{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T17:48:42Z","timestamp":1771350522861,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,10,28]],"date-time":"2017-10-28T00:00:00Z","timestamp":1509148800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","award":["1062470"],"award-info":[{"award-number":["1062470"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000925","name":"NHMRC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The branchpoint element is required for the first lariat-forming reaction in splicing. However current catalogues of human branchpoints remain incomplete due to the difficulty in experimentally identifying these splicing elements. To address this limitation, we have developed a machine-learning algorithm\u2014branchpointer\u2014to identify branchpoint elements solely from gene annotations and genomic sequence.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Using branchpointer, we annotate branchpoint elements in 85% of human gene introns with sensitivity (61.8%) and specificity (97.8%). In addition to annotation, branchpointer can evaluate the impact of SNPs on branchpoint architecture to inform functional interpretation of genetic variants. Branchpointer identifies all published deleterious branchpoint mutations annotated in clinical variant databases, and finds thousands of additional clinical and common genetic variants with similar predicted effects. This genome-wide annotation of branchpoints provides a reference for the genetic analysis of splicing, and the interpretation of noncoding variation.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Branchpointer is written and implemented in the statistical programming language R and is freely available under a BSD license as a package through Bioconductor.<\/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\/btx688","type":"journal-article","created":{"date-parts":[[2017,10,27]],"date-time":"2017-10-27T19:11:45Z","timestamp":1509131505000},"page":"920-927","source":"Crossref","is-referenced-by-count":62,"title":["Machine learning annotation of human branchpoints"],"prefix":"10.1093","volume":"34","author":[{"given":"Bethany","family":"Signal","sequence":"first","affiliation":[{"name":"Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW, Australia"},{"name":"St Vincent\u2019s Clinical School, University of New South Wales, Sydney, NSW, Australia"}]},{"given":"Brian S","family":"Gloss","sequence":"additional","affiliation":[{"name":"Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW, Australia"},{"name":"St Vincent\u2019s Clinical School, University of New South Wales, Sydney, NSW, Australia"}]},{"given":"Marcel E","family":"Dinger","sequence":"additional","affiliation":[{"name":"Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW, Australia"},{"name":"St Vincent\u2019s Clinical School, University of New South Wales, Sydney, NSW, Australia"}]},{"given":"Tim R","family":"Mercer","sequence":"additional","affiliation":[{"name":"Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, NSW, Australia"},{"name":"St Vincent\u2019s Clinical School, University of New South Wales, Sydney, NSW, Australia"},{"name":"Altius Institute for Biomedical Sciences, Seattle, WA, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,10,28]]},"reference":[{"key":"2023012712464882600_btx688-B1","doi-asserted-by":"crossref","first-page":"D789","DOI":"10.1093\/nar\/gku1205","article-title":"OMIM.org: Online Mendelian Inheritance in Man (OMIM\u00ae), an online catalog of human genes and genetic disorders","volume":"43","author":"Amberger","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023012712464882600_btx688-B2","doi-asserted-by":"crossref","first-page":"2008","DOI":"10.1101\/gr.133744.111","article-title":"Detecting differential usage of exons from RNA-seq data","volume":"22","author":"Anders","year":"2012","journal-title":"Genome Res"},{"key":"2023012712464882600_btx688-B3","doi-asserted-by":"crossref","first-page":"884","DOI":"10.1101\/gr.185371.114","article-title":"Widespread exon skipping triggers degradation by nuclear RNA surveillance in fission yeast","volume":"25","author":"Bitton","year":"2015","journal-title":"Genome Res"},{"key":"2023012712464882600_btx688-B4","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/ng940","article-title":"Selection for short introns in highly expressed genes","volume":"31","author":"Castillo-Davis","year":"2002","journal-title":"Nat. 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