{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T15:26:23Z","timestamp":1782401183241,"version":"3.54.5"},"reference-count":229,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T00:00:00Z","timestamp":1737331200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,11]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Tumor-specific antigens, also known as neoantigens, have potential utility in anti-cancer immunotherapy, including immune checkpoint blockade (ICB), neoantigen-specific T cell receptor-engineered T (TCR-T), chimeric antigen receptor T (CAR-T), and therapeutic cancer vaccines (TCVs). After recognizing presented neoantigens, the immune system becomes activated and triggers the death of tumor cells. Neoantigens may be derived from multiple origins, including somatic mutations (single nucleotide variants, insertions\/deletions, and gene fusions), circular RNAs, alternative splicing, RNA editing, and polymorphic microbiomes. An increasing amount of bioinformatics tools and algorithms are being developed to predict tumor neoantigens derived from different sources, which may require inputs from different multi-omics data. In addition, calculating the peptide\u2013major histocompatibility complex (MHC) affinity can aid in selecting putative neoantigens, as high binding affinities facilitate antigen presentation. Based on these approaches and previous experiments, many resources have been developed to reveal the landscape of tumor neoantigens across multiple cancer types. Herein, we summarize these tools, algorithms, and resources to provide an overview of computational analysis for neoantigen discovery and prioritization, as well as the future development of potential clinical utilities in this field.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf001","type":"journal-article","created":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T13:29:01Z","timestamp":1737379741000},"source":"Crossref","is-referenced-by-count":9,"title":["Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0009-0000-8726-3409","authenticated-orcid":false,"given":"Yunzhe","family":"Wang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9641-4560","authenticated-orcid":false,"given":"James","family":"Wengler","sequence":"additional","affiliation":[{"name":"Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University , Houston, TX 77030,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2086-8170","authenticated-orcid":false,"given":"Yuzhu","family":"Fang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6994-2639","authenticated-orcid":false,"given":"Joseph","family":"Zhou","sequence":"additional","affiliation":[{"name":"Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University , Houston, TX 77030,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7506-3805","authenticated-orcid":false,"given":"Hang","family":"Ruan","sequence":"additional","affiliation":[{"name":"Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University , Suzhou 215123,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3757-8469","authenticated-orcid":false,"given":"Zhao","family":"Zhang","sequence":"additional","affiliation":[{"name":"MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University , Shanghai 200032,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7380-2640","authenticated-orcid":false,"given":"Leng","family":"Han","sequence":"additional","affiliation":[{"name":"Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University , Houston, TX 77030,","place":["USA"]},{"name":"Brown Center for Immunotherapy, School of Medicine, Indiana University , Indianapolis, IN 46202,","place":["USA"]},{"name":"Department of Biostatistics and Health 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