{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,19]],"date-time":"2026-02-19T08:26:06Z","timestamp":1771489566571,"version":"3.50.1"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2021,1,20]],"date-time":"2021-01-20T00:00:00Z","timestamp":1611100800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01 HL141424"],"award-info":[{"award-number":["R01 HL141424"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Institutional Funds"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>MicroRNA (miRNA) precursor arms give rise to multiple isoforms simultaneously called \u2018isomiRs.\u2019 IsomiRs from the same arm typically differ by a few nucleotides at either their 5\u2032 or 3\u2032 termini or both. In humans, the identities and abundances of isomiRs depend on a person\u2019s sex and genetic ancestry as well as on tissue type, tissue state and disease type\/subtype. Moreover, nearly half of the time the most abundant isomiR differs from the miRNA sequence found in public databases. Accurate mining of isomiRs from deep sequencing data is thus important.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed isoMiRmap, a fast, standalone, user-friendly mining tool that identifies and quantifies all isomiRs by directly processing short RNA-seq datasets. IsoMiRmap is a portable \u2018plug-and-play\u2019 tool, requires minimal setup, has modest computing and storage requirements, and can process an RNA-seq dataset with 50 million reads in just a few minutes on an average laptop. IsoMiRmap deterministically and exhaustively reports all isomiRs in a given deep sequencing dataset and quantifies them accurately (no double-counting). IsoMiRmap comprehensively reports all miRNA precursor locations from which an isomiR may be transcribed, tags as \u2018ambiguous\u2019 isomiRs whose sequences exist both inside and outside of the space of known miRNA sequences and reports the public identifiers of common single-nucleotide polymorphisms and documented somatic mutations that may be present in an isomiR. IsoMiRmap also identifies isomiRs with 3\u2019 non-templated post-transcriptional additions. Compared to similar tools, isoMiRmap is the fastest, reports more bona fide isomiRs, and provides the most comprehensive information related to an isomiR\u2019s transcriptional origin.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The codes for isoMiRmap are freely available at https:\/\/cm.jefferson.edu\/isoMiRmap\/ and https:\/\/github.com\/TJU-CMC-Org\/isoMiRmap\/. IsomiR profiles for the datasets of the 1000 Genomes Project, spanning five population groups, and The Cancer Genome Atlas (TCGA), spanning 33 cancer studies, are also available at https:\/\/cm.jefferson.edu\/isoMiRmap\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab016","type":"journal-article","created":{"date-parts":[[2021,1,10]],"date-time":"2021-01-10T20:19:55Z","timestamp":1610309995000},"page":"1828-1838","source":"Crossref","is-referenced-by-count":31,"title":["IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets"],"prefix":"10.1093","volume":"37","author":[{"given":"Phillipe","family":"Loher","sequence":"first","affiliation":[{"name":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"}]},{"given":"Nestoras","family":"Karathanasis","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"}]},{"given":"Eric","family":"Londin","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"}]},{"given":"Paul","family":"F. Bray","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, University of Utah , Salt Lake City, UT 84112, USA"}]},{"given":"Venetia","family":"Pliatsika","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"}]},{"given":"Aristeidis G.","family":"Telonis","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"},{"name":"Department of Human Genetics, Miller School of Medicine, University of Miami , Miami, FL 33136, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1529-8631","authenticated-orcid":false,"given":"Isidore","family":"Rigoutsos","sequence":"additional","affiliation":[{"name":"Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University , Philadelphia, PA 19107, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,1,20]]},"reference":[{"key":"2023051611465941200_btab016-B1","doi-asserted-by":"crossref","first-page":"2773","DOI":"10.1101\/gad.1705308","article-title":"Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs","volume":"22","author":"Babiarz","year":"2008","journal-title":"Genes Dev"},{"key":"2023051611465941200_btab016-B2","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":"2023051611465941200_btab016-B3","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":"2023051611465941200_btab016-B4","doi-asserted-by":"crossref","first-page":"e0143066","DOI":"10.1371\/journal.pone.0143066","article-title":"miRge \u2013 a multiplexed method of processing small RNA-seq data to determine MicroRNA entropy","volume":"10","author":"Baras","year":"2015","journal-title":"PLoS One"},{"key":"2023051611465941200_btab016-B5","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0092-8674(04)00045-5","article-title":"MicroRNAs: genomics, biogenesis, mechanism, and function","volume":"116","author":"Bartel","year":"2004","journal-title":"Cell"},{"key":"2023051611465941200_btab016-B6","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1016\/j.cell.2009.01.002","article-title":"MicroRNAs: target recognition and regulatory functions","volume":"136","author":"Bartel","year":"2009","journal-title":"Cell"},{"key":"2023051611465941200_btab016-B7","doi-asserted-by":"crossref","first-page":"1398","DOI":"10.1101\/gr.106054.110","article-title":"A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness","volume":"20","author":"Burroughs","year":"2010","journal-title":"Genome Res"},{"key":"2023051611465941200_btab016-B8","doi-asserted-by":"crossref","first-page":"857","DOI":"10.1038\/nrc1997","article-title":"MicroRNA signatures in human cancers","volume":"6","author":"Calin","year":"2006","journal-title":"Nat. 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