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This work presents a computational pipeline that integrates diverse computational tools and machine learning models to accelerate the identification and optimization of antigen candidates. The pipeline employs efficient filtering and consensus-based strategies to highlight epitopes with high therapeutic potential. We demonstrate its utility by significantly narrowing the antigen search space for Rift Valley fever virus (RVFV) and Mayaro virus (MAYV), and by effectively identifying conserved neutralizing epitopes in SARS-CoV-2. Our proposed computational antigen pipeline offers a powerful framework for expediting the development of future vaccines and therapeutics in response to emerging pathogens.<\/jats:p>","DOI":"10.1093\/narmme\/ugag024","type":"journal-article","created":{"date-parts":[[2026,5,9]],"date-time":"2026-05-09T11:41:35Z","timestamp":1778326895000},"source":"Crossref","is-referenced-by-count":0,"title":["An integrated computational antigen discovery pipeline with hierarchical filtering for emerging viral variants"],"prefix":"10.1093","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2400-7210","authenticated-orcid":false,"given":"Raj S","family":"Roy","sequence":"first","affiliation":[{"name":"Department of Electrical and Computer Engineering, Texas A&M University , 77843 TX ,","place":["United 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