{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:50:56Z","timestamp":1778226656250,"version":"3.51.4"},"reference-count":144,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,2,21]],"date-time":"2022-02-21T00:00:00Z","timestamp":1645401600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Hainan Province Science and Technology Special Fund","award":["ZDYF2021SHFZ051"],"award-info":[{"award-number":["ZDYF2021SHFZ051"]}]},{"name":"Hainan Province Science and Technology Special Fund","award":["ZDYF2020132"],"award-info":[{"award-number":["ZDYF2020132"]}]},{"name":"Hainan Provincial Natural Science Foundation of China","award":["820MS053"],"award-info":[{"award-number":["820MS053"]}]},{"name":"Marshal Initiative Funding of Hainan Medical University","award":["JBGS202103"],"award-info":[{"award-number":["JBGS202103"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871338"],"award-info":[{"award-number":["31871338"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31970646"],"award-info":[{"award-number":["31970646"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61873075"],"award-info":[{"award-number":["61873075"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32060152"],"award-info":[{"award-number":["32060152"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070673"],"award-info":[{"award-number":["32070673"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32170676"],"award-info":[{"award-number":["32170676"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81960528"],"award-info":[{"award-number":["81960528"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81760553"],"award-info":[{"award-number":["81760553"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Hainan Province Clinical Medical Center"},{"name":"Major Science and Technology Program of Hainan Province","award":["ZDKJ202003"],"award-info":[{"award-number":["ZDKJ202003"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFC2000100"],"award-info":[{"award-number":["2018YFC2000100"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Natural Science Foundation for Distinguished Young Scholars of Heilongjiang Province","award":["JQ2019C004"],"award-info":[{"award-number":["JQ2019C004"]}]},{"name":"Hainan Provincial Key Laboratory of Carcinogenesis and Intervention","award":["JCKF2021003"],"award-info":[{"award-number":["JCKF2021003"]}]},{"name":"Innovation Research Fund for Graduate Students","award":["Qhys2021-348"],"award-info":[{"award-number":["Qhys2021-348"]}]},{"name":"Innovation Research Fund for Graduate Students","award":["Qhys2021-350"],"award-info":[{"award-number":["Qhys2021-350"]}]},{"name":"Innovation Research Fund for Graduate Students","award":["Qhys2021-351"],"award-info":[{"award-number":["Qhys2021-351"]}]},{"name":"Innovation Research Fund for Graduate Students","award":["Qhys2021-377"],"award-info":[{"award-number":["Qhys2021-377"]}]},{"name":"Innovation Research Fund for Graduate Students","award":["HYYB2021A01"],"award-info":[{"award-number":["HYYB2021A01"]}]},{"name":"Innovation Research Fund for Graduate Students","award":["HYYS2021A31"],"award-info":[{"award-number":["HYYS2021A31"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,10]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Unrestrained cellular growth and immune escape of a tumor are associated with the incidental errors of the genome and transcriptome. Advances in next-generation sequencing have identified thousands of genomic and transcriptomic aberrations that generate variant peptides that assemble the hidden proteome, further expanding the immunopeptidome. Emerging next-generation sequencing technologies and a number of computational methods estimated the abundance of immune infiltration from bulk transcriptome have advanced our understanding of tumor microenvironments. Here, we will characterize several major types of tumor-specific antigens arising from single-nucleotide variants, insertions and deletions, gene fusion, alternative splicing, RNA editing and non-coding RNAs. Finally, we summarize the current state-of-the-art computational and experimental approaches or resources and provide an integrative pipeline for the identification of candidate tumor antigens. Together, the systematic investigation of the hidden proteome in cancer will help facilitate the development of effective and durable immunotherapy targets for cancer.<\/jats:p>","DOI":"10.1093\/bib\/bbac034","type":"journal-article","created":{"date-parts":[[2022,1,26]],"date-time":"2022-01-26T12:10:29Z","timestamp":1643199029000},"source":"Crossref","is-referenced-by-count":7,"title":["Shedding light on the hidden human proteome expands immunopeptidome in cancer"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1914-0727","authenticated-orcid":false,"given":"Yongsheng","family":"Li","sequence":"first","affiliation":[{"name":"College of Biomedical Information and Engineering, Hainan Women and Children\u2019s Medical Center, Hainan Medical University, Haikou 571199, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3709-3656","authenticated-orcid":false,"given":"Yunpeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tao","family":"Pan","sequence":"additional","affiliation":[{"name":"College of Biomedical Information and Engineering, Hainan Women and Children\u2019s Medical Center, Hainan Medical University, Haikou 571199, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ping","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Radiotherapy, the First Affiliated Hospital of Hainan Medical University, Hainan, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Weiwei","family":"Zhou","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yueying","family":"Gao","sequence":"additional","affiliation":[{"name":"College of Biomedical Information and Engineering, Hainan Women and Children\u2019s Medical Center, Hainan Medical University, Haikou 571199, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaojiang","family":"Zheng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Emergency and Trauma of Ministry of Education, Tumor Institute of the First Affiliated Hospital, Hainan Medical University, Haikou, 571199, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3709-4165","authenticated-orcid":false,"given":"Juan","family":"Xu","sequence":"additional","affiliation":[{"name":"College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,2,21]]},"reference":[{"key":"2022031506401534000_ref1","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.canlet.2016.01.043","article-title":"Tumor microenvironment and therapeutic response","volume":"387","author":"Wu","year":"2017","journal-title":"Cancer Lett"},{"key":"2022031506401534000_ref2","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1093\/carcin\/bgp127","article-title":"Cancer-related inflammation, the seventh hallmark of cancer: links to genetic instability","volume":"30","author":"Colotta","year":"2009","journal-title":"Carcinogenesis"},{"key":"2022031506401534000_ref3","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nmeth.3337","article-title":"Robust enumeration of cell subsets from tissue expression profiles","volume":"12","author":"Newman","year":"2015","journal-title":"Nat Methods"},{"key":"2022031506401534000_ref4","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1186\/s13059-017-1349-1","article-title":"xCell: digitally portraying the tissue cellular heterogeneity landscape","volume":"18","author":"Aran","year":"2017","journal-title":"Genome Biol"},{"key":"2022031506401534000_ref5","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nri.2017.76","article-title":"Single-cell RNA sequencing to explore immune cell heterogeneity","volume":"18","author":"Papalexi","year":"2018","journal-title":"Nat Rev Immunol"},{"key":"2022031506401534000_ref6","doi-asserted-by":"crossref","first-page":"3335","DOI":"10.1172\/JCI83871","article-title":"Cancer immunotherapy: harnessing the immune system to battle cancer","volume":"125","author":"Yang","year":"2015","journal-title":"J Clin Invest"},{"key":"2022031506401534000_ref7","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s12943-020-01174-w","article-title":"MIR22HG acts as a tumor suppressor via TGFbeta\/SMAD signaling and facilitates immunotherapy in colorectal cancer","volume":"19","author":"Xu","year":"2020","journal-title":"Mol Cancer"},{"key":"2022031506401534000_ref8","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1016\/j.ymthe.2020.02.004","article-title":"RBP EIF2S2 promotes tumorigenesis and progression by regulating MYC-mediated inhibition via FHIT-related enhancers","volume":"28","author":"Zhang","year":"2020","journal-title":"Mol Ther"},{"key":"2022031506401534000_ref9","doi-asserted-by":"crossref","first-page":"2509","DOI":"10.1056\/NEJMoa1500596","article-title":"PD-1 blockade in tumors with mismatch-repair deficiency","volume":"372","author":"Le","year":"2015","journal-title":"N Engl J Med"},{"key":"2022031506401534000_ref10","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1056\/NEJMoa1504627","article-title":"Nivolumab versus docetaxel in advanced squamous-cell non-small-cell lung cancer","volume":"373","author":"Brahmer","year":"2015","journal-title":"N Engl J Med"},{"key":"2022031506401534000_ref11","doi-asserted-by":"crossref","DOI":"10.3390\/cancers13194883","article-title":"Immunomodulating therapies in breast cancer-from prognosis to clinical practice","volume":"13","author":"Schmidt","year":"2021","journal-title":"Cancers (Basel)"},{"key":"2022031506401534000_ref12","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1126\/science.aaa4971","article-title":"Neoantigens in cancer immunotherapy","volume":"348","author":"Schumacher","year":"2015","journal-title":"Science"},{"key":"2022031506401534000_ref13","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1186\/s12943-019-1055-6","article-title":"Neoantigen vaccine: an emerging tumor immunotherapy","volume":"18","author":"Peng","year":"2019","journal-title":"Mol Cancer"},{"key":"2022031506401534000_ref14","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/s41591-018-0014-x","article-title":"Understanding the tumor immune microenvironment (TIME) for effective therapy","volume":"24","author":"Binnewies","year":"2018","journal-title":"Nat Med"},{"key":"2022031506401534000_ref15","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/nrc.2016.154","article-title":"Targeting neoantigens to augment antitumour immunity","volume":"17","author":"Yarchoan","year":"2017","journal-title":"Nat Rev Cancer"},{"key":"2022031506401534000_ref16","doi-asserted-by":"crossref","first-page":"xii11","DOI":"10.1093\/annonc\/mdx681","article-title":"Preclinical and clinical development of neoantigen vaccines","volume":"28","author":"Li","year":"2017","journal-title":"Ann Oncol"},{"key":"2022031506401534000_ref17","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1038\/nature19947","article-title":"Proteome complexity and the forces that drive proteome imbalance","volume":"537","author":"Harper","year":"2016","journal-title":"Nature"},{"key":"2022031506401534000_ref18","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nature13302","article-title":"A draft map of the human proteome","volume":"509","author":"Kim","year":"2014","journal-title":"Nature"},{"key":"2022031506401534000_ref19","doi-asserted-by":"crossref","first-page":"2067","DOI":"10.1158\/0008-5472.CAN-19-2687","article-title":"LncSpA: LncRNA spatial atlas of expression across normal and cancer tissues","volume":"80","author":"Lv","year":"2020","journal-title":"Cancer Res"},{"key":"2022031506401534000_ref20","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/nature19949","article-title":"Mass-spectrometric exploration of proteome structure and function","volume":"537","author":"Aebersold","year":"2016","journal-title":"Nature"},{"key":"2022031506401534000_ref21","doi-asserted-by":"crossref","first-page":"e8503","DOI":"10.15252\/msb.20188503","article-title":"A deep proteome and transcriptome abundance atlas of 29 healthy human tissues","volume":"15","author":"Wang","year":"2019","journal-title":"Mol Syst Biol"},{"key":"2022031506401534000_ref22","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.cell.2019.12.023","article-title":"Quantitative proteomics of the cancer cell line Encyclopedia","volume":"180","author":"Nusinow","year":"2020","journal-title":"Cell"},{"key":"2022031506401534000_ref23","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/s41576-020-0268-2","article-title":"Genetics meets proteomics: perspectives for large population-based studies","volume":"22","author":"Suhre","year":"2021","journal-title":"Nat Rev Genet"},{"key":"2022031506401534000_ref24","doi-asserted-by":"crossref","first-page":"3060","DOI":"10.7150\/thno.54150","article-title":"Systematic analysis of enhancer regulatory circuit perturbation driven by copy number variations in malignant glioma","volume":"11","author":"Xiao","year":"2021","journal-title":"Theranostics"},{"key":"2022031506401534000_ref25","doi-asserted-by":"crossref","first-page":"2287","DOI":"10.1093\/nar\/gkaa041","article-title":"Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types","volume":"48","author":"Wang","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref26","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1016\/j.ccell.2020.08.002","article-title":"Integrated omics of metastatic colorectal cancer","volume":"38","author":"Li","year":"2020","journal-title":"Cancer Cell"},{"key":"2022031506401534000_ref27","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1186\/s13045-020-01013-x","article-title":"Proteomic signatures of 16 major types of human cancer reveal universal and cancer-type-specific proteins for the identification of potential therapeutic targets","volume":"13","author":"Zhou","year":"2020","journal-title":"J Hematol Oncol"},{"key":"2022031506401534000_ref28","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1586\/14789450.2015.1070100","article-title":"Proteogenomics meets cancer immunology: mass spectrometric discovery and analysis of neoantigens","volume":"12","author":"Polyakova","year":"2015","journal-title":"Expert Rev Proteomics"},{"key":"2022031506401534000_ref29","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1056\/NEJMcibr1814237","article-title":"Alternative splicing in tumors\u2014a path to immunogenicity?","volume":"380","author":"Slansky","year":"2019","journal-title":"N Engl J Med"},{"key":"2022031506401534000_ref30","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1038\/s41571-020-0387-x","article-title":"Towards new horizons: characterization, classification and implications of the tumour antigenic repertoire","volume":"17","author":"Haen","year":"2020","journal-title":"Nat Rev Clin Oncol"},{"key":"2022031506401534000_ref31","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.semradonc.2019.12.001","article-title":"Diverse neoantigens and the development of cancer therapies","volume":"30","author":"Srivastava","year":"2020","journal-title":"Semin Radiat Oncol"},{"key":"2022031506401534000_ref32","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1084\/jem.183.3.1185","article-title":"A mutated beta-catenin gene encodes a melanoma-specific antigen recognized by tumor infiltrating lymphocytes","volume":"183","author":"Robbins","year":"1996","journal-title":"J Exp Med"},{"key":"2022031506401534000_ref33","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1084\/jem.186.5.785","article-title":"A CASP-8 mutation recognized by cytolytic T lymphocytes on a human head and neck carcinoma","volume":"186","author":"Mandruzzato","year":"1997","journal-title":"J Exp Med"},{"key":"2022031506401534000_ref34","doi-asserted-by":"crossref","first-page":"16013","DOI":"10.1073\/pnas.0500090102","article-title":"The response of autologous T cells to a human melanoma is dominated by mutated neoantigens","volume":"102","author":"Lennerz","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2022031506401534000_ref35","doi-asserted-by":"crossref","first-page":"1109","DOI":"10.1172\/JCI123791","article-title":"Neoantigen screening identifies broad TP53 mutant immunogenicity in patients with epithelial cancers","volume":"129","author":"Malekzadeh","year":"2019","journal-title":"J Clin Invest"},{"key":"2022031506401534000_ref36","doi-asserted-by":"crossref","DOI":"10.1186\/s12943-021-01465-w","article-title":"Tumor antigens and immune subtypes guided mRNA vaccine development for kidney renal clear cell carcinoma","volume":"20","author":"Xu","year":"2021","journal-title":"Mol Cancer"},{"key":"2022031506401534000_ref37","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1016\/S1470-2045(17)30516-8","article-title":"Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis","volume":"18","author":"Turajlic","year":"2017","journal-title":"Lancet Oncol"},{"key":"2022031506401534000_ref38","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1007\/s002620100222","article-title":"A TGF betaRII frameshift-mutation-derived CTL epitope recognised by HLA-A2-restricted CD8+ T cells","volume":"50","author":"Saeterdal","year":"2001","journal-title":"Cancer Immunol Immunother"},{"key":"2022031506401534000_ref39","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1038\/s41568-019-0162-4","article-title":"Alternative tumour-specific antigens","volume":"19","author":"Smith","year":"2019","journal-title":"Nat Rev Cancer"},{"key":"2022031506401534000_ref40","doi-asserted-by":"crossref","first-page":"1807","DOI":"10.1016\/j.jtho.2019.06.016","article-title":"Clinical and immunological implications of frameshift mutations in lung cancer","volume":"14","author":"Chae","year":"2019","journal-title":"J Thorac Oncol"},{"key":"2022031506401534000_ref41","doi-asserted-by":"crossref","first-page":"4156","DOI":"10.1002\/cncr.33033","article-title":"Nivolumab versus everolimus in patients with advanced renal cell carcinoma: updated results with long-term follow-up of the randomized, open-label, phase 3 CheckMate 025 trial","volume":"126","author":"Motzer","year":"2020","journal-title":"Cancer"},{"key":"2022031506401534000_ref42","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nrc2091","article-title":"The impact of translocations and gene fusions on cancer causation","volume":"7","author":"Mitelman","year":"2007","journal-title":"Nat Rev Cancer"},{"key":"2022031506401534000_ref43","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1038\/s41598-019-38550-6","article-title":"Identification of recurrent fusion genes across multiple cancer types","volume":"9","author":"Yu","year":"2019","journal-title":"Sci Rep"},{"key":"2022031506401534000_ref44","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.canlet.2021.02.023","article-title":"Gene fusion neoantigens: emerging targets for cancer immunotherapy","volume":"506","author":"Wang","year":"2021","journal-title":"Cancer Lett"},{"key":"2022031506401534000_ref45","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/j.celrep.2018.03.050","article-title":"Driver fusions and their implications in the development and treatment of human cancers","volume":"23","author":"Gao","year":"2018","journal-title":"Cell Rep"},{"key":"2022031506401534000_ref46","first-page":"3863","article-title":"HLA-B8 and HLA-A3 coexpressed with HLA-B8 are associated with a reduced risk of the development of chronic myeloid leukemia","volume":"93","author":"Posthuma","year":"1999","journal-title":"The Chronic Leukemia Working Party of the EBMT, Blood"},{"key":"2022031506401534000_ref47","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1182\/blood-2003-03-0954","article-title":"A multivalent bcr-abl fusion peptide vaccination trial in patients with chronic myeloid leukemia","volume":"103","author":"Cathcart","year":"2004","journal-title":"Blood"},{"key":"2022031506401534000_ref48","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1038\/s41591-019-0434-2","article-title":"Immunogenic neoantigens derived from gene fusions stimulate T cell responses","volume":"25","author":"Yang","year":"2019","journal-title":"Nat Med"},{"key":"2022031506401534000_ref49","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1093\/bioinformatics\/btw674","article-title":"INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery","volume":"33","author":"Zhang","year":"2017","journal-title":"Bioinformatics"},{"key":"2022031506401534000_ref50","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1016\/j.tips.2021.01.006","article-title":"RNA dysregulation: an expanding source of cancer immunotherapy targets","volume":"42","author":"Pan","year":"2021","journal-title":"Trends Pharmacol Sci"},{"key":"2022031506401534000_ref51","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1016\/j.trecan.2018.09.009","article-title":"Maximizing the utility of cancer transcriptomic data","volume":"4","author":"Xiang","year":"2018","journal-title":"Trends Cancer"},{"key":"2022031506401534000_ref52","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.tibs.2018.05.002","article-title":"Gene regulatory network perturbation by genetic and epigenetic variation","volume":"43","author":"Li","year":"2018","journal-title":"Trends Biochem Sci"},{"key":"2022031506401534000_ref53","doi-asserted-by":"crossref","first-page":"792","DOI":"10.1016\/j.omtn.2021.04.005","article-title":"Alternative splicing perturbation landscape identifies RNA binding proteins as potential therapeutic targets in cancer","volume":"24","author":"Li","year":"2021","journal-title":"Mol Ther Nucleic Acids"},{"key":"2022031506401534000_ref54","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1016\/j.celrep.2017.09.071","article-title":"Revealing the determinants of widespread alternative splicing perturbation in cancer","volume":"21","author":"Li","year":"2017","journal-title":"Cell Rep"},{"key":"2022031506401534000_ref55","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1016\/j.ccell.2018.07.001","article-title":"Comprehensive analysis of alternative splicing across tumors from 8,705 patients","volume":"34","author":"Kahles","year":"2018","journal-title":"Cancer Cell"},{"key":"2022031506401534000_ref56","doi-asserted-by":"crossref","first-page":"1056","DOI":"10.1038\/nbt.4239","article-title":"Intron retention is a source of neoepitopes in cancer","volume":"36","author":"Smart","year":"2018","journal-title":"Nat Biotechnol"},{"key":"2022031506401534000_ref57","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2021.05.038","article-title":"Pharmacologic modulation of RNA splicing enhances anti-tumor immunity","volume":"184","author":"Lu","year":"2021","journal-title":"Cell"},{"key":"2022031506401534000_ref58","doi-asserted-by":"crossref","first-page":"2246","DOI":"10.1016\/j.molcel.2021.03.028","article-title":"A pan-cancer transcriptome analysis of exitron splicing identifies novel cancer driver genes and neoepitopes","volume":"81","author":"Wang","year":"2021","journal-title":"Mol Cell"},{"key":"2022031506401534000_ref59","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1038\/nature24041","article-title":"Dynamic landscape and regulation of RNA editing in mammals","volume":"550","author":"Tan","year":"2017","journal-title":"Nature"},{"key":"2022031506401534000_ref60","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1016\/j.ccell.2018.03.026","article-title":"A-to-I RNA editing contributes to proteomic diversity in cancer","volume":"33","author":"Peng","year":"2018","journal-title":"Cancer Cell"},{"key":"2022031506401534000_ref61","doi-asserted-by":"crossref","first-page":"e23","DOI":"10.5808\/GI.2019.17.3.e23","article-title":"Identification of neoantigens derived from alternative splicing and RNA modification","volume":"17","author":"Park","year":"2019","journal-title":"Genomics Inform"},{"key":"2022031506401534000_ref62","doi-asserted-by":"crossref","first-page":"593989","DOI":"10.3389\/fonc.2020.593989","article-title":"Systematically characterizing A-to-I RNA editing neoantigens in cancer","volume":"10","author":"Zhou","year":"2020","journal-title":"Front Oncol"},{"key":"2022031506401534000_ref63","doi-asserted-by":"crossref","first-page":"3919","DOI":"10.1038\/s41467-018-06405-9","article-title":"RNA editing derived epitopes function as cancer antigens to elicit immune responses","volume":"9","author":"Zhang","year":"2018","journal-title":"Nat Commun"},{"key":"2022031506401534000_ref64","first-page":"1","article-title":"The cancer\/testis genes: review, standardization, and commentary","volume":"4","author":"Scanlan","year":"2004","journal-title":"Cancer Immun"},{"key":"2022031506401534000_ref65","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1034\/j.1600-065X.2002.18803.x","article-title":"Cancer\/testis antigens: an expanding family of targets for cancer immunotherapy","volume":"188","author":"Scanlan","year":"2002","journal-title":"Immunol Rev"},{"key":"2022031506401534000_ref66","doi-asserted-by":"crossref","first-page":"726","DOI":"10.1002\/(SICI)1097-0215(20000301)85:5<726::AID-IJC21>3.0.CO;2-F","article-title":"CT10: a new cancer-testis (CT) antigen homologous to CT7 and the MAGE family, identified by representational-difference analysis","volume":"85","author":"Gure","year":"2000","journal-title":"Int J Cancer"},{"key":"2022031506401534000_ref67","first-page":"3848","article-title":"Identification on a human sarcoma of two new genes with tumor-specific expression","volume":"60","author":"Martelange","year":"2000","journal-title":"Cancer Res"},{"key":"2022031506401534000_ref68","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1038\/s41467-020-14802-2","article-title":"Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers","volume":"11","author":"Li","year":"2020","journal-title":"Nat Commun"},{"key":"2022031506401534000_ref69","doi-asserted-by":"crossref","first-page":"e203","DOI":"10.1093\/nar\/gkt1054","article-title":"Comprehensive analysis of the functional microRNA-mRNA regulatory network identifies miRNA signatures associated with glioma malignant progression","volume":"41","author":"Li","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref70","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1093\/nar\/gkq832","article-title":"MiRNA-miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features","volume":"39","author":"Xu","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref71","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/s12943-020-1147-3","article-title":"Emerging role of tumor-related functional peptides encoded by lncRNA and circRNA","volume":"19","author":"Wu","year":"2020","journal-title":"Mol Cancer"},{"key":"2022031506401534000_ref72","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.molcel.2017.09.015","article-title":"A peptide encoded by a putative lncRNA HOXB-AS3 suppresses colon cancer growth","volume":"68","author":"Huang","year":"2017","journal-title":"Mol Cell"},{"key":"2022031506401534000_ref73","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/nchembio.2249","article-title":"A human microprotein that interacts with the mRNA decapping complex","volume":"13","author":"D'Lima","year":"2017","journal-title":"Nat Chem Biol"},{"key":"2022031506401534000_ref74","doi-asserted-by":"crossref","first-page":"4750","DOI":"10.1038\/s41388-018-0281-5","article-title":"The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation","volume":"37","author":"Polycarpou-Schwarz","year":"2018","journal-title":"Oncogene"},{"key":"2022031506401534000_ref75","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/nature11993","article-title":"Natural RNA circles function as efficient microRNA sponges","volume":"495","author":"Hansen","year":"2013","journal-title":"Nature"},{"key":"2022031506401534000_ref76","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1038\/s41388-017-0019-9","article-title":"A novel protein encoded by the circular form of the SHPRH gene suppresses glioma tumorigenesis","volume":"37","author":"Zhang","year":"2018","journal-title":"Oncogene"},{"key":"2022031506401534000_ref77","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1186\/s12943-019-1056-5","article-title":"A novel tumor suppressor protein encoded by circular AKT3 RNA inhibits glioblastoma tumorigenicity by competing with active phosphoinositide-dependent Kinase-1","volume":"18","author":"Xia","year":"2019","journal-title":"Mol Cancer"},{"key":"2022031506401534000_ref78","doi-asserted-by":"crossref","DOI":"10.1093\/jnci\/djx166","article-title":"Novel role of FBXW7 circular RNA in repressing glioma tumorigenesis","volume":"110","author":"Yang","year":"2018","journal-title":"J Natl Cancer Inst"},{"key":"2022031506401534000_ref79","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/s12943-019-1010-6","article-title":"A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via hippo-YAP signaling","volume":"18","author":"Zheng","year":"2019","journal-title":"Mol Cancer"},{"key":"2022031506401534000_ref80","first-page":"zcaa015","article-title":"Pan-cancer proteogenomic analysis reveals long and circular noncoding RNAs encoding peptides, NAR","volume":"2","author":"Othoum","year":"2020","journal-title":"Cancer"},{"key":"2022031506401534000_ref81","doi-asserted-by":"crossref","first-page":"2180","DOI":"10.1111\/cas.14034","article-title":"circMAN1A2 could serve as a novel serum biomarker for malignant tumors","volume":"110","author":"Fan","year":"2019","journal-title":"Cancer Sci"},{"key":"2022031506401534000_ref82","doi-asserted-by":"crossref","first-page":"59704","DOI":"10.18632\/oncotarget.10923","article-title":"IRES-dependent translation of the long non coding RNA meloe in melanoma cells produces the most immunogenic MELOE antigens","volume":"7","author":"Charpentier","year":"2016","journal-title":"Oncotarget"},{"key":"2022031506401534000_ref83","doi-asserted-by":"crossref","first-page":"e75233","DOI":"10.1371\/journal.pone.0075233","article-title":"The melanoma antigens MELOE-1 and MELOE-2 are translated from a bona fide polycistronic mRNA containing functional IRES sequences","volume":"8","author":"Carbonnelle","year":"2013","journal-title":"PLoS One"},{"key":"2022031506401534000_ref84","doi-asserted-by":"crossref","first-page":"1786","DOI":"10.1002\/eji.200940132","article-title":"Frequent occurrence of high affinity T cells against MELOE-1 makes this antigen an attractive target for melanoma immunotherapy","volume":"40","author":"Godet","year":"2010","journal-title":"Eur J Immunol"},{"key":"2022031506401534000_ref85","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aau5516","article-title":"Noncoding regions are the main source of targetable tumor-specific antigens","volume":"10","author":"Laumont","year":"2018","journal-title":"Sci Transl Med"},{"key":"2022031506401534000_ref86","article-title":"Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer","volume":"40","author":"Ouspenskaia","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2022031506401534000_ref87","doi-asserted-by":"crossref","first-page":"D276","DOI":"10.1093\/nar\/gkx1004","article-title":"lncRNASNP2: an updated database of functional SNPs and mutations in human and mouse lncRNAs","volume":"46","author":"Miao","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref88","doi-asserted-by":"crossref","DOI":"10.3390\/ijms22010323","article-title":"Role of host-mediated post-translational modifications (PTMs) in RNA virus pathogenesis","volume":"22","author":"Kumar","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2022031506401534000_ref89","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.immuni.2016.06.020","article-title":"Post-translational modification control of innate immunity","volume":"45","author":"Liu","year":"2016","journal-title":"Immunity"},{"key":"2022031506401534000_ref90","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1080\/14789450.2017.1345633","article-title":"Understanding type 1 diabetes through proteomics","volume":"14","author":"Crevecoeur","year":"2017","journal-title":"Expert Rev Proteomics"},{"key":"2022031506401534000_ref91","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1080\/14789450.2020.1845147","article-title":"Using phosphoproteomics and next generation sequencing to discover novel therapeutic targets in patient antibodies","volume":"17","author":"Zeneyedpour","year":"2020","journal-title":"Expert Rev Proteomics"},{"key":"2022031506401534000_ref92","doi-asserted-by":"crossref","first-page":"e1114","DOI":"10.1371\/journal.pone.0001114","article-title":"Treating cancer as an infectious disease--viral antigens as novel targets for treatment and potential prevention of tumors of viral etiology","volume":"2","author":"Wang","year":"2007","journal-title":"PLoS One"},{"key":"2022031506401534000_ref93","doi-asserted-by":"crossref","first-page":"889","DOI":"10.1016\/S0140-6736(13)60022-7","article-title":"Human papillomavirus and cervical cancer","volume":"382","author":"Crosbie","year":"2013","journal-title":"Lancet"},{"key":"2022031506401534000_ref94","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1158\/1078-0432.CCR-18-1763","article-title":"Immunotherapy targeting HPV16\/18 generates potent immune responses in HPV-associated head and neck cancer","volume":"25","author":"Aggarwal","year":"2019","journal-title":"Clin Cancer Res"},{"key":"2022031506401534000_ref95","doi-asserted-by":"crossref","first-page":"218","DOI":"10.1126\/science.1168978","article-title":"Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling","volume":"324","author":"Ingolia","year":"2009","journal-title":"Science"},{"key":"2022031506401534000_ref96","doi-asserted-by":"crossref","first-page":"4493","DOI":"10.1016\/j.molcel.2021.08.033","article-title":"The oncomicropeptide APPLE promotes hematopoietic malignancy by enhancing translation initiation","volume":"81","author":"Sun","year":"2021","journal-title":"Mol Cell"},{"key":"2022031506401534000_ref97","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1016\/j.tibs.2016.05.003","article-title":"New peptides under the s(ORF)ace of the genome","volume":"41","author":"Pueyo","year":"2016","journal-title":"Trends Biochem Sci"},{"key":"2022031506401534000_ref98","doi-asserted-by":"crossref","first-page":"41929","DOI":"10.1038\/srep41929","article-title":"SpotLight proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics","volume":"7","author":"Lundstrom","year":"2017","journal-title":"Sci Rep"},{"key":"2022031506401534000_ref99","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1093\/bib\/bbz160","article-title":"Human body-fluid proteome: quantitative profiling and computational prediction","volume":"22","author":"Huang","year":"2021","journal-title":"Brief Bioinform"},{"key":"2022031506401534000_ref100","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.coi.2016.04.005","article-title":"Mass spectrometry-based antigen discovery for cancer immunotherapy","volume":"41","author":"Bassani-Sternberg","year":"2016","journal-title":"Curr Opin Immunol"},{"key":"2022031506401534000_ref101","doi-asserted-by":"crossref","first-page":"109542","DOI":"10.1016\/j.biopha.2019.109542","article-title":"Application of mass spectrometry-based MHC immunopeptidome profiling in neoantigen identification for tumor immunotherapy","volume":"120","author":"Zhang","year":"2019","journal-title":"Biomed Pharmacother"},{"key":"2022031506401534000_ref102","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/s13045-019-0787-5","article-title":"Tumor neoantigens: from basic research to clinical applications","volume":"12","author":"Jiang","year":"2019","journal-title":"J Hematol Oncol"},{"key":"2022031506401534000_ref103","doi-asserted-by":"crossref","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","article-title":"NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data","volume":"48","author":"Reynisson","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref104","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nbt.2514","article-title":"Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples","volume":"31","author":"Cibulskis","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2022031506401534000_ref105","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/s41592-018-0051-x","article-title":"Strelka2: fast and accurate calling of germline and somatic variants","volume":"15","author":"Kim","year":"2018","journal-title":"Nat Methods"},{"key":"2022031506401534000_ref106","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1101\/gr.129684.111","article-title":"VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing","volume":"22","author":"Koboldt","year":"2012","journal-title":"Genome Res"},{"key":"2022031506401534000_ref107","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/s42003-018-0023-9","article-title":"Genome-wide somatic variant calling using localized colored de Bruijn graphs","volume":"1","author":"Narzisi","year":"2018","journal-title":"Commun Biol"},{"key":"2022031506401534000_ref108","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/s13059-019-1842-9","article-title":"Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods","volume":"20","author":"Haas","year":"2019","journal-title":"Genome Biol"},{"key":"2022031506401534000_ref109","doi-asserted-by":"crossref","first-page":"e26","DOI":"10.5808\/GI.2019.17.3.e26","article-title":"FusionScan: accurate prediction of fusion genes from RNA-Seq data","volume":"17","author":"Kim","year":"2019","journal-title":"Genomics Inform"},{"key":"2022031506401534000_ref110","doi-asserted-by":"crossref","first-page":"R72","DOI":"10.1186\/gb-2011-12-8-r72","article-title":"TopHat-fusion: an algorithm for discovery of novel fusion transcripts","volume":"12","author":"Kim","year":"2011","journal-title":"Genome Biol"},{"key":"2022031506401534000_ref111","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1101\/gr.186114.114","article-title":"INTEGRATE: gene fusion discovery using whole genome and transcriptome data","volume":"26","author":"Zhang","year":"2016","journal-title":"Genome Res"},{"key":"2022031506401534000_ref112","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1038\/nbt.2450","article-title":"Differential analysis of gene regulation at transcript resolution with RNA-seq","volume":"31","author":"Trapnell","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2022031506401534000_ref113","doi-asserted-by":"crossref","first-page":"2633","DOI":"10.1093\/bioinformatics\/btr458","article-title":"FDM: a graph-based statistical method to detect differential transcription using RNA-seq data","volume":"27","author":"Singh","year":"2011","journal-title":"Bioinformatics"},{"key":"2022031506401534000_ref114","doi-asserted-by":"crossref","first-page":"e39","DOI":"10.1093\/nar\/gks1026","article-title":"DiffSplice: the genome-wide detection of differential splicing events with RNA-seq","volume":"41","author":"Hu","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref115","doi-asserted-by":"crossref","first-page":"E5593","DOI":"10.1073\/pnas.1419161111","article-title":"rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data","volume":"111","author":"Shen","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2022031506401534000_ref116","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1093\/bib\/bbx129","article-title":"Elucidating the editome: bioinformatics approaches for RNA editing detection","volume":"20","author":"Diroma","year":"2019","journal-title":"Brief Bioinform"},{"key":"2022031506401534000_ref117","doi-asserted-by":"crossref","first-page":"1098","DOI":"10.1038\/s41596-019-0279-7","article-title":"Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal","volume":"15","author":"Lo Giudice","year":"2020","journal-title":"Nat Protoc"},{"key":"2022031506401534000_ref118","first-page":"993","article-title":"RNAEditor: easy detection of RNA editing events and the introduction of editing islands","volume":"18","author":"John","year":"2017","journal-title":"Brief Bioinform"},{"key":"2022031506401534000_ref119","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1186\/gm396","article-title":"Derivation of HLA types from shotgun sequence datasets","volume":"4","author":"Warren","year":"2012","journal-title":"Genome Med"},{"key":"2022031506401534000_ref120","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1186\/gm403","article-title":"HLA typing from RNA-Seq sequence reads","volume":"4","author":"Boegel","year":"2012","journal-title":"Genome Med"},{"key":"2022031506401534000_ref121","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s13073-015-0145-3","article-title":"HLAreporter: a tool for HLA typing from next generation sequencing data","volume":"7","author":"Huang","year":"2015","journal-title":"Genome Med"},{"key":"2022031506401534000_ref122","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1186\/1471-2164-15-325","article-title":"Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads","volume":"15","author":"Bai","year":"2014","journal-title":"BMC Genomics"},{"key":"2022031506401534000_ref123","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1111\/tan.14244","article-title":"Systematic comparative study of computational methods for HLA typing from next-generation sequencing","volume":"97","author":"Yu","year":"2021","journal-title":"HLA"},{"key":"2022031506401534000_ref124","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1186\/1471-2105-8-280","article-title":"PepBank--a database of peptides based on sequence text mining and public peptide data sources","volume":"8","author":"Shtatland","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"2022031506401534000_ref125","doi-asserted-by":"crossref","first-page":"D65","DOI":"10.1093\/nar\/gkaa791","article-title":"cncRNAdb: a manually curated resource of experimentally supported RNAs with both protein-coding and noncoding function","volume":"49","author":"Huang","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref126","doi-asserted-by":"crossref","first-page":"D230","DOI":"10.1093\/nar\/gky978","article-title":"RPFdb v2.0: an updated database for genome-wide information of translated mRNA generated from ribosome profiling","volume":"47","author":"Wang","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref127","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s13059-021-02300-7","article-title":"riboCIRC: a comprehensive database of translatable circRNAs","volume":"22","author":"Li","year":"2021","journal-title":"Genome Biol"},{"key":"2022031506401534000_ref128","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1038\/s41588-020-00774-y","article-title":"Comprehensive characterization of protein-protein interactions perturbed by disease mutations","volume":"53","author":"Cheng","year":"2021","journal-title":"Nat Genet"},{"key":"2022031506401534000_ref129","doi-asserted-by":"crossref","first-page":"10368","DOI":"10.1093\/nar\/gkaa704","article-title":"Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts","volume":"48","author":"Ho-Xuan","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref130","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.gpb.2020.03.001","article-title":"IRESbase: a comprehensive database of experimentally validated internal ribosome entry sites","volume":"18","author":"Zhao","year":"2020","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2022031506401534000_ref131","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1038\/cr.2017.31","article-title":"Extensive translation of circular RNAs driven by N(6)-methyladenosine","volume":"27","author":"Yang","year":"2017","journal-title":"Cell Res"},{"key":"2022031506401534000_ref132","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1186\/s12943-019-1066-3","article-title":"Molecular characterization and clinical relevance of m(6)A regulators across 33 cancer types","volume":"18","author":"Li","year":"2019","journal-title":"Mol Cancer"},{"key":"2022031506401534000_ref133","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s12943-021-01324-8","article-title":"Pan-cancer characterization of expression and clinical relevance of m(6)A-related tissue-elevated long non-coding RNAs","volume":"20","author":"Xu","year":"2021","journal-title":"Mol Cancer"},{"key":"2022031506401534000_ref134","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkab847","article-title":"TransLnc: a comprehensive resource for translatable lncRNAs extends immunopeptidome","volume":"50","author":"Lv","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2022031506401534000_ref135","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1038\/nprot.2016.136","article-title":"The MaxQuant computational platform for mass spectrometry-based shotgun proteomics","volume":"11","author":"Tyanova","year":"2016","journal-title":"Nat Protoc"},{"key":"2022031506401534000_ref136","doi-asserted-by":"crossref","first-page":"1522","DOI":"10.1002\/pmic.200900759","article-title":"XTandem parser: an open-source library to parse and analyse X!Tandem MS\/MS search results","volume":"10","author":"Muth","year":"2010","journal-title":"Proteomics"},{"key":"2022031506401534000_ref137","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1002\/pmic.201200439","article-title":"Comet: an open-source MS\/MS sequence database search tool","volume":"13","author":"Eng","year":"2013","journal-title":"Proteomics"},{"key":"2022031506401534000_ref138","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1038\/s41587-019-0289-6","article-title":"Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes","volume":"37","author":"Racle","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2022031506401534000_ref139","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.1038\/s41587-019-0280-2","article-title":"Predicting HLA class II antigen presentation through integrated deep learning","volume":"37","author":"Chen","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2022031506401534000_ref140","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1158\/2326-6066.CIR-19-0401","article-title":"pVACtools: a computational toolkit to identify and visualize cancer neoantigens","volume":"8","author":"Hundal","year":"2020","journal-title":"Cancer Immunol Res"},{"key":"2022031506401534000_ref141","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/s13073-019-0679-x","article-title":"pTuneos: prioritizing tumor neoantigens from next-generation sequencing data","volume":"11","author":"Zhou","year":"2019","journal-title":"Genome Med"},{"key":"2022031506401534000_ref142","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.1038\/s41467-020-15456-w","article-title":"Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis","volume":"11","author":"Wen","year":"2020","journal-title":"Nat Commun"},{"key":"2022031506401534000_ref143","article-title":"nextNEOpi: a comprehensive pipeline for computational neoantigen prediction","volume":"38","author":"Rieder","year":"2021","journal-title":"Bioinformatics"},{"key":"2022031506401534000_ref144","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/ni.3682","article-title":"'Final common pathway' of human cancer immunotherapy: targeting random somatic mutations","volume":"18","author":"Tran","year":"2017","journal-title":"Nat Immunol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/2\/bbac034\/42805371\/bbac034.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/2\/bbac034\/42805371\/bbac034.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,16]],"date-time":"2023-11-16T08:41:03Z","timestamp":1700124063000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac034\/6533503"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,2,21]]},"references-count":144,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2022,3,10]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac034","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,3]]},"published":{"date-parts":[[2022,2,21]]},"article-number":"bbac034"}}