{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,3]],"date-time":"2026-03-03T15:17:25Z","timestamp":1772551045474,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2016,12,6]],"date-time":"2016-12-06T00:00:00Z","timestamp":1480982400000},"content-version":"vor","delay-in-days":12,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000054","name":"NIH National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NIH National Cancer Institute","doi-asserted-by":"publisher","award":["R00CA149182"],"award-info":[{"award-number":["R00CA149182"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>INTEGRATE-Neo is implemented in C\u2009++\u2009and Python. Full source code and installation instructions are freely available from https:\/\/github.com\/ChrisMaherLab\/INTEGRATE-Neo.<\/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\/btw674","type":"journal-article","created":{"date-parts":[[2016,10,21]],"date-time":"2016-10-21T19:05:23Z","timestamp":1477076723000},"page":"555-557","source":"Crossref","is-referenced-by-count":103,"title":["INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery"],"prefix":"10.1093","volume":"33","author":[{"given":"Jin","family":"Zhang","sequence":"first","affiliation":[{"name":"McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA"}]},{"given":"Elaine R","family":"Mardis","sequence":"additional","affiliation":[{"name":"McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA"}]},{"given":"Christopher A","family":"Maher","sequence":"additional","affiliation":[{"name":"McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA"},{"name":"Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO, USA"}]}],"member":"286","published-online":{"date-parts":[[2016,11,24]]},"reference":[{"key":"2023020204421574500_btw674-B1","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/bioinformatics\/btv639","article-title":"Gapped sequence alignment using artificial neural networks: application to the MHC class I system","volume":"32","author":"Andreatta","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020204421574500_btw674-B2","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1126\/science.aaa3828","article-title":"Cancer immunotherapy. 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