{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T19:36:22Z","timestamp":1768592182806,"version":"3.49.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,7,29]],"date-time":"2022-07-29T00:00:00Z","timestamp":1659052800000},"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\/501100010877","name":"Science, Technology and Innovation Commission of Shenzhen Municipality","doi-asserted-by":"publisher","award":["JCYJ20210324141814037"],"award-info":[{"award-number":["JCYJ20210324141814037"]}],"id":[{"id":"10.13039\/501100010877","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Extracellular vesicles (EVs) carrying various small non-coding RNAs (sncRNAs) play a vital roles in cell communication and diseases. Correct quantification of multiple sncRNA biotypes simultaneously in EVs is a challenge due to the short reads (&amp;lt;30\u00a0bp) could be mapped to multiple sncRNA types. To address this question, we developed an optimized reads assignment algorithm (ORAA) to dynamically map multi-mapping reads to the sncRNA type with a higher proportion. We integrated ORAA with reads processing steps into EVAtool Python-package (http:\/\/bioinfo.life.hust.edu.cn\/EVAtool) to quantify sncRNAs, especially for sncRNA-seq from EV samples. EVAtool allows users to specify interested sncRNA types in advanced mode or use default seven sncRNAs (microRNA, small nucleolar RNA, PIWI-interacting RNAs, small nuclear RNA, ribosomal RNA, transfer RNA and Y RNA). To prove the utilities of EVAtool, we quantified the sncRNA expression profiles for 200 samples from cognitive decline and multiple sclerosis. We found that more than 20% of short reads on average were mapped to multiple sncRNA biotypes in multiple sclerosis. In cognitive decline, the proportion of Y RNA is significantly higher than other sncRNA types. EVAtool is a flexible and extensible tool that would benefit to mine potential biomarkers and functional molecules in EVs.<\/jats:p>","DOI":"10.1093\/bib\/bbac310","type":"journal-article","created":{"date-parts":[[2022,7,28]],"date-time":"2022-07-28T20:29:06Z","timestamp":1659040146000},"source":"Crossref","is-referenced-by-count":5,"title":["EVAtool: an optimized reads assignment tool for small ncRNA quantification and its application in extracellular vesicle datasets"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2924-5306","authenticated-orcid":false,"given":"Gui-Yan","family":"Xie","sequence":"first","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3008-3375","authenticated-orcid":false,"given":"Chun-Jie","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5099-7465","authenticated-orcid":false,"given":"An-Yuan","family":"Guo","sequence":"additional","affiliation":[{"name":"Center for Artificial Intelligence Biology, Hubei Bioinformatics & Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology ; Wuhan, 430074, China"},{"name":"Shenzhen Huazhong University of Science and Technology Research Institute , Shenzhen, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,7,29]]},"reference":[{"key":"2022092013214851200_ref1","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/s41556-018-0250-9","article-title":"Specificities of secretion and uptake of exosomes and other extracellular vesicles for cell-to-cell communication","volume":"21","author":"Mathieu","year":"2019","journal-title":"Nat Cell Biol"},{"key":"2022092013214851200_ref2","doi-asserted-by":"crossref","DOI":"10.3402\/jev.v4.27066","article-title":"Biological properties of extracellular vesicles and their physiological functions","volume":"4","author":"Y\u00e1\u00f1ez-M\u00f3","year":"2015","journal-title":"J Extracell Vesicles"},{"key":"2022092013214851200_ref3","doi-asserted-by":"crossref","first-page":"721","DOI":"10.3389\/fimmu.2018.00721","article-title":"Extracellular vesicles: packages sent with complement","volume":"9","author":"Karasu","year":"2018","journal-title":"Front Immunol"},{"key":"2022092013214851200_ref4","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1186\/s13046-019-1317-6","article-title":"Large oncosomes overexpressing integrin alpha-V promote prostate cancer adhesion and invasion via AKT activation","volume":"38","author":"Ciardiello","year":"2019","journal-title":"J Exp Clin Cancer Res"},{"key":"2022092013214851200_ref5","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/s41423-020-0391-1","article-title":"The function and clinical application of extracellular vesicles in innate immune regulation","volume":"17","author":"Zhou","year":"2020","journal-title":"Cell Mol Immunol"},{"key":"2022092013214851200_ref6","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.semcancer.2020.11.022","article-title":"Diverse roles of EV-RNA in cancer progression","volume":"75","author":"Cocks","year":"2021","journal-title":"Semin Cancer Biol"},{"key":"2022092013214851200_ref7","doi-asserted-by":"crossref","first-page":"1985","DOI":"10.1002\/stem.1161","article-title":"Human liver stem cell-derived microvesicles inhibit hepatoma growth in SCID mice by delivering antitumor MicroRNAs","volume":"30","author":"Fonsato","year":"2012","journal-title":"Stem Cells"},{"key":"2022092013214851200_ref8","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1038\/nrc.2017.99","article-title":"Non-coding RNA networks in cancer","volume":"18","author":"Anastasiadou","year":"2018","journal-title":"Nat Rev Cancer"},{"key":"2022092013214851200_ref9","doi-asserted-by":"crossref","first-page":"2901","DOI":"10.1158\/0008-5472.CAN-15-2120","article-title":"miR-146b-5p within BCR-ABL1\u2013positive microvesicles promotes leukemic transformation of hematopoietic cells","volume":"76","author":"Zhang","year":"2016","journal-title":"Cancer Res"},{"key":"2022092013214851200_ref10","doi-asserted-by":"crossref","first-page":"196","DOI":"10.7150\/thno.27550","article-title":"Tumor-derived extracellular vesicles inhibit osteogenesis and exacerbate myeloma bone disease","volume":"9","author":"Zhang","year":"2019","journal-title":"Theranostics"},{"key":"2022092013214851200_ref11","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1038\/nrg3074","article-title":"Non-coding RNAs in human disease","volume":"12","author":"Esteller","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2022092013214851200_ref12","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1016\/j.cca.2011.05.015","article-title":"piRNA, the new non-coding RNA, is aberrantly expressed in human cancer cells","volume":"412","author":"Cheng","year":"2011","journal-title":"Clin Chim Acta"},{"key":"2022092013214851200_ref13","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.semcancer.2014.04.010","article-title":"Extracellular RNA mediates and marks cancer progression","volume":"28","author":"Redzic","year":"2014","journal-title":"Semin Cancer Biol"},{"key":"2022092013214851200_ref14","doi-asserted-by":"crossref","first-page":"D111","DOI":"10.1093\/nar\/gkab668","article-title":"EVAtlas: a comprehensive database for ncRNA expression in human extracellular vesicles","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2022092013214851200_ref15","doi-asserted-by":"crossref","first-page":"4552","DOI":"10.1038\/s41598-020-61495-0","article-title":"COMPSRA: a COMprehensive platform for small RNA-Seq data analysis","volume":"10","author":"Li","year":"2020","journal-title":"Sci Rep"},{"key":"2022092013214851200_ref16","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.cels.2019.03.004","article-title":"exceRpt: a comprehensive analytic platform for extracellular RNA profiling","volume":"8","author":"Rozowsky","year":"2019","journal-title":"Cell Syst"},{"key":"2022092013214851200_ref17","doi-asserted-by":"crossref","first-page":"D216","DOI":"10.1093\/nar\/gkv1188","article-title":"DASHR: database of small human noncoding RNAs","volume":"44","author":"Leung","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2022092013214851200_ref18","doi-asserted-by":"crossref","first-page":"D285","DOI":"10.1093\/nar\/gks1238","article-title":"YM500: a small RNA sequencing (smRNA-seq) database for microRNA research","volume":"41","author":"Cheng","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2022092013214851200_ref19","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1080\/15476286.2014.996465","article-title":"Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing","volume":"11","author":"Gong","year":"2015","journal-title":"RNA Biol"},{"key":"2022092013214851200_ref20","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"2022092013214851200_ref21","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2022092013214851200_ref22","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2022092013214851200_ref23","doi-asserted-by":"crossref","first-page":"323","DOI":"10.3389\/fnagi.2017.00323","article-title":"miRNA in circulating microvesicles as biomarkers for age-related cognitive decline","volume":"9","author":"Rani","year":"2017","journal-title":"Front Aging Neurosci"},{"key":"2022092013214851200_ref24","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1007\/s12035-019-01792-6","article-title":"Serum exosome MicroRNAs predict multiple sclerosis disease activity after Fingolimod treatment","volume":"57","author":"Ebrahimkhani","year":"2020","journal-title":"Mol Neurobiol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/5\/bbac310\/45936850\/bbac310.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/5\/bbac310\/45936850\/bbac310.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,20]],"date-time":"2022-09-20T17:48:45Z","timestamp":1663696125000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac310\/6651306"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,7,29]]},"references-count":24,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2022,9,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac310","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,9]]},"published":{"date-parts":[[2022,7,29]]},"article-number":"bbac310"}}