{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T06:21:42Z","timestamp":1771914102207,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2017,6,26]],"date-time":"2017-06-26T00:00:00Z","timestamp":1498435200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008890","name":"University of Dundee","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008890","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/K006568\/1"],"award-info":[{"award-number":["BB\/K006568\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000268","name":"BBSRC","doi-asserted-by":"publisher","award":["BB\/N022807\/1"],"award-info":[{"award-number":["BB\/N022807\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>An alternative splicing isoform switch is where a pair of transcript isoforms reverse their relative expression abundances in response to external or internal stimuli. Although computational methods are available to study differential alternative splicing, few tools for detection of isoform switches exist and these are based on pairwise comparisons. Here, we provide the TSIS R package, which is the first tool for detecting significant transcript isoform switches in time-series data. The main steps of TSIS are to search for the isoform switch points in the time-series, characterize the switches and filter the results with user input parameters. All the functions are integrated into a Shiny App for ease of implementation of the analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The TSIS package is available on GitHub: https:\/\/github.com\/wyguo\/TSIS.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx411","type":"journal-article","created":{"date-parts":[[2017,6,22]],"date-time":"2017-06-22T19:40:10Z","timestamp":1498160410000},"page":"3308-3310","source":"Crossref","is-referenced-by-count":41,"title":["TSIS: an R package to infer alternative splicing isoform switches for time-series data"],"prefix":"10.1093","volume":"33","author":[{"given":"Wenbin","family":"Guo","sequence":"first","affiliation":[{"name":"Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK"},{"name":"Plant Sciences Division, School of Life Sciences, University of Dundee, Invergowrie, Dundee, Scotland, UK"}]},{"given":"Cristiane P G","family":"Calixto","sequence":"additional","affiliation":[{"name":"Plant Sciences Division, School of Life Sciences, University of Dundee, Invergowrie, Dundee, Scotland, UK"}]},{"given":"John W S","family":"Brown","sequence":"additional","affiliation":[{"name":"Plant Sciences Division, School of Life Sciences, University of Dundee, Invergowrie, Dundee, Scotland, UK"},{"name":"Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK"}]},{"given":"Runxuan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, UK"}]}],"member":"286","published-online":{"date-parts":[[2017,6,26]]},"reference":[{"key":"2023020207511942700_btx411-B1","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.molp.2014.10.011","article-title":"Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis","volume":"8","author":"Filichkin","year":"2015","journal-title":"Mol. Plant"},{"key":"2023020207511942700_btx411-B2","article-title":"Identification, annotation and visualisation of extreme changes in splicing from RNA-seq experiments with SwitchSeq","author":"Gonz\u00e0lez-Porta","year":"2014","journal-title":"bioRxiv"},{"key":"2023020207511942700_btx411-B3","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1105\/tpc.111.093948","article-title":"Alternative splicing mediates responses of the Arabidopsis circadian clock to temperature changes","volume":"24","author":"James","year":"2012","journal-title":"Plant Cell"},{"key":"2023020207511942700_btx411-B4","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.4161\/psb.21491","article-title":"Thermoplasticity in the plant circadian clock: how plants tell the time-perature","volume":"7","author":"James","year":"2012","journal-title":"Plant. Signal. Behav"},{"key":"2023020207511942700_btx411-B5","doi-asserted-by":"crossref","first-page":"1345","DOI":"10.1093\/nar\/gku1392","article-title":"Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer","volume":"43","author":"Sebestyen","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020207511942700_btx411-B6","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/1471-2105-15-81","article-title":"spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data","volume":"15","author":"Vitting-Seerup","year":"2014","journal-title":"BMC Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/20\/3308\/49042821\/bioinformatics_33_20_3308.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/20\/3308\/49042821\/bioinformatics_33_20_3308.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T07:56:35Z","timestamp":1675324595000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/20\/3308\/3892390"}},"subtitle":[],"editor":[{"given":"Ziv","family":"Bar-Joseph","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,6,26]]},"references-count":6,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2017,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx411","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,10,15]]},"published":{"date-parts":[[2017,6,26]]}}}