{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:20Z","timestamp":1772138060831,"version":"3.50.1"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T00:00:00Z","timestamp":1684108800000},"content-version":"vor","delay-in-days":14,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"University of North Carolina University Cancer Research Fund"},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1F30CA268748"],"award-info":[{"award-number":["1F30CA268748"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["5R37CA247676-03"],"award-info":[{"award-number":["5R37CA247676-03"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Elimination of cancer cells by T cells is a critical mechanism of anti-tumor immunity and cancer immunotherapy response. T cells recognize cancer cells by engagement of T cell receptors with peptide epitopes presented by major histocompatibility complex molecules on the cancer cell surface. Peptide epitopes can be derived from antigen proteins coded for by multiple genomic sources. Bioinformatics tools used to identify tumor-specific epitopes via analysis of DNA and RNA-sequencing data have largely focused on epitopes derived from somatic variants, though a smaller number have evaluated potential antigens from other genomic sources.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We report here an open-source workflow utilizing the Nextflow DSL2 workflow manager, Landscape of Effective Neoantigens Software (LENS), which predicts tumor-specific and tumor-associated antigens from single nucleotide variants, insertions and deletions, fusion events, splice variants, cancer-testis antigens, overexpressed self-antigens, viruses, and endogenous retroviruses. The primary advantage of LENS is that it expands the breadth of genomic sources of discoverable tumor antigens using genomics data. Other advantages include modularity, extensibility, ease of use, and harmonization of relative expression level and immunogenicity prediction across multiple genomic sources. We present an analysis of 115 acute myeloid leukemia samples to demonstrate the utility of LENS. We expect LENS will be a valuable platform and resource for T cell epitope discovery bioinformatics, especially in cancers with few somatic variants where tumor-specific epitopes from alternative genomic sources are an elevated priority.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>More information about LENS, including code, workflow documentation, and instructions, can be found at (https:\/\/gitlab.com\/landscape-of-effective-neoantigens-software).<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad322","type":"journal-article","created":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T11:48:18Z","timestamp":1684151298000},"source":"Crossref","is-referenced-by-count":17,"title":["LENS: Landscape of Effective Neoantigens Software"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9399-5999","authenticated-orcid":false,"suffix":"II","given":"Steven P","family":"Vensko","sequence":"first","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"}]},{"given":"Kelly","family":"Olsen","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"}]},{"given":"Dante","family":"Bortone","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6517-0439","authenticated-orcid":false,"given":"Christof C","family":"Smith","sequence":"additional","affiliation":[{"name":"Department of Medicine, Brigham and Women\u2019s Hospital , Boston, MA, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6445-9457","authenticated-orcid":false,"given":"Shengjie","family":"Chai","sequence":"additional","affiliation":[{"name":"Uber Technologies, Inc. , San Francisco, CA, United States"}]},{"given":"Wolfgang","family":"Beckabir","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"}]},{"given":"Misha","family":"Fini","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"}]},{"given":"Othmane","family":"Jadi","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"}]},{"given":"Alex","family":"Rubinsteyn","sequence":"additional","affiliation":[{"name":"Department of Genetics, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"},{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"},{"name":"Computational Medicine Program, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"}]},{"given":"Benjamin G","family":"Vincent","sequence":"additional","affiliation":[{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"},{"name":"Department of Microbiology and Immunology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"},{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"},{"name":"Computational Medicine Program, University of North Carolina\u2014Chapel Hill , Chapel Hill, NC, United States"},{"name":"Division of Hematology, Department of 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