{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T10:32:37Z","timestamp":1770978757046,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,4,16]],"date-time":"2019-04-16T00:00:00Z","timestamp":1555372800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"The Ultimate Corporate Bike Challenge"},{"DOI":"10.13039\/501100001227","name":"Office of Health and Medical Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001227","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NSW State Government"},{"name":"National Health and Medical Research Council Principal Research Fellowship","award":["1135886"],"award-info":[{"award-number":["1135886"]}]},{"name":"NSW Health Early-Mid Career Fellowship"},{"name":"National Heart Foundation of Australia Future Leader Fellowship","award":["101204"],"award-info":[{"award-number":["101204"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>In silico prediction tools are essential for identifying variants which create or disrupt cis-splicing motifs. However, there are limited options for genome-scale discovery of splice-altering variants.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed Spliceogen, a highly scalable pipeline integrating predictions from some of the individually best performing models for splice motif prediction: MaxEntScan, GeneSplicer, ESRseq and Branchpointer.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Spliceogen is available as a command line tool which accepts VCF\/BED inputs and handles both single nucleotide variants (SNVs) and indels (https:\/\/github.com\/VCCRI\/Spliceogen). SNV databases with prediction scores are also available, covering all possible SNVs at all genomic positions within all Gencode-annotated multi-exon transcripts.<\/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\/btz263","type":"journal-article","created":{"date-parts":[[2019,4,10]],"date-time":"2019-04-10T11:14:22Z","timestamp":1554894862000},"page":"4405-4407","source":"Crossref","is-referenced-by-count":12,"title":["Spliceogen: an integrative, scalable tool for the discovery of splice-altering variants"],"prefix":"10.1093","volume":"35","author":[{"given":"Steven","family":"Monger","sequence":"first","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael","family":"Troup","sequence":"additional","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eddie","family":"Ip","sequence":"additional","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"},{"name":"St Vincent\u2019s Clinical School , UNSW Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sally L","family":"Dunwoodie","sequence":"additional","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"},{"name":"St Vincent\u2019s Clinical School , UNSW Sydney, Australia"},{"name":"School of Biotechnology and Biomolecular Sciences , UNSW Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7084-6736","authenticated-orcid":false,"given":"Eleni","family":"Giannoulatou","sequence":"additional","affiliation":[{"name":"Victor Chang Cardiac Research Institute , Sydney, Australia"},{"name":"St Vincent\u2019s Clinical School , UNSW Sydney, Australia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,4,16]]},"reference":[{"key":"2023062712522267000_btz263-B1","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"},{"key":"2023062712522267000_btz263-B2","doi-asserted-by":"crossref","first-page":"13534","DOI":"10.1093\/nar\/gku1206","article-title":"In silico prediction of splice-altering single nucleotide variants in the human genome","volume":"42","author":"Jian","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023062712522267000_btz263-B3","doi-asserted-by":"crossref","first-page":"1360","DOI":"10.1101\/gr.119628.110","article-title":"Quantitative evaluation of all hexamers as exonic splicing elements","volume":"21","author":"Ke","year":"2011","journal-title":"Genome Res"},{"key":"2023062712522267000_btz263-B4","doi-asserted-by":"crossref","first-page":"11093","DOI":"10.1073\/pnas.1101135108","article-title":"Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes","volume":"108","author":"Lim","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062712522267000_btz263-B5","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1093\/nar\/29.5.1185","article-title":"GeneSplicer: a new computational method for splice site prediction","volume":"29","author":"Pertea","year":"2001","journal-title":"Nucleic Acids Res"},{"key":"2023062712522267000_btz263-B6","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/gim.2015.30","article-title":"Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology","volume":"17","author":"Richards","year":"2015","journal-title":"Genet. Med"},{"key":"2023062712522267000_btz263-B7","article-title":"A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity","author":"Shamsani","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062712522267000_btz263-B8","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1101\/gr.231951.117","article-title":"A comprehensive characterization of cis-acting splicing-associated variants in human cancer","volume":"28","author":"Shiraishi","year":"2018","journal-title":"Genome Res"},{"key":"2023062712522267000_btz263-B9","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1093\/bioinformatics\/btx688","article-title":"Machine learning annotation of human branchpoints","volume":"34","author":"Signal","year":"2018","journal-title":"Bioinformatics"},{"key":"2023062712522267000_btz263-B10","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1101\/gr.202820.115","article-title":"Large-scale analysis of branchpoint usage across species and cell lines","volume":"27","author":"Taggart","year":"2017","journal-title":"Genome Res"},{"key":"2023062712522267000_btz263-B11","doi-asserted-by":"crossref","first-page":"e164.","DOI":"10.1093\/nar\/gkq603","article-title":"ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2023062712522267000_btz263-B12","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1089\/1066527041410418","article-title":"Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals","volume":"11","author":"Yeo","year":"2004","journal-title":"J. Comput. Biol"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz263\/29213253\/btz263.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4405\/50721905\/bioinformatics_35_21_4405.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4405\/50721905\/bioinformatics_35_21_4405.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T12:52:48Z","timestamp":1687870368000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/21\/4405\/5472338"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,4,16]]},"references-count":12,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz263","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,11,1]]},"published":{"date-parts":[[2019,4,16]]}}}