{"id":"https://openalex.org/W4400060956","doi":"https://doi.org/10.1093/bib/bbae302","title":"HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses","display_name":"HLAIImaster: a deep learning method with adaptive domain knowledge predicts HLA II neoepitope immunogenic responses","publication_year":2024,"publication_date":"2024-05-23","ids":{"openalex":"https://openalex.org/W4400060956","doi":"https://doi.org/10.1093/bib/bbae302","pmid":"https://pubmed.ncbi.nlm.nih.gov/38920343"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae302","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae302","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae302/58336834/bbae302.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae302/58336834/bbae302.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101648196","display_name":"Qiang Yang","orcid":"https://orcid.org/0000-0002-6524-9443"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiang Yang","raw_affiliation_strings":["School of Medicine and Health, Harbin Institute of Technology , Yikuang Street, Harbin 150000 , China"],"raw_orcid":"https://orcid.org/0000-0002-6524-9443","affiliations":[{"raw_affiliation_string":"School of Medicine and Health, Harbin Institute of Technology , Yikuang Street, Harbin 150000 , China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100713766","display_name":"Long Xu","orcid":"https://orcid.org/0000-0003-4952-9178"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Long Xu","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology , West Dazhi Street, Harbin 150001 , China"],"raw_orcid":"https://orcid.org/0000-0003-4952-9178","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology , West Dazhi Street, Harbin 150001 , China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038137938","display_name":"Weihe Dong","orcid":"https://orcid.org/0000-0001-8022-9793"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weihe Dong","raw_affiliation_strings":["College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, Harbin 150004 , China"],"raw_orcid":"https://orcid.org/0000-0001-8022-9793","affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, Harbin 150004 , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100628723","display_name":"Xiaokun Li","orcid":"https://orcid.org/0000-0002-6645-6890"},"institutions":[{"id":"https://openalex.org/I1300757298","display_name":"Heilongjiang University of Science and Technology","ror":"https://ror.org/030xwyx96","country_code":"CN","type":"education","lineage":["https://openalex.org/I1300757298"]},{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaokun Li","raw_affiliation_strings":["Postdoctoral Program of Heilongjiang Hengxun Technology Co., Ltd. , Xuefu Road, Harbin 150090 , China","School of Computer Science and Technology, Harbin Institute of Technology , West Dazhi Street, Harbin 150001 , China","School of Computer Science and Technology, Heilongjiang University , Xuefu Road, Harbin 150080 , China","Shandong Hengxun Technology Co., Ltd. , Miaoling Road, Qingdao 266100 , China"],"raw_orcid":"https://orcid.org/0000-0002-6645-6890","affiliations":[{"raw_affiliation_string":"Postdoctoral Program of Heilongjiang Hengxun Technology Co., Ltd. , Xuefu Road, Harbin 150090 , China","institution_ids":[]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology , West Dazhi Street, Harbin 150001 , China","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"School of Computer Science and Technology, Heilongjiang University , Xuefu Road, Harbin 150080 , China","institution_ids":["https://openalex.org/I1300757298"]},{"raw_affiliation_string":"Shandong Hengxun Technology Co., Ltd. , Miaoling Road, Qingdao 266100 , China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049558861","display_name":"Kuanquan Wang","orcid":"https://orcid.org/0000-0003-1347-3491"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kuanquan Wang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology , West Dazhi Street, Harbin 150001 , China"],"raw_orcid":"https://orcid.org/0000-0003-1347-3491","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology , West Dazhi Street, Harbin 150001 , China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024430250","display_name":"Suyu Dong","orcid":"https://orcid.org/0000-0001-7521-8782"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Suyu Dong","raw_affiliation_strings":["College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, Harbin 150004 , China"],"raw_orcid":"https://orcid.org/0000-0001-7521-8782","affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, Harbin 150004 , China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101574471","display_name":"Xianyu Zhang","orcid":"https://orcid.org/0000-0002-9738-2361"},"institutions":[{"id":"https://openalex.org/I156144747","display_name":"Harbin Medical University","ror":"https://ror.org/05jscf583","country_code":"CN","type":"education","lineage":["https://openalex.org/I156144747"]},{"id":"https://openalex.org/I4210103956","display_name":"Third Affiliated Hospital of Harbin Medical University","ror":"https://ror.org/01f77gp95","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210103956"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xianyu Zhang","raw_affiliation_strings":["Department of Breast Surgery, Harbin Medical University Cancer Hospital , Haping Road, Harbin 150081 , China"],"raw_orcid":"https://orcid.org/0000-0002-9738-2361","affiliations":[{"raw_affiliation_string":"Department of Breast Surgery, Harbin Medical University Cancer Hospital , Haping Road, Harbin 150081 , China","institution_ids":["https://openalex.org/I156144747","https://openalex.org/I4210103956"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090875515","display_name":"Tiansong Yang","orcid":"https://orcid.org/0000-0002-4008-702X"},"institutions":[{"id":"https://openalex.org/I4210102855","display_name":"First Affiliated Hospital of Heilongjiang University of Chinese Medicine","ror":"https://ror.org/01c0exk17","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210102855"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tiansong Yang","raw_affiliation_strings":["Department of Rehabilitation, The First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, and Traditional Chinese Medicine Informatics Key Laboratory of Heilongjiang Province , Heping Road, Harbin 150040 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Rehabilitation, The First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, and Traditional Chinese Medicine Informatics Key Laboratory of Heilongjiang Province , Heping Road, Harbin 150040 , China","institution_ids":["https://openalex.org/I4210102855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100726088","display_name":"Feng Jiang","orcid":"https://orcid.org/0000-0002-7407-7604"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Jiang","raw_affiliation_strings":["School of Medicine and Health, Harbin Institute of Technology , Yikuang Street, Harbin 150000 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Medicine and Health, Harbin Institute of Technology , Yikuang Street, Harbin 150000 , China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100392792","display_name":"Bin Zhang","orcid":"https://orcid.org/0000-0001-8835-8370"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Bin Zhang","raw_affiliation_strings":["Computer , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","King Abdullah University of Science and Technology , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0001-8835-8370","affiliations":[{"raw_affiliation_string":"Computer , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091843570","display_name":"Gongning Luo","orcid":"https://orcid.org/0000-0003-3662-0335"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Gongning Luo","raw_affiliation_strings":["Computer , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","King Abdullah University of Science and Technology , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0003-3662-0335","affiliations":[{"raw_affiliation_string":"Computer , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Xin Gao","raw_affiliation_strings":["Computer , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","King Abdullah University of Science and Technology , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0002-7108-3574","affiliations":[{"raw_affiliation_string":"Computer , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"King Abdullah University of Science and Technology , Electrical and Mathematical Sciences & Engineering Division, , 4700 KAUST, Thuwal 23955 , Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100649978","display_name":"Guohua Wang","orcid":"https://orcid.org/0000-0001-7381-2374"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guohua Wang","raw_affiliation_strings":["College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, Harbin 150004 , China"],"raw_orcid":"https://orcid.org/0000-0001-7381-2374","affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Northeast Forestry University , Hexing Road, Harbin 150004 , China","institution_ids":["https://openalex.org/I47689461"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.9634,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.92094555,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"25","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/immunogenicity","display_name":"Immunogenicity","score":0.7535822987556458},{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.7019142508506775},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6227058172225952},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.4468112587928772},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3903646469116211},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.3841598629951477},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.3822484016418457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3817330598831177},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.32858142256736755}],"concepts":[{"id":"https://openalex.org/C2780868878","wikidata":"https://www.wikidata.org/wiki/Q1660197","display_name":"Immunogenicity","level":3,"score":0.7535822987556458},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.7019142508506775},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6227058172225952},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.4468112587928772},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3903646469116211},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.3841598629951477},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.3822484016418457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3817330598831177},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.32858142256736755}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D018984","descriptor_name":"Epitopes, T-Lymphocyte","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae302","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae302","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae302/58336834/bbae302.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38920343","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38920343","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11200192","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11200192","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11200192/pdf/bbae302.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae302","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae302","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae302/58336834/bbae302.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1445374915","display_name":null,"funder_award_id":"62272135","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1745487217","display_name":null,"funder_award_id":"62372135","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2058729345","display_name":null,"funder_award_id":"FCC/1/1976-45-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5289953175","display_name":null,"funder_award_id":"REI/1/5234-01-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"},{"id":"https://openalex.org/G5644938599","display_name":null,"funder_award_id":"62202092","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5660135745","display_name":null,"funder_award_id":"2022YFF1202100","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8253667702","display_name":null,"funder_award_id":"FCC/1/1976-44-01","funder_id":"https://openalex.org/F4320322320","funder_display_name":"King Abdullah University of Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400060956.pdf","grobid_xml":"https://content.openalex.org/works/W4400060956.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1501531009","https://openalex.org/W1728842521","https://openalex.org/W1966023886","https://openalex.org/W1972103487","https://openalex.org/W1993772622","https://openalex.org/W2006759360","https://openalex.org/W2040594411","https://openalex.org/W2049553585","https://openalex.org/W2050407789","https://openalex.org/W2059385530","https://openalex.org/W2059874211","https://openalex.org/W2079018735","https://openalex.org/W2111695773","https://openalex.org/W2127284149","https://openalex.org/W2154509769","https://openalex.org/W2167991773","https://openalex.org/W2201214180","https://openalex.org/W2560367415","https://openalex.org/W2589139221","https://openalex.org/W2599601523","https://openalex.org/W2604278061","https://openalex.org/W2724264513","https://openalex.org/W2728365508","https://openalex.org/W2737196618","https://openalex.org/W2747623286","https://openalex.org/W2761575992","https://openalex.org/W2782837367","https://openalex.org/W2784995911","https://openalex.org/W2793859699","https://openalex.org/W2806895459","https://openalex.org/W2806925824","https://openalex.org/W2886770018","https://openalex.org/W2895264449","https://openalex.org/W2898389621","https://openalex.org/W2901218091","https://openalex.org/W2904711643","https://openalex.org/W2953065444","https://openalex.org/W2979293383","https://openalex.org/W2979882137","https://openalex.org/W2982049472","https://openalex.org/W2983176158","https://openalex.org/W2995389725","https://openalex.org/W3024570138","https://openalex.org/W3177828909","https://openalex.org/W3198942356","https://openalex.org/W3205542661","https://openalex.org/W4210348552","https://openalex.org/W4212774754","https://openalex.org/W4233120011","https://openalex.org/W4310215464","https://openalex.org/W4313492115","https://openalex.org/W4313830530","https://openalex.org/W4360752063","https://openalex.org/W4384934897","https://openalex.org/W4385245566","https://openalex.org/W4388899046","https://openalex.org/W4389670882","https://openalex.org/W6637572315","https://openalex.org/W6739901393","https://openalex.org/W6750109254","https://openalex.org/W6851362381"],"related_works":["https://openalex.org/W1581415616","https://openalex.org/W1552738310","https://openalex.org/W4250292386","https://openalex.org/W2021824670","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W2470318958","https://openalex.org/W2428121789","https://openalex.org/W2019183242","https://openalex.org/W203802859"],"abstract_inverted_index":{"While":[0],"significant":[1],"strides":[2],"have":[3],"been":[4],"made":[5],"in":[6,136],"predicting":[7,116],"neoepitopes":[8],"that":[9],"trigger":[10],"autologous":[11],"CD4+":[12],"T":[13],"cell":[14],"responses,":[15],"accurately":[16,150],"identifying":[17],"the":[18,62,71,76,155,161,166,185,192],"antigen":[19,24],"presentation":[20],"by":[21,93],"human":[22,72],"leukocyte":[23],"(HLA)":[25],"class":[26,65],"II":[27],"molecules":[28],"remains":[29],"a":[30,50,181],"challenge.":[31],"This":[32],"identification":[33],"is":[34,130],"critical":[35],"for":[36,115,168],"developing":[37],"vaccines":[38],"and":[39,57,89,100,123,160,164],"cancer":[40],"immunotherapies.":[41],"Current":[42],"prediction":[43],"methods":[44],"are":[45],"limited,":[46],"primarily":[47],"due":[48],"to":[49,80,172],"lack":[51],"of":[52,70,138,184,189,195],"high-quality":[53],"training":[54],"epitope":[55],"datasets":[56],"algorithmic":[58],"constraints.":[59],"To":[60],"predict":[61],"exogenous":[63],"HLA":[64],"II-restricted":[66],"peptides":[67],"across":[68,142],"most":[69],"population,":[73],"we":[74,103,179],"utilized":[75],"mass":[77],"spectrometry":[78],"data":[79,96],"profile":[81],">223":[82],"000":[83],"eluted":[84],"ligands":[85],"over":[86],"HLA-DR,":[87],"-DQ,":[88],"-DP":[90],"alleles.":[91],"Here,":[92],"integrating":[94],"these":[95],"with":[97,111],"peptide":[98],"processing":[99],"gene":[101],"expression,":[102],"introduce":[104],"HLAIImaster,":[105],"an":[106],"attention-based":[107],"deep":[108,126],"learning":[109,127,149],"framework":[110],"adaptive":[112],"domain":[113,147],"knowledge":[114,148],"neoepitope":[117,152,187],"immunogenicity.":[118],"Leveraging":[119],"diverse":[120],"biological":[121],"characteristics":[122],"our":[124],"enhanced":[125],"framework,":[128],"HLAIImaster":[129],"significantly":[131],"improved":[132],"against":[133],"existing":[134],"tools":[135],"terms":[137],"positive":[139],"predictive":[140],"value":[141],"various":[143],"neoantigen":[144,158],"studies.":[145],"Robust":[146],"identifies":[151],"immunogenicity,":[153],"bridging":[154],"gap":[156],"between":[157],"biology":[159],"clinical":[162,175],"setting":[163],"paving":[165],"way":[167],"future":[169],"neoantigen-based":[170],"therapies":[171],"provide":[173],"greater":[174],"benefit.":[176],"In":[177],"summary,":[178],"present":[180],"comprehensive":[182],"exploitation":[183],"immunogenic":[186],"repertoire":[188],"cancers,":[190],"facilitating":[191],"effective":[193],"development":[194],"\"just-in-time\"":[196],"personalized":[197],"vaccines.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
