{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T21:36:13Z","timestamp":1773869773888,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2021,5,1]],"date-time":"2021-05-01T00:00:00Z","timestamp":1619827200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["1R01AI081062"],"award-info":[{"award-number":["1R01AI081062"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the first web-based vaccine design program using reverse vaccinology with machine learning. Vaxign2 is a comprehensive web server for rational vaccine design, consisting of predictive and computational workflow components. The predictive part includes the original Vaxign filtering-based method and a new machine learning-based method, Vaxign-ML. The benchmarking results using a validation dataset showed that Vaxign-ML had superior prediction performance compared to other RV tools. Besides the prediction component, Vaxign2 implemented various post-prediction analyses to significantly enhance users\u2019 capability to refine the prediction results based on different vaccine design rationales and considerably reduce user time to analyze the Vaxign\/Vaxign-ML prediction results. Users provide proteome sequences as input data, select candidates based on Vaxign outputs and Vaxign-ML scores, and perform post-prediction analysis. Vaxign2 also includes precomputed results from approximately 1 million proteins in 398 proteomes of 36 pathogens. As a demonstration, Vaxign2 was used to effectively analyse SARS-CoV-2, the coronavirus causing COVID-19. The comprehensive framework of Vaxign2 can support better and more rational vaccine design. Vaxign2 is publicly accessible at http:\/\/www.violinet.org\/vaxign2.<\/jats:p>","DOI":"10.1093\/nar\/gkab279","type":"journal-article","created":{"date-parts":[[2021,4,16]],"date-time":"2021-04-16T21:01:58Z","timestamp":1618606918000},"page":"W671-W678","source":"Crossref","is-referenced-by-count":105,"title":["Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning"],"prefix":"10.1093","volume":"49","author":[{"given":"Edison","family":"Ong","sequence":"first","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA"}]},{"given":"Michael F","family":"Cooke","sequence":"additional","affiliation":[{"name":"School of Information, University of Michigan, Ann Arbor, MI\u00a048109, USA"},{"name":"Undergraduate Research Opportunity Program, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA"}]},{"given":"Anthony","family":"Huffman","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA"}]},{"given":"Zuoshuang","family":"Xiang","sequence":"additional","affiliation":[{"name":"Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA"}]},{"given":"Mei U","family":"Wong","sequence":"additional","affiliation":[{"name":"Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA"}]},{"given":"Haihe","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pathogenobiology, Daqing Branch of Harbin Medical University, Daqing, Helongjiang, China"}]},{"given":"Meenakshi","family":"Seetharaman","sequence":"additional","affiliation":[{"name":"Undergraduate Research Opportunity Program, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA"}]},{"given":"Ninotchka","family":"Valdez","sequence":"additional","affiliation":[{"name":"Undergraduate Research Opportunity Program, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI 48109, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9189-9661","authenticated-orcid":false,"given":"Yongqun","family":"He","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"}]}],"member":"286","published-online":{"date-parts":[[2021,5,1]]},"reference":[{"key":"2021070812035600400_B1","author":"World Health Organization","year":"2020"},{"key":"2021070812035600400_B2","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1080\/08998280.2005.11928028","article-title":"Edward Jenner and the history of smallpox and vaccination","volume":"18","author":"Riedel","year":"2005","journal-title":"Baylor Univ. 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