{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T20:46:54Z","timestamp":1770065214573,"version":"3.49.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"20","license":[{"start":{"date-parts":[[2019,3,19]],"date-time":"2019-03-19T00:00:00Z","timestamp":1552953600000},"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\/100000892","name":"Prostate Cancer Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000892","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100001797","name":"PhRMA foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100001797","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Summary<\/jats:title><jats:p>Insertion and deletion (indels) have been recognized as an important source generating tumor-specific mutant peptides (neoantigens). The focus of indel-derived neoantigen identification has been on leveraging DNA sequencing such as whole exome sequencing, with the effort of using RNA-seq less well explored. Here we present ScanNeo, a fast-streamlined computational pipeline for analyzing RNA-seq to predict neoepitopes derived from small to large-sized indels. We applied ScanNeo in a prostate cancer cell line and validated our predictions with matched mass spectrometry data. Finally, we demonstrated that indel neoantigens predicted from RNA-seq were associated with checkpoint inhibitor response in a cohort of melanoma patients.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>ScanNeo is implemented in Python. It is freely accessible at the GitHub repository (https:\/\/github.com\/ylab-hi\/ScanNeo).<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz193","type":"journal-article","created":{"date-parts":[[2019,3,16]],"date-time":"2019-03-16T04:01:30Z","timestamp":1552708890000},"page":"4159-4161","source":"Crossref","is-referenced-by-count":45,"title":["ScanNeo: identifying indel-derived neoantigens using RNA-Seq data"],"prefix":"10.1093","volume":"35","author":[{"given":"Ting-You","family":"Wang","sequence":"first","affiliation":[{"name":"The Hormel Institute, University of Minnesota , Austin, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Wang","sequence":"additional","affiliation":[{"name":"The Hormel Institute, University of Minnesota , Austin, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sk Kayum","family":"Alam","sequence":"additional","affiliation":[{"name":"The Hormel Institute, University of Minnesota , Austin, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luke H","family":"Hoeppner","sequence":"additional","affiliation":[{"name":"The Hormel Institute, University of Minnesota , Austin, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rendong","family":"Yang","sequence":"additional","affiliation":[{"name":"The Hormel Institute, University of Minnesota , Austin, MN, USA"},{"name":"Masonic Cancer Center, University of Minnesota , Minneapolis, MN, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,3,19]]},"reference":[{"key":"2023013108281463700_btz193-B1","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1038\/nature11003","article-title":"The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity","volume":"483","author":"Barretina","year":"2012","journal-title":"Nature"},{"key":"2023013108281463700_btz193-B2","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1126\/science.aaa3828","article-title":"Cancer immunotherapy. 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