{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:32:31Z","timestamp":1778635951651,"version":"3.51.4"},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2016,3,10]],"date-time":"2016-03-10T00:00:00Z","timestamp":1457568000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2016,3,10]],"date-time":"2016-03-10T00:00:00Z","timestamp":1457568000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>We examine several of the choices that went into the design of tDRmapper, a recently reported tool for identifying transfer RNA (tRNA) fragments in deep sequencing data, evaluate them in the context of currently available knowledge, and discuss their potential impact on the output that the tool generates.<\/jats:p>","DOI":"10.1186\/s12859-016-0921-0","type":"journal-article","created":{"date-parts":[[2016,3,9]],"date-time":"2016-03-09T16:56:56Z","timestamp":1457542616000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":36,"title":["Consequential considerations when mapping tRNA fragments"],"prefix":"10.1186","volume":"17","author":[{"given":"Aristeidis G.","family":"Telonis","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Phillipe","family":"Loher","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yohei","family":"Kirino","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isidore","family":"Rigoutsos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,3,10]]},"reference":[{"key":"921_CR1","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1186\/s12859-015-0800-0","volume":"16","author":"SR Selitsky","year":"2015","unstructured":"Selitsky SR, Sethupathy P. tDRmapper: challenges and solutions to mapping, naming, and quantifying tRNA-derived RNAs from human small RNA-sequencing data. BMC Bioinformatics. 2015;16:354.","journal-title":"BMC Bioinformatics"},{"issue":"12","key":"921_CR2","doi-asserted-by":"publisher","first-page":"1798","DOI":"10.4161\/rna.27177","volume":"10","author":"J Gebetsberger","year":"2013","unstructured":"Gebetsberger J, Polacek N. Slicing tRNAs to boost functional ncRNA diversity. RNA Biol. 2013;10(12):1798\u2013806.","journal-title":"RNA Biol"},{"key":"921_CR3","first-page":"2","volume":"1","author":"M Shigematsu","year":"2014","unstructured":"Shigematsu M, Honda S, Kirino Y. Tranfer RNA as a source of small functional RNA. J Mol Biol Mol Imaging. 2014;1:2.","journal-title":"J Mol Biol Mol Imaging"},{"issue":"6","key":"921_CR4","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1002\/wrna.96","volume":"2","author":"A Sobala","year":"2011","unstructured":"Sobala A, Hutvagner G. Transfer RNA-derived fragments: origins, processing, and functions. Wiley Interdiscip Rev RNA. 2011;2(6):853\u201362.","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"921_CR5","doi-asserted-by":"publisher","first-page":"344","DOI":"10.3389\/fgene.2014.00344","volume":"5","author":"AG Telonis","year":"2014","unstructured":"Telonis AG, Loher P, Kirino Y, Rigoutsos I. Nuclear and mitochondrial tRNA-lookalikes in the human genome. Front Genet. 2014;5:344.","journal-title":"Front Genet"},{"issue":"28","key":"921_CR6","doi-asserted-by":"publisher","first-page":"24797","DOI":"10.18632\/oncotarget.4695","volume":"6","author":"AG Telonis","year":"2015","unstructured":"Telonis AG, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y, et al. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015;6(28):24797\u2013822.","journal-title":"Oncotarget"},{"issue":"1","key":"921_CR7","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/s12915-014-0078-0","volume":"12","author":"P Kumar","year":"2014","unstructured":"Kumar P, Anaya J, Mudunuri SB, Dutta A. Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Biol. 2014;12(1):78.","journal-title":"BMC Biol"},{"issue":"4","key":"921_CR8","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1080\/15476286.2015.1017239","volume":"12","author":"AG Telonis","year":"2015","unstructured":"Telonis AG, Kirino Y, Rigoutsos I. Mitochondrial tRNA-lookalikes in nuclear chromosomes: could they be functional? RNA Biol. 2015;12(4):375\u201380.","journal-title":"RNA Biol"},{"issue":"17","key":"921_CR9","doi-asserted-by":"publisher","first-page":"6605","DOI":"10.1073\/pnas.0601688103","volume":"103","author":"I Rigoutsos","year":"2006","unstructured":"Rigoutsos I, Huynh T, Miranda K, Tsirigos A, McHardy A, Platt D. Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc Natl Acad Sci U S A. 2006;103(17):6605\u201310.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"921_CR10","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1186\/1471-2164-14-104","volume":"14","author":"F Llorens","year":"2013","unstructured":"Llorens F, Banez-Coronel M, Pantano L, del Rio JA, Ferrer I, Estivill X, et al. A highly expressed miR-101 isomiR is a functional silencing small RNA. BMC Genomics. 2013;14:104.","journal-title":"BMC Genomics"},{"key":"921_CR11","doi-asserted-by":"publisher","first-page":"390","DOI":"10.1186\/1756-0500-6-390","volume":"6","author":"C Vaz","year":"2013","unstructured":"Vaz C, Ahmad HM, Bharti R, Pandey P, Kumar L, Kulshreshtha R, et al. Analysis of the microRNA transcriptome and expression of different isomiRs in human peripheral blood mononuclear cells. BMC Res Notes. 2013;6:390.","journal-title":"BMC Res Notes"},{"issue":"18","key":"921_CR12","doi-asserted-by":"publisher","first-page":"8790","DOI":"10.18632\/oncotarget.2405","volume":"5","author":"P Loher","year":"2014","unstructured":"Loher P, Londin ER, Rigoutsos I. IsomiR expression profiles in human lymphoblastoid cell lines exhibit population and gender dependencies. Oncotarget. 2014;5(18):8790\u2013802.","journal-title":"Oncotarget"},{"issue":"19","key":"921_CR13","doi-asserted-by":"publisher","first-page":"9158","DOI":"10.1093\/nar\/gkv922","volume":"43","author":"AG Telonis","year":"2015","unstructured":"Telonis AG, Loher P, Jing Y, Londin E, Rigoutsos I. Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity. Nucleic Acids Res. 2015;43(19):9158\u201375.","journal-title":"Nucleic Acids Res"},{"key":"921_CR14","doi-asserted-by":"publisher","first-page":"E3816","DOI":"10.1073\/pnas.1510077112","volume":"112","author":"S Honda","year":"2015","unstructured":"Honda S, Loher P, Shigematsu M, Palazzo JP, Suzuki R, Imoto I, Rigoutsos I, Kirino Y. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc Natl Acad Sci USA, 2015;112:E3816\u201325.","journal-title":"Proc Natl Acad Sci USA"},{"key":"921_CR15","doi-asserted-by":"publisher","first-page":"24797","DOI":"10.18632\/oncotarget.4695","volume":"6","author":"AG Telonis","year":"2015","unstructured":"Telonis AG, Loher P, Honda S, Jing Y, Palazzo J, Kirino Y, Rigoutsos I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget, 2015;6:24797\u2013822.","journal-title":"Oncotarget"},{"key":"921_CR16","doi-asserted-by":"crossref","unstructured":"Selitsky SR, Baran-Gale J, Honda M, Yamane D, Masaki T, Fannin EE, Guerra B, Shirasaki T, Shimakami T,  Kaneko S, Lanford RE, Lemon SM, Sethupathy P. Scientific Reports. 2015;5:7675.","DOI":"10.1038\/srep07675"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-0921-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-016-0921-0\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-0921-0","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-016-0921-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T18:19:31Z","timestamp":1706811571000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-016-0921-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,3,10]]},"references-count":16,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["921"],"URL":"https:\/\/doi.org\/10.1186\/s12859-016-0921-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,3,10]]},"assertion":[{"value":"9 December 2015","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 January 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"10 March 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"123"}}