":"crossref","first-page":"8713","DOI":"10.1093\/nar\/gkv871","article-title":"A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm","volume":"43","author":"Jha","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B26","doi-asserted-by":"crossref","first-page":"D862","DOI":"10.1093\/nar\/gku1156","article-title":"YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research","volume":"43","author":"Cheng","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B27","doi-asserted-by":"crossref","first-page":"3353","DOI":"10.1093\/nar\/gkz097","article-title":"An estimate of the total number of true human miRNAs","volume":"47","author":"Alles","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B28","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/j.cell.2012.04.005","article-title":"Roles for microRNAs in conferring robustness to biological processes","volume":"149","author":"Ebert","year":"2012","journal-title":"Cell"},{"key":"2020010521380690100_B29","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1016\/j.celrep.2015.12.031","article-title":"Elucidating MicroRNA regulatory networks using transcriptional, Post-transcriptional, and histone modification measurements","volume":"14","author":"Gosline","year":"2016","journal-title":"Cell Rep."},{"key":"2020010521380690100_B30","doi-asserted-by":"crossref","first-page":"2548","DOI":"10.1242\/dev.146613","article-title":"A framework for understanding the roles of miRNAs in animal development","volume":"144","author":"Alberti","year":"2017","journal-title":"Development"},{"key":"2020010521380690100_B31","doi-asserted-by":"crossref","first-page":"769","DOI":"10.1038\/nature03315","article-title":"Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs","volume":"433","author":"Lim","year":"2005","journal-title":"Nature"},{"key":"2020010521380690100_B32","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nature03702","article-title":"MicroRNA expression profiles classify human cancers","volume":"435","author":"Lu","year":"2005","journal-title":"Nature"},{"key":"2020010521380690100_B33","doi-asserted-by":"crossref","first-page":"2257","DOI":"10.1073\/pnas.0510565103","article-title":"A microRNA expression signature of human solid tumors defines cancer gene targets","volume":"103","author":"Volinia","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020010521380690100_B34","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1261\/rna.2183803","article-title":"A uniform system for microRNA annotation","volume":"9","author":"Ambros","year":"2003","journal-title":"RNA"},{"key":"2020010521380690100_B35","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1038\/s42003-017-0001-7","article-title":"Non-coding RNA fragments account for the majority of annotated piRNAs expressed in somatic non-gonadal tissues","volume":"1","author":"Tosar","year":"2018","journal-title":"Commun. Biol."},{"key":"2020010521380690100_B36","first-page":"1622","article-title":"MiR-1182 inhibited metastasis and proliferation of ovarian cancer by targeting hTERT","volume":"22","author":"Hou","year":"2018","journal-title":"Eur. Rev. Med. Pharmacol. Sci."},{"key":"2020010521380690100_B37","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.canlet.2015.01.044","article-title":"miR-1182 attenuates gastric cancer proliferation and metastasis by targeting the open reading frame of hTERT","volume":"360","author":"Zhang","year":"2015","journal-title":"Cancer Lett."},{"key":"2020010521380690100_B38","doi-asserted-by":"crossref","first-page":"445","DOI":"10.1016\/j.bbrc.2016.01.014","article-title":"miR-1182 inhibits growth and mediates the chemosensitivity of bladder cancer by targeting hTERT","volume":"470","author":"Zhou","year":"2016","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"2020010521380690100_B39","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":"2020010521380690100_B40","doi-asserted-by":"crossref","first-page":"D160","DOI":"10.1093\/nar\/gkx851","article-title":"miRCarta: a central repository for collecting miRNA candidates","volume":"46","author":"Backes","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B41","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1093\/gbe\/evy096","article-title":"Well-annotated microRNAomes do not evidence pervasive miRNA loss","volume":"10","author":"Tarver","year":"2018","journal-title":"Genome Biol. Evol."},{"key":"2020010521380690100_B42","doi-asserted-by":"crossref","first-page":"9655","DOI":"10.1038\/s41598-017-10189-1","article-title":"Analysis of the miR-34 family functions in breast cancer reveals annotation error of miR-34b","volume":"7","author":"Engkvist","year":"2017","journal-title":"Sci Rep."},{"key":"2020010521380690100_B43","doi-asserted-by":"crossref","first-page":"1506","DOI":"10.1093\/jn\/nxy144","article-title":"Human and Cow Have Identical miR-21-5p and miR-30a-5p Sequences, Which Are Likely Unsuited to Study Dietary Uptake from Cow Milk","volume":"148","author":"Fromm","year":"2018","journal-title":"The Journal of Nutrition"},{"key":"2020010521380690100_B44","first-page":"bau080","article-title":"miRBase Tracker: keeping track of microRNA annotation changes","volume":"2014","author":"Van\u00a0Peer","year":"2014","journal-title":"Database"},{"key":"2020010521380690100_B45","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.1080\/15476286.2019.1637680","article-title":"miRBaseMiner, a tool for investigating miRBase content","volume":"16","author":"Zhong","year":"2019","journal-title":"RNA Biol."},{"key":"2020010521380690100_B46","doi-asserted-by":"crossref","first-page":"e42390","DOI":"10.1371\/journal.pone.0042390","article-title":"miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets","volume":"7","author":"Lu","year":"2012","journal-title":"PLoS One"},{"key":"2020010521380690100_B47","doi-asserted-by":"crossref","first-page":"W487","DOI":"10.1093\/nar\/gkv381","article-title":"miRiadne: a web tool for consistent integration of miRNA nomenclature","volume":"43","author":"Bonnal","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B48","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1186\/s12859-018-2531-5","article-title":"miRBaseConverter: an R\/Bioconductor package for converting and retrieving miRNA name, accession, sequence and family information in different versions of miRBase","volume":"19","author":"Xu","year":"2018","journal-title":"BMC Bioinformatics. BioMed Central"},{"key":"2020010521380690100_B49","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1093\/bioinformatics\/btw660","article-title":"miRNAmeConverter: an R\/bioconductor package for translating mature miRNA names to different miRBase versions","volume":"33","author":"Haunsberger","year":"2017","journal-title":"Bioinformatics"},{"key":"2020010521380690100_B50","first-page":"65","article-title":"MicroRNA nomenclature and the need for a revised naming prescription","volume":"15","author":"Budak","year":"2016","journal-title":"Brief. Funct. Genomics"},{"key":"2020010521380690100_B51","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1038\/nature07415","article-title":"Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals","volume":"455","author":"Grimson","year":"2008","journal-title":"Nature"},{"key":"2020010521380690100_B52","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nature09616","article-title":"Formation, regulation and evolution of Caenorhabditis elegans 3\u2032UTRs","volume":"469","author":"Jan","year":"2011","journal-title":"Nature"},{"key":"2020010521380690100_B53","doi-asserted-by":"crossref","first-page":"3407","DOI":"10.1101\/gad.1476406","article-title":"A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana","volume":"20","author":"Rajagopalan","year":"2006","journal-title":"Genes Dev."},{"key":"2020010521380690100_B54","doi-asserted-by":"crossref","first-page":"1193","DOI":"10.1016\/j.cell.2006.10.040","article-title":"Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans","volume":"127","author":"Ruby","year":"2006","journal-title":"Cell"},{"key":"2020010521380690100_B55","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1101\/gr.6597907","article-title":"Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs","volume":"17","author":"Ruby","year":"2007","journal-title":"Genome Res."},{"key":"2020010521380690100_B56","doi-asserted-by":"crossref","first-page":"W530","DOI":"10.1093\/nar\/gkz415","article-title":"sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression","volume":"47","author":"Aparicio-Puerta","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B57","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/s13059-018-1588-9","article-title":"miRTrace reveals the organismal origins of microRNA sequencing data","volume":"19","author":"Kang","year":"2018","journal-title":"Genome Biol. BioMed Central"},{"key":"2020010521380690100_B58","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1038\/nbt.3947","article-title":"An integrated expression atlas of miRNAs and their promoters in human and mouse","volume":"35","author":"de\u00a0Rie","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"2020010521380690100_B59","doi-asserted-by":"crossref","first-page":"E1881","DOI":"10.1073\/pnas.1602532113","article-title":"Re-evaluation of the roles of DROSHA, Export in 5, and DICER in microRNA biogenesis","volume":"113","author":"Kim","year":"2016","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020010521380690100_B60","doi-asserted-by":"crossref","first-page":"1769","DOI":"10.1101\/gr.222067.117","article-title":"Toward the human cellular microRNAome","volume":"27","author":"McCall","year":"2017","journal-title":"Genome Res."},{"key":"2020010521380690100_B61","doi-asserted-by":"crossref","first-page":"9290","DOI":"10.1093\/nar\/gkx706","article-title":"A comprehensive, cell specific microRNA catalogue of human peripheral blood","volume":"45","author":"Juzenas","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B62","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.tig.2017.12.015","article-title":"Big strides in cellular MicroRNA Expression","volume":"34","author":"Halushka","year":"2018","journal-title":"Trends Genet. Elsevier Curr. Trends"},{"key":"2020010521380690100_B63","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btz675","article-title":"Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API","author":"Desvignes","year":"2019","journal-title":"Bioinformatics"},{"key":"2020010521380690100_B64","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1016\/j.tig.2012.07.005","article-title":"IsomiRs\u2013the overlooked repertoire in the dynamic microRNAome","volume":"28","author":"Neilsen","year":"2012","journal-title":"Trends Genet."},{"key":"2020010521380690100_B65","doi-asserted-by":"crossref","first-page":"1801","DOI":"10.15252\/embj.201590931","article-title":"TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms","volume":"34","author":"Kim","year":"2015","journal-title":"EMBO J."},{"key":"2020010521380690100_B66","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1016\/j.cell.2012.09.022","article-title":"Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs","volume":"151","author":"Heo","year":"2012","journal-title":"Cell"},{"key":"2020010521380690100_B67","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/j.molcel.2015.08.015","article-title":"The menu of features that define primary MicroRNAs and Enable de novo design of MicroRNA Genes","volume":"60","author":"Fang","year":"2015","journal-title":"Mol. Cell"},{"key":"2020010521380690100_B68","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":"2020010521380690100_B69","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1016\/j.cell.2013.01.031","article-title":"Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing","volume":"152","author":"Auyeung","year":"2013","journal-title":"Cell"},{"key":"2020010521380690100_B70","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1261\/rna.048876.114","article-title":"Divergent target recognition by coexpressed 5\u2032-isomiRs of miR-142-3p and selective viral mimicry","volume":"21","author":"Manzano","year":"2015","journal-title":"RNA"},{"key":"2020010521380690100_B71","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1101\/gad.1615208","article-title":"Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci","volume":"22","author":"Tyler","year":"2008","journal-title":"Genes Dev."},{"key":"2020010521380690100_B72","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/nature06642","article-title":"A skin microRNA promotes differentiation by repressing \u201cstemness\u201d","volume":"452","author":"Yi","year":"2008","journal-title":"Nature"},{"key":"2020010521380690100_B73","doi-asserted-by":"crossref","first-page":"D68","DOI":"10.1093\/nar\/gkt1181","article-title":"miRBase: annotating high confidence microRNAs using deep sequencing data","volume":"42","author":"Kozomara","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B74","doi-asserted-by":"crossref","first-page":"2369","DOI":"10.1093\/molbev\/mst133","article-title":"miRNAs: small genes with big potential in metazoan phylogenetics","volume":"30","author":"Tarver","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"2020010521380690100_B75","doi-asserted-by":"crossref","first-page":"e53","DOI":"10.1093\/nar\/gkv1335","article-title":"Prioritizing and selecting likely novel miRNAs from NGS data","volume":"44","author":"Backes","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B76","doi-asserted-by":"crossref","first-page":"E3659","DOI":"10.1073\/pnas.1407207111","article-title":"A critical appraisal of the use of microRNA data in phylogenetics","volume":"111","author":"Thomson","year":"2014","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2020010521380690100_B77","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1089\/10665270050081478","article-title":"A greedy algorithm for aligning DNA sequences","volume":"7","author":"Zhang","year":"2000","journal-title":"J. Comput. Biol."},{"key":"2020010521380690100_B78","doi-asserted-by":"crossref","first-page":"D140","DOI":"10.1093\/nar\/gkj112","article-title":"miRBase: microRNA sequences, targets and gene nomenclature","volume":"34","author":"Griffiths-Jones","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2020010521380690100_B79","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/35040556","article-title":"Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA","volume":"408","author":"Pasquinelli","year":"2000","journal-title":"Nature"},{"key":"2020010521380690100_B80","first-page":"372","article-title":"Expression of the 22 nucleotide let-7 heterochronic RNA throughout the Metazoa: a role in life history evolution? Evol Dev","volume":"5","author":"Pasquinelli","year":"2003","journal-title":"Wiley Online Library"},{"key":"2020010521380690100_B81","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1038\/nature04336","article-title":"Tunicates and not cephalochordates are the closest living relatives of vertebrates","volume":"439","author":"Delsuc","year":"2006","journal-title":"Nature"},{"key":"2020010521380690100_B82","doi-asserted-by":"crossref","first-page":"231","DOI":"10.4161\/rna.18974","article-title":"Evolution of the let-7 microRNA Family","volume":"9","author":"Hertel","year":"2012","journal-title":"RNA Biol."},{"key":"2020010521380690100_B83","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1038\/ng865","article-title":"Micro RNAs are complementary to 3\u2032 UTR sequence motifs that mediate negative post-transcriptional regulation","volume":"30","author":"Lai","year":"2002","journal-title":"Nat. Genet."},{"key":"2020010521380690100_B84","doi-asserted-by":"crossref","first-page":"787","DOI":"10.1016\/S0092-8674(03)01018-3","article-title":"Prediction of mammalian microRNA targets","volume":"115","author":"Lewis","year":"2003","journal-title":"Cell"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D132\/31697416\/gkz885.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D132\/31697416\/gkz885.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,21]],"date-time":"2023-09-21T00:30:57Z","timestamp":1695256257000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D132\/5584683"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,10,10]]},"references-count":84,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2019,10,10]]},"published-print":{"date-parts":[[2020,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz885","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/258749","asserted-by":"object"}]},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,1,8]]},"published":{"date-parts":[[2019,10,10]]}}}