{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T06:20:40Z","timestamp":1773382840604,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,3,17]],"date-time":"2024-03-17T00:00:00Z","timestamp":1710633600000},"content-version":"vor","delay-in-days":55,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Computational predictors of immunogenic peptides, or epitopes, are traditionally built based on data from a broad range of pathogens without consideration for taxonomic information. While this approach may be reasonable if one aims to develop one-size-fits-all models, it may be counterproductive if the proteins for which the model is expected to generalize are known to come from a specific subset of phylogenetically related pathogens. There is mounting evidence that, for these cases, taxon-specific models can outperform generalist ones, even when trained with substantially smaller amounts of data. In this comment, we provide some perspective on the current state of taxon-specific modelling for the prediction of linear B-cell epitopes, and the challenges faced when building and deploying these predictors.<\/jats:p>","DOI":"10.1093\/bib\/bbae092","type":"journal-article","created":{"date-parts":[[2024,3,17]],"date-time":"2024-03-17T03:33:38Z","timestamp":1710646418000},"source":"Crossref","is-referenced-by-count":3,"title":["The rise of taxon-specific epitope predictors"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8432-4325","authenticated-orcid":false,"given":"Felipe","family":"Campelo","sequence":"first","affiliation":[{"name":"Aston University Aston Centre for Artificial Intelligence Research and Application, , Aston Triangle, B4 7ET, Birmingham, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9671-9313","authenticated-orcid":false,"given":"Francisco P","family":"Lobo","sequence":"additional","affiliation":[{"name":"Universidade Federal de Minas Gerais Department of Genetics, Ecology and Evolution, , Av. Antonio Carlos 6627, 31270-901, Belo Horizonte, MG, Brazil"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,3,16]]},"reference":[{"issue":"D1","key":"2024031703333343300_ref1","doi-asserted-by":"crossref","first-page":"D339","DOI":"10.1093\/nar\/gky1006","article-title":"The immune epitope database (IEDB): 2018 update","volume":"47","author":"Vita","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"24","key":"2024031703333343300_ref2","doi-asserted-by":"crossref","first-page":"4826","DOI":"10.1093\/bioinformatics\/btab536","article-title":"Organism-specific training improves performance of linear B-cell epitope prediction","volume":"37","author":"Ashford","year":"2021","journal-title":"Bioinformatics"},{"key":"2024031703333343300_ref3","doi-asserted-by":"crossref","DOI":"10.1101\/2022.09.08.507179","article-title":"Phylogeny-aware linear B-cell epitope predictor detects candidate targets for specific immune responses to Monkeypox virus","author":"Campelo","year":"2022"},{"issue":"3","key":"2024031703333343300_ref4","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbad114","article-title":"epitope1D: accurate taxonomy-aware B-cell linear epitope prediction","volume":"24","author":"da Silva","year":"2023","journal-title":"Brief Bioinformatics"},{"issue":"6","key":"2024031703333343300_ref5","doi-asserted-by":"crossref","first-page":"3669","DOI":"10.1109\/TCBB.2023.3311444","article-title":"Family-specific training improves linear b cell epitope prediction for emerging viruses","volume":"20","author":"Liu","year":"2023","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"5","key":"2024031703333343300_ref6","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbac281","article-title":"A framework for predicting variable-length epitopes of human-adapted viruses using machine learning methods","volume":"23","author":"Yin","year":"2022","journal-title":"Brief Bioinform"},{"key":"2024031703333343300_ref7","volume-title":"International Code of Zoological Nomenclature - Glossary","author":"International Commission on Zoological Nomenclature","year":"2000"},{"issue":"6","key":"2024031703333343300_ref8","doi-asserted-by":"crossref","first-page":"100728","DOI":"10.1016\/j.patter.2023.100728","article-title":"CALANGO: a phylogeny-aware comparative genomics tool for discovering quantitative genotype-phenotype associations across species","volume":"4","author":"Hongo","year":"2023","journal-title":"Patterns"},{"key":"2024031703333343300_ref9","article-title":"Estimated limits of organism-specific training for epitope prediction","volume-title":"Proceedings of the 2023 IEEE International Conference on Bioinformatics and Biomedicine, Istanbul, Turkyie","author":"Ashford","year":"2023"},{"issue":"23","key":"2024031703333343300_ref10","doi-asserted-by":"crossref","first-page":"4517","DOI":"10.1093\/bioinformatics\/btab467","article-title":"EpitopeVec: linear epitope prediction using deep protein sequence embeddings","volume":"37","author":"Bahai","year":"2021","journal-title":"Bioinformatics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/2\/bbae092\/56993007\/bbae092.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/2\/bbae092\/56993007\/bbae092.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,3,17]],"date-time":"2024-03-17T03:33:43Z","timestamp":1710646423000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae092\/7630284"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,22]]},"references-count":10,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,1,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae092","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,3,1]]},"published":{"date-parts":[[2024,1,22]]},"article-number":"bbae092"}}