{"doi":"10.1002/advs.202508896","title":"B‐EPIC: A Transformer‐Based Language Model for Decoding B Cell Immunodominance Patterns","abstract":"Vaccine development for pathogens has faced significant challenges, contributing to a public health burden. B-cell epitope (BCE) prediction is a crucial process in vaccine development, but is hindered by limited efficiency and accuracy. To address this, B-Epic, the first pipeline applying Transformer to predict BCEs is independently developed. B-Epic's robustness is validated through multiple testing datasets, including distinguishing clinically-approved vaccine targets, identifying BCEs (the Immune Epitope Database testing dataset; n = 23,888) and immunoreactive peptides (Trypanosoma cruzi peptidome; n = 239,575) with high AUCs of 0.882 and 0.945, respectively, outperforming widely used tools. Based on its superior performance, B-Epic is applied to the prevention of carcinogenic pathogens. In the application to Helicobacter pylori, peptides screened by B-Epic can activate B cells in experiments, suggesting their potential as vaccine targets. In another application to Epstein-Barr virus, B-Epic identifies pan-immunoreactive peptides in a clinical cohort (n = 899). These peptides exhibit higher reactogenicity in nasopharyngeal carcinoma patients than in healthy controls (n = 140), indicating their viability as immunodiagnostic targets. Overall, B-Epic utilizes self-attention, high-dimensional feature projection, and convolutional neural networks to autonomously extract complicated BCE features, enabling accurate BCE prediction and thereby facilitating efforts to prevent infectious diseases and cancers.","journal":"Advanced Science","year":2025,"id":577047,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9523,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1486290,"name":"Youtao Wang","orcid":null,"position":1,"is_corresponding":false},{"id":1485799,"name":"Cong Sun","orcid":"0000-0003-1786-7420","position":2,"is_corresponding":false},{"id":1485800,"name":"Tao Liu","orcid":"0000-0001-8090-1447","position":3,"is_corresponding":false},{"id":1485801,"name":"Zhongtao Wu","orcid":"0000-0001-7991-0194","position":4,"is_corresponding":false},{"id":1485802,"name":"Lipeng Chen","orcid":"0000-0003-2169-2766","position":5,"is_corresponding":false},{"id":850884,"name":"Lina Chen","orcid":"0000-0002-4576-6814","position":6,"is_corresponding":false},{"id":1485803,"name":"Penglin Li","orcid":"0000-0003-4440-8457","position":7,"is_corresponding":false},{"id":1486291,"name":"Zhengkang Li","orcid":null,"position":8,"is_corresponding":false},{"id":1486292,"name":"Cangui Zhang","orcid":null,"position":9,"is_corresponding":false},{"id":1485804,"name":"Bingyun Lu","orcid":"0000-0002-0358-1379","position":10,"is_corresponding":false},{"id":451820,"name":"Ye Chen","orcid":"0000-0002-7964-7899","position":11,"is_corresponding":false},{"id":1485805,"name":"Bing Gu","orcid":"0000-0001-7764-3213","position":12,"is_corresponding":false},{"id":635157,"name":"Qian Zhong","orcid":"0000-0003-1071-6996","position":13,"is_corresponding":false},{"id":239664,"name":"Sophie Wang","orcid":"0000-0001-9735-606X","position":14,"is_corresponding":false},{"id":469649,"name":"Mu‐Sheng Zeng","orcid":"0000-0003-3509-5591","position":15,"is_corresponding":false},{"id":857720,"name":"Jinping Liu","orcid":"0000-0002-4854-1610","position":16,"is_corresponding":false},{"id":1486289,"name":"Junze Liang","orcid":null,"position":0,"is_corresponding":true}],"reference_count":65,"raw_metadata":null,"created_at":"2026-07-19T02:58:00.620755Z","pmid":"41054859","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}