{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,20]],"date-time":"2026-02-20T17:45:08Z","timestamp":1771609508143,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2019,5,28]],"date-time":"2019-05-28T00:00:00Z","timestamp":1559001600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["CA13106"],"award-info":[{"award-number":["CA13106"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Cancer Institute Cancer Center","award":["5P30CA045508"],"award-info":[{"award-number":["5P30CA045508"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Percent Spliced-In (PSI) values are commonly used to report alternative pre-mRNA splicing (AS) changes. Previous PSI-detection tools were limited to specific AS events and were evaluated by in silico RNA-seq data. We developed PSI-Sigma, which uses a new PSI index, and we employed actual (non-simulated) RNA-seq data from spliced synthetic genes (RNA Sequins) to benchmark its performance (i.e. precision, recall, false positive rate and correlation) in comparison with three leading tools (rMATS, SUPPA2 and Whippet).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>PSI-Sigma outperformed these tools, especially in the case of AS events with multiple alternative exons and intron-retention events. We also briefly evaluated its performance in long-read RNA-seq analysis, by sequencing a mixture of human RNAs and RNA Sequins with nanopore long-read sequencers.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PSI-Sigma is implemented is available at https:\/\/github.com\/wososa\/PSI-Sigma.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz438","type":"journal-article","created":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T19:39:30Z","timestamp":1558553970000},"page":"5048-5054","source":"Crossref","is-referenced-by-count":53,"title":["PSI-Sigma: a comprehensive splicing-detection method for short-read and long-read RNA-seq analysis"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1294-1142","authenticated-orcid":false,"given":"Kuan-Ting","family":"Lin","sequence":"first","affiliation":[{"name":"Cold Spring Harbor Laboratory, Cold Spring Harbor , NY, USA"}]},{"given":"Adrian R","family":"Krainer","sequence":"additional","affiliation":[{"name":"Cold Spring Harbor Laboratory, Cold Spring Harbor , NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,5,28]]},"reference":[{"key":"2023013108325876800_btz438-B1","doi-asserted-by":"crossref","first-page":"2503","DOI":"10.1128\/MCB.00070-15","article-title":"Regulated intron retention and nuclear pre-mRNA decay contribute to PABPN1 autoregulation","volume":"35","author":"Bergeron","year":"2015","journal-title":"Mol. 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