{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,15]],"date-time":"2026-06-15T17:41:03Z","timestamp":1781545263707,"version":"3.54.5"},"reference-count":20,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T00:00:00Z","timestamp":1686614400000},"content-version":"vor","delay-in-days":163,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771373"],"award-info":[{"award-number":["31771373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Shanghai Science and Technology Commission","doi-asserted-by":"publisher","award":["21ZR1442400"],"award-info":[{"award-number":["21ZR1442400"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012600","name":"ShanghaiTech University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012600","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771373"],"award-info":[{"award-number":["31771373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Shanghai Science and Technology Commission","doi-asserted-by":"publisher","award":["21ZR1442400"],"award-info":[{"award-number":["21ZR1442400"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012600","name":"ShanghaiTech University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012600","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Neoantigens derived from somatic deoxyribonucleic acid alterations are ideal cancer-specific targets. However, integrated platform for neoantigen discovery is urgently needed. Recently, many scattered experimental evidences suggest that some neoantigens are immunogenic, and comprehensive collection of these experimentally validated neoantigens is still lacking. Here, we have integrated the commonly used tools in the current neoantigen discovery process to form a comprehensive web-based analysis platform. To identify experimental evidences supporting the immunogenicity of neoantigens, we performed comprehensive literature search and constructed the database. The collection of public neoantigens was obtained by using comprehensive features to filter the potential neoantigens from recurrent driver mutations. Importantly, we constructed a graph neural network (GNN) model (Immuno-GNN) using an attention mechanism to consider the spatial interactions between human leukocyte antigen and antigenic peptides for neoantigen immunogenicity prediction. The new easy-to-use R\/Shiny web\u2013based neoantigen database and discovery platform, Neodb, contains currently the largest number of experimentally validated neoantigens. In addition to validated neoantigen, Neodb also includes three additional modules for facilitating neoantigen prediction and analysis, including \u2018Tools\u2019 module (comprehensive neoantigen prediction tools); \u2018Driver-Neo\u2019 module (collection of public neoantigens derived from recurrent mutations) and \u2018Immuno-GNN\u2019 module (a novel immunogenicity prediction tool based on a GNN). Immuno-GNN shows improved performance compared with known methods and also represents the first application of GNN model in neoantigen immunogenicity prediction. The construction of Neodb will facilitate the study of neoantigen immunogenicity and the clinical application of neoantigen-based cancer immunotherapy.<\/jats:p>\n               <jats:p>Database URL https:\/\/liuxslab.com\/Neodb\/<\/jats:p>","DOI":"10.1093\/database\/baad041","type":"journal-article","created":{"date-parts":[[2023,6,13]],"date-time":"2023-06-13T18:23:52Z","timestamp":1686680632000},"source":"Crossref","is-referenced-by-count":21,"title":["Neodb: a comprehensive neoantigen database and\u00a0discovery platform for\u00a0cancer immunotherapy"],"prefix":"10.1093","volume":"2023","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8999-9628","authenticated-orcid":false,"given":"Tao","family":"Wu","sequence":"first","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 393 Middle Huaxia Road, Pudong, Shanghai 201203, China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , 320 Yue Yang Road, Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences , 1 Yanqihu East Rd, Huairou District, Beijing 101408, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 393 Middle Huaxia Road, Pudong, Shanghai 201203, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaixuan","family":"Diao","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 393 Middle Huaxia Road, Pudong, Shanghai 201203, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangshuai","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 393 Middle Huaxia Road, Pudong, Shanghai 201203, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinyu","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 393 Middle Huaxia Road, Pudong, Shanghai 201203, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huizi","family":"Yao","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 393 Middle Huaxia Road, Pudong, Shanghai 201203, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7736-0077","authenticated-orcid":false,"given":"Xue-Song","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , 393 Middle Huaxia Road, Pudong, Shanghai 201203, China"},{"name":"Shanghai Clinical Research and Trial Center , 1599 Keyuan Road, Pudong New Area, Shanghai 201203, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,6,13]]},"reference":[{"key":"2023061318425287200_R1","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1126\/science.aaa4971","article-title":"Neoantigens in\u00a0cancer immunotherapy","volume":"348","author":"Schumacher","year":"2015","journal-title":"Science"},{"key":"2023061318425287200_R2","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1038\/s43018-021-00210-y","article-title":"Targeting public neoantigens for\u00a0cancer immunotherapy","volume":"2","author":"Pearlman","year":"2021","journal-title":"Nat. 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