{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T09:20:46Z","timestamp":1780392046300,"version":"3.54.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2021,11,12]],"date-time":"2021-11-12T00:00:00Z","timestamp":1636675200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Austrian Science Fund","award":["T 974-B30"],"award-info":[{"award-number":["T 974-B30"]}]},{"DOI":"10.13039\/501100004061","name":"Oesterreichische Nationalbank","doi-asserted-by":"crossref","award":["18496"],"award-info":[{"award-number":["18496"]}],"id":[{"id":"10.13039\/501100004061","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Research Council","award":["786295"],"award-info":[{"award-number":["786295"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Somatic mutations and gene fusions can produce immunogenic neoantigens mediating anticancer immune responses. However, their computational prediction from sequencing data requires complex computational workflows to identify tumor-specific aberrations, derive the resulting peptides, infer patients\u2019 Human Leukocyte Antigen types and predict neoepitopes binding to them, together with a set of features underlying their immunogenicity. Here, we present nextNEOpi (nextflow NEOantigen prediction pipeline) a comprehensive and fully automated bioinformatic pipeline to predict tumor neoantigens from raw DNA and RNA sequencing data. In addition, nextNEOpi quantifies neoepitope- and patient-specific features associated with tumor immunogenicity and response to immunotherapy.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>nextNEOpi source code and documentation are available at https:\/\/github.com\/icbi-lab\/nextNEOpi<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>dietmar.rieder@i-med.ac.at or francesca.finotello@uibk.ac.at<\/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\/btab759","type":"journal-article","created":{"date-parts":[[2021,11,9]],"date-time":"2021-11-09T20:18:03Z","timestamp":1636489083000},"page":"1131-1132","source":"Crossref","is-referenced-by-count":46,"title":["nextNEOpi: a comprehensive pipeline for computational neoantigen prediction"],"prefix":"10.1093","volume":"38","author":[{"given":"Dietmar","family":"Rieder","sequence":"first","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georgios","family":"Fotakis","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markus","family":"Ausserhofer","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geyeregger","family":"Ren\u00e9","sequence":"additional","affiliation":[{"name":"St. Anna Children\u2019s Cancer Research Institute , Vienna 1090, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wolfgang","family":"Paster","sequence":"additional","affiliation":[{"name":"St. Anna Children\u2019s Cancer Research Institute , Vienna 1090, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zlatko","family":"Trajanoski","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0712-4658","authenticated-orcid":false,"given":"Francesca","family":"Finotello","sequence":"additional","affiliation":[{"name":"Biocenter, Institute of Bioinformatics, Medical University of Innsbruck , Innsbruck 6020, Austria"},{"name":"Institute of Molecular Biology, University Innsbruck , Innsbruck 6020, Austria"},{"name":"Digital Science Center (DiSC), University Innsbruck , Innsbruck 6020, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,11,12]]},"reference":[{"key":"2023020108521211000_btab759-B1","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1038\/nmeth.3364","article-title":"MiXCR: software for comprehensive adaptive immunity profiling","volume":"12","author":"Bolotin","year":"2015","journal-title":"Nat. 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