{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T03:52:26Z","timestamp":1773719546311,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2017,9,14]],"date-time":"2017-09-14T00:00:00Z","timestamp":1505347200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>As sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major expressed isoform.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The package is freely available under the LGPL license from the Bioconductor web site.<\/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\/btx578","type":"journal-article","created":{"date-parts":[[2017,9,13]],"date-time":"2017-09-13T07:11:39Z","timestamp":1505286699000},"page":"524-526","source":"Crossref","is-referenced-by-count":16,"title":["Identification and visualization of differential isoform expression in RNA-seq time series"],"prefix":"10.1093","volume":"34","author":[{"given":"Mar\u00eda Jos\u00e9","family":"Nueda","sequence":"first","affiliation":[{"name":"Mathematics Department, University of Alicante, Alicante, Spain"}]},{"given":"Jordi","family":"Martorell-Marugan","sequence":"additional","affiliation":[{"name":"Genomics of Gene Expression Laboratory, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe, Valencia, Spain"}]},{"given":"Cristina","family":"Mart\u00ed","sequence":"additional","affiliation":[{"name":"Genomics of Gene Expression Laboratory, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe, Valencia, Spain"}]},{"given":"Sonia","family":"Tarazona","sequence":"additional","affiliation":[{"name":"Genomics of Gene Expression Laboratory, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe, Valencia, Spain"},{"name":"Applied Statistics, Operational Research and Quality Department, Politechnic University of Valencia, Valencia, Spain"}]},{"given":"Ana","family":"Conesa","sequence":"additional","affiliation":[{"name":"Genomics of Gene Expression Laboratory, Centro de Investigaci\u00f3n Pr\u00edncipe Felipe, Valencia, Spain"},{"name":"Microbiology and Cell Science Department, Institute for Food and Agricultural Research, University of Florida, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,9,14]]},"reference":[{"key":"2023012712315900200_btx578-B1","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1186\/s12864-017-3656-z","article-title":"Herboxidiene triggers splicing repression and abiotic stress responses in plants","volume":"18","author":"AlShareef","year":"2017","journal-title":"BMC Genomics"},{"key":"2023012712315900200_btx578-B2","doi-asserted-by":"crossref","first-page":"2965","DOI":"10.1093\/bioinformatics\/btw364","article-title":"Statistical modeling of isoform splicing dynamics from RNA-seq time series data","volume":"32","author":"Huang","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012712315900200_btx578-B3","doi-asserted-by":"crossref","first-page":"2598","DOI":"10.1093\/bioinformatics\/btu333","article-title":"Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series","volume":"30","author":"Nueda","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012712315900200_btx578-B4","doi-asserted-by":"crossref","first-page":"i147","DOI":"10.1093\/bioinformatics\/btw283","article-title":"Analysis of differential splicing suggests different modes of short-term splicing regulation","volume":"32","author":"Topa","year":"2016","journal-title":"Bioinformatics"},{"key":"2023012712315900200_btx578-B5","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/nrn.2016.27","article-title":"The neurogenetics of alternative splicing","volume":"17","author":"Vuong","year":"2016","journal-title":"Nat. Rev. Neurosci"},{"key":"2023012712315900200_btx578-B6","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/nmeth.2251","article-title":"Streaming fragment assignment for real-time analysis of sequencing experiments","volume":"10","author":"Roberts","year":"2013","journal-title":"Nat. Methods"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/3\/524\/48912944\/bioinformatics_34_3_524.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/3\/524\/48912944\/bioinformatics_34_3_524.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T08:18:49Z","timestamp":1674807529000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/3\/524\/4158165"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,9,14]]},"references-count":6,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2018,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx578","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/155135","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,2,1]]},"published":{"date-parts":[[2017,9,14]]}}}