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Biol."},{"issue":"8","key":"10.1016\/j.biotechadv.2026.109063_bb0965","doi-asserted-by":"crossref","DOI":"10.3390\/ijms27083622","article-title":"Targeting the pMHC-TCR interaction: molecular strategies and therapeutic potential in autoimmunity","volume":"27","author":"Nechaeva","year":"2026","journal-title":"Int. J. Mol. Sci."},{"key":"10.1016\/j.biotechadv.2026.109063_bb0970","doi-asserted-by":"crossref","DOI":"10.1016\/j.biotechadv.2023.108283","article-title":"Influence of glycosylation on the immunogenicity and antigenicity of viral immunogens","volume":"70","author":"Newby","year":"2024","journal-title":"Biotechnol. 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Immunol."},{"issue":"5","key":"10.1016\/j.biotechadv.2026.109063_bb0990","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1038\/s41587-026-03018-2","article-title":"The promises and challenges of neoantigen cancer vaccines","volume":"44","author":"Ott","year":"2026","journal-title":"Nat. Biotechnol."},{"issue":"7662","key":"10.1016\/j.biotechadv.2026.109063_bb0995","doi-asserted-by":"crossref","first-page":"217","DOI":"10.1038\/nature22991","article-title":"An immunogenic personal neoantigen vaccine for patients with melanoma","volume":"547","author":"Ott","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.biotechadv.2026.109063_bb1000","doi-asserted-by":"crossref","DOI":"10.1016\/j.sbi.2022.102348","article-title":"Glycosylation as a key parameter in the design of nucleic acid vaccines","volume":"73","author":"Ozdilek","year":"2022","journal-title":"Curr. Opin. Struct. Biol."},{"issue":"2","key":"10.1016\/j.biotechadv.2026.109063_bb1005","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/j.ccell.2023.12.016","article-title":"A comprehensive clinically informed map of dependencies in cancer cells and framework for target prioritization","volume":"42","author":"Pacini","year":"2024","journal-title":"Cancer Cell"},{"issue":"35","key":"10.1016\/j.biotechadv.2026.109063_bb1010","doi-asserted-by":"crossref","first-page":"E7348","DOI":"10.1073\/pnas.1707304114","article-title":"Immunogenicity and structures of a rationally designed prefusion MERS-CoV spike antigen","volume":"114","author":"Pallesen","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"12","key":"10.1016\/j.biotechadv.2026.109063_bb1015","doi-asserted-by":"crossref","DOI":"10.1172\/JCI178540","article-title":"Epigenetic regulation of tumor immunity","volume":"134","author":"Pang","year":"2024","journal-title":"J. Clin. 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