{"id":"https://openalex.org/W4406917211","doi":"https://doi.org/10.1038/s42256-024-00971-y","title":"Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens","display_name":"Deep learning enhances the prediction of HLA class I-presented CD8+ T cell epitopes in foreign pathogens","publication_year":2025,"publication_date":"2025-01-28","ids":{"openalex":"https://openalex.org/W4406917211","doi":"https://doi.org/10.1038/s42256-024-00971-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/40008296"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-024-00971-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00971-y","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1038/s42256-024-00971-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082461467","display_name":"Jeremy Wohlwend","orcid":"https://orcid.org/0000-0002-1993-2380"},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy Wohlwend","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA","Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA USA","Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA, USA","Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054370453","display_name":"Anusha Nathan","orcid":"https://orcid.org/0000-0002-4418-1005"},"institutions":[{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anusha Nathan","raw_affiliation_strings":["Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA USA","Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","institution_ids":["https://openalex.org/I2802422659"]},{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I2802422659","https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008684312","display_name":"Nitan Shalon","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nitan Shalon","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA","Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA USA","Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA, USA","Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022908215","display_name":"Charles R. Crain","orcid":null},"institutions":[{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Charles R. Crain","raw_affiliation_strings":["Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","institution_ids":["https://openalex.org/I2802422659"]},{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I2802422659","https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081736167","display_name":"Rhoda Tano-Menka","orcid":null},"institutions":[{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rhoda Tano-Menka","raw_affiliation_strings":["Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","institution_ids":["https://openalex.org/I2802422659"]},{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I2802422659","https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Benjamin Goldberg","orcid":"https://orcid.org/0009-0007-0403-6181"},"institutions":[{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin Goldberg","raw_affiliation_strings":["Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0009-0007-0403-6181","affiliations":[{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","institution_ids":["https://openalex.org/I2802422659"]},{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I2802422659","https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015923466","display_name":"Esther Richards","orcid":"https://orcid.org/0000-0003-3568-9023"},"institutions":[{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Emma Richards","raw_affiliation_strings":["Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","institution_ids":["https://openalex.org/I2802422659"]},{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I2802422659","https://openalex.org/I4210087915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007482995","display_name":"Gaurav D. Gaiha","orcid":"https://orcid.org/0000-0001-6875-4472"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I2802422659","display_name":"Ragon Institute of MGH, MIT and Harvard","ror":"https://ror.org/053r20n13","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I48633490","https://openalex.org/I63966007"]},{"id":"https://openalex.org/I4210087915","display_name":"Massachusetts General Hospital","ror":"https://ror.org/002pd6e78","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210087915","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gaurav D. Gaiha","raw_affiliation_strings":["Division of Gastroenterology, Massachusetts General Hospital, Boston, MA USA","Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA USA","Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA, USA","Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA"],"raw_orcid":"https://orcid.org/0000-0001-6875-4472","affiliations":[{"raw_affiliation_string":"Division of Gastroenterology, Massachusetts General Hospital, Boston, MA USA","institution_ids":["https://openalex.org/I4210087915"]},{"raw_affiliation_string":"Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA USA","institution_ids":["https://openalex.org/I2802422659"]},{"raw_affiliation_string":"Program in Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Boston, MA, USA","institution_ids":["https://openalex.org/I136199984","https://openalex.org/I63966007"]},{"raw_affiliation_string":"Ragon Institute of Mass General, MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I2802422659","https://openalex.org/I4210087915"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5010124873","display_name":"Regina Barzilay","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Regina Barzilay","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA","Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA USA","Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA, USA","Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Jameel Clinic, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA","institution_ids":["https://openalex.org/I63966007"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5007482995","https://openalex.org/A5010124873"],"corresponding_institution_ids":["https://openalex.org/I136199984","https://openalex.org/I2802422659","https://openalex.org/I4210087915","https://openalex.org/I63966007"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":{"value":9750,"currency":"EUR","value_usd":11690},"fwci":13.3491,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.99280489,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"7","issue":"2","first_page":"232","last_page":"243"},"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":0.9980999827384949,"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":0.9869999885559082,"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/epitope","display_name":"Epitope","score":0.8596035242080688},{"id":"https://openalex.org/keywords/immunogenicity","display_name":"Immunogenicity","score":0.77997225522995},{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.6981813311576843},{"id":"https://openalex.org/keywords/cd8","display_name":"CD8","score":0.6020570397377014},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5597871541976929},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5162796378135681},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.4825548529624939},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.46171805262565613},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4231563210487366},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.34314224123954773},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.3312642574310303},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.32620730996131897},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14058709144592285},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10215607285499573}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.8596035242080688},{"id":"https://openalex.org/C2780868878","wikidata":"https://www.wikidata.org/wiki/Q1660197","display_name":"Immunogenicity","level":3,"score":0.77997225522995},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.6981813311576843},{"id":"https://openalex.org/C167672396","wikidata":"https://www.wikidata.org/wiki/Q417800","display_name":"CD8","level":3,"score":0.6020570397377014},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5597871541976929},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5162796378135681},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.4825548529624939},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.46171805262565613},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4231563210487366},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.34314224123954773},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3312642574310303},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.32620730996131897},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14058709144592285},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10215607285499573}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1038/s42256-024-00971-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00971-y","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},{"id":"pmid:40008296","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40008296","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":"Nature machine intelligence","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11847706","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11847706","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11847706/pdf/42256_2024_Article_971.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":"Nat Mach Intell","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1038/s42256-024-00971-y","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00971-y","pdf_url":null,"source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G1330203626","display_name":null,"funder_award_id":"T32GM144273","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2316316837","display_name":null,"funder_award_id":"T32GM144273","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4484206110","display_name":null,"funder_award_id":"T32GM007753","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G5513406193","display_name":null,"funder_award_id":"T32 GM144273","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G674738779","display_name":null,"funder_award_id":"T32GM007753, T32GM144273","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G707340384","display_name":null,"funder_award_id":"T32GM007753","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7638773934","display_name":null,"funder_award_id":"T32GM144273","funder_id":"https://openalex.org/F4320306085","funder_display_name":"U.S. Department of Health and Human Services"},{"id":"https://openalex.org/G783456948","display_name":"The General Hospital Corporation d/b/a Massachusetts General Hospital - to develop a vaccine against HPV","funder_award_id":"INV-027454","funder_id":"https://openalex.org/F4320306137","funder_display_name":"Bill and Melinda Gates Foundation"},{"id":"https://openalex.org/G8911445315","display_name":null,"funder_award_id":"T32GM007753","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306085","display_name":"U.S. Department of Health and Human Services","ror":"https://ror.org/033jnv181"},{"id":"https://openalex.org/F4320306133","display_name":"Burroughs Wellcome Fund","ror":"https://ror.org/01d35cw23"},{"id":"https://openalex.org/F4320306137","display_name":"Bill and Melinda Gates Foundation","ror":"https://ror.org/0456r8d26"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1540078095","https://openalex.org/W1973980688","https://openalex.org/W1993417435","https://openalex.org/W2064675550","https://openalex.org/W2097398162","https://openalex.org/W2129225392","https://openalex.org/W2158882181","https://openalex.org/W2162567066","https://openalex.org/W2168688111","https://openalex.org/W2303521084","https://openalex.org/W2337777524","https://openalex.org/W2509856146","https://openalex.org/W2605808699","https://openalex.org/W2613978126","https://openalex.org/W2792754198","https://openalex.org/W2808143659","https://openalex.org/W2898389621","https://openalex.org/W2911366108","https://openalex.org/W2979330275","https://openalex.org/W2987502822","https://openalex.org/W2995389725","https://openalex.org/W2998313390","https://openalex.org/W3005830045","https://openalex.org/W3009999407","https://openalex.org/W3014003872","https://openalex.org/W3016322638","https://openalex.org/W3023033208","https://openalex.org/W3024570138","https://openalex.org/W3042910002","https://openalex.org/W3091991776","https://openalex.org/W3094126920","https://openalex.org/W3101796750","https://openalex.org/W3127841695","https://openalex.org/W3132833117","https://openalex.org/W3146944767","https://openalex.org/W3163762505","https://openalex.org/W3170322470","https://openalex.org/W3176494753","https://openalex.org/W3179554769","https://openalex.org/W3196626346","https://openalex.org/W4205972999","https://openalex.org/W4210664421","https://openalex.org/W4210792795","https://openalex.org/W4213149192","https://openalex.org/W4220655797","https://openalex.org/W4220726792","https://openalex.org/W4290774080","https://openalex.org/W4313453360","https://openalex.org/W4313492115","https://openalex.org/W4327550249","https://openalex.org/W4362633841","https://openalex.org/W4380225153","https://openalex.org/W4384934897","https://openalex.org/W4385507310","https://openalex.org/W4389127896","https://openalex.org/W6968463214"],"related_works":["https://openalex.org/W1581415616","https://openalex.org/W1552738310","https://openalex.org/W4250292386","https://openalex.org/W2021824670","https://openalex.org/W2030908446","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W2470318958","https://openalex.org/W2019183242","https://openalex.org/W203802859"],"abstract_inverted_index":{"Abstract":[0],"Accurate":[1],"in":[2,73,110,127],"silico":[3],"determination":[4],"of":[5,41,87,98,129,143],"CD8":[6,78,144],"+":[7,79,145],"T":[8,14,80,115,146,151],"cell":[9,81,116,147,152],"epitopes":[10,104,148],"would":[11],"greatly":[12],"enhance":[13],"cell-based":[15],"vaccine":[16,153],"development,":[17],"but":[18],"current":[19],"prediction":[20],"models":[21,72],"are":[22],"not":[23],"reliably":[24],"successful.":[25],"Here,":[26],"motivated":[27],"by":[28,62,109],"recent":[29],"successes":[30],"applying":[31],"machine":[32],"learning":[33,56,135],"to":[34,89,95,122],"complex":[35],"biology,":[36],"we":[37],"curated":[38],"a":[39,54],"dataset":[40],"651,237":[42],"unique":[43],"human":[44],"leukocyte":[45],"antigen":[46],"class":[47],"I":[48],"(HLA-I)":[49],"ligands":[50],"and":[51,77,101,114,140],"developed":[52],"MUNIS,":[53],"deep":[55,134],"model":[57],"that":[58,133],"identifies":[59],"peptides":[60],"presented":[61],"HLA-I":[63,103],"alleles.":[64],"MUNIS":[65,88,119],"shows":[66],"improved":[67],"performance":[68],"compared":[69],"with":[70],"existing":[71],"predicting":[74],"peptide":[75],"presentation":[76],"epitope":[82],"immunodominance":[83],"hierarchies.":[84],"Moreover,":[85],"application":[86],"proteins":[90],"from":[91],"Epstein\u2013Barr":[92],"virus":[93],"led":[94],"successful":[96],"identification":[97,142],"both":[99],"established":[100],"novel":[102],"which":[105],"were":[106],"experimentally":[107],"validated":[108],"vitro":[111],"HLA-I-peptide":[112],"stability":[113,125],"immunogenicity":[117,130],"assays.":[118],"performs":[120],"comparably":[121],"an":[123],"experimental":[124,138],"assay":[126],"terms":[128],"prediction,":[131],"suggesting":[132],"can":[136],"reduce":[137],"burden":[139],"accelerate":[141],"for":[149],"rapid":[150],"development.":[154]},"counts_by_year":[{"year":2026,"cited_by_count":19},{"year":2025,"cited_by_count":12}],"updated_date":"2026-07-17T09:13:05.818461","created_date":"2025-01-29T00:00:00"}