{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T06:11:21Z","timestamp":1763705481544,"version":"3.32.0"},"reference-count":28,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2018,9,1]],"date-time":"2018-09-01T00:00:00Z","timestamp":1535760000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"},{"start":{"date-parts":[[2018,9,1]],"date-time":"2018-09-01T00:00:00Z","timestamp":1535760000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Quant. Biol."],"published-print":{"date-parts":[[2018,9]]},"abstract":"<jats:sec><jats:title>Background<\/jats:title><jats:p>Most intronic lariats are rapidly turned over after splicing. However, new research suggests that some introns may have additional post\u2010splicing functions. Current bioinformatics methods used to identify lariats require a sequencing read that traverses the lariat branchpoint. This method provides precise branchpoint sequence and position information, but is limited in its ability to quantify abundance of stabilized lariat species in a given RNAseq sample. Bioinformatic tools are needed to better address these emerging biological questions.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We used an unsupervised machine learning approach on sequencing reads from publicly available ENCODE data to learn to identify and quantify lariats based on RNAseq read coverage shape.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed ShapeShifter, a novel approach for identifying and quantifying stable lariat species in RNAseq datasets. We learned a characteristic \u201clariat\u201d curve from ENCODE RNAseq data and were able to estimate abundances for introns based on read coverage. Using this method we discovered new stable introns in these samples that were not represented using the older, branchpoint\u2010traversing read method.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>ShapeShifter provides a robust approach towards detecting and quantifying stable lariat species.<\/jats:p><\/jats:sec>","DOI":"10.1007\/s40484-018-0141-x","type":"journal-article","created":{"date-parts":[[2018,7,25]],"date-time":"2018-07-25T05:39:27Z","timestamp":1532497167000},"page":"267-274","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data"],"prefix":"10.1002","volume":"6","author":[{"given":"Allison J","family":"Taggart","sequence":"first","affiliation":[{"name":"<!--1--> Department of Molecular Biology Cell Biology and Biochemistry Brown University Providence RI 02912 USA"}]},{"given":"William G","family":"Fairbrother","sequence":"additional","affiliation":[{"name":"<!--1--> Department of Molecular Biology Cell Biology and Biochemistry Brown University Providence RI 02912 USA"},{"name":"<!--2--> Center for Computational Molecular Biology Brown University Providence RI 02912 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