{"id":"https://openalex.org/W4388843713","doi":"https://doi.org/10.1371/journal.pcbi.1011664","title":"Neural network models for sequence-based TCR and HLA association prediction","display_name":"Neural network models for sequence-based TCR and HLA association prediction","publication_year":2023,"publication_date":"2023-11-20","ids":{"openalex":"https://openalex.org/W4388843713","doi":"https://doi.org/10.1371/journal.pcbi.1011664","pmid":"https://pubmed.ncbi.nlm.nih.gov/37983288"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011664","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011664","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011664&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011664&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009625485","display_name":"Si Liu","orcid":"https://orcid.org/0000-0003-1289-7241"},"institutions":[{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Si Liu","raw_affiliation_strings":["Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067744380","display_name":"Philip Bradley","orcid":"https://orcid.org/0000-0002-0224-6464"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip Bradley","raw_affiliation_strings":["Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","Institute for Protein Design. University of Washington, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Institute for Protein Design. University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086153438","display_name":"Wei Sun","orcid":"https://orcid.org/0000-0002-6350-1107"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]},{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I4210089486","display_name":"Fred Hutch Cancer Center","ror":"https://ror.org/007ps6h72","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210089486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wei Sun","raw_affiliation_strings":["Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America","Department of Biostatistics, University of Washington, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-6350-1107","affiliations":[{"raw_affiliation_string":"Biostatistics Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I4210089486"]},{"raw_affiliation_string":"Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America","institution_ids":["https://openalex.org/I114027177"]},{"raw_affiliation_string":"Department of Biostatistics, University of Washington, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009625485","https://openalex.org/A5086153438"],"corresponding_institution_ids":["https://openalex.org/I114027177","https://openalex.org/I201448701","https://openalex.org/I4210089486"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.2056,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.78244008,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"19","issue":"11","first_page":"e1011664","last_page":"e1011664"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"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":0.9998999834060669,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.9998000264167786,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9998000264167786,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.7925403118133545},{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.7585701942443848},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5484946966171265},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.5151501893997192},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4739121198654175},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.4366093873977661},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.4216201901435852},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.41584861278533936},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3857088088989258},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.3716033101081848},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.3204286992549896},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1834145486354828}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.7925403118133545},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.7585701942443848},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5484946966171265},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.5151501893997192},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4739121198654175},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.4366093873977661},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.4216201901435852},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.41584861278533936},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3857088088989258},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.3716033101081848},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.3204286992549896},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1834145486354828}],"mesh":[{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000949","descriptor_name":"Histocompatibility Antigens Class II","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011664","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011664","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011664&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37983288","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37983288","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10695368","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10695368","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10695368/pdf/pcbi.1011664.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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:5416700ae9fd4612a1e4c89c9b0c9eee","is_oa":true,"landing_page_url":"https://doaj.org/article/5416700ae9fd4612a1e4c89c9b0c9eee","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 11, p e1011664 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011664","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011664","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011664&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6800000071525574}],"awards":[{"id":"https://openalex.org/G2972819009","display_name":null,"funder_award_id":"R56 AI169192","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5172056821","display_name":null,"funder_award_id":"R35GM141457","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G686205711","display_name":null,"funder_award_id":"R01 CA 222833","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G736634319","display_name":null,"funder_award_id":"R01 GM105785","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7641855279","display_name":null,"funder_award_id":"R35GM141457","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388843713.pdf","grobid_xml":"https://content.openalex.org/works/W4388843713.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W2112752664","https://openalex.org/W2140323624","https://openalex.org/W2142739377","https://openalex.org/W2158485828","https://openalex.org/W2166593999","https://openalex.org/W2587374790","https://openalex.org/W2605177850","https://openalex.org/W2613978126","https://openalex.org/W2671261300","https://openalex.org/W2774712455","https://openalex.org/W2794804602","https://openalex.org/W2795989238","https://openalex.org/W2796207838","https://openalex.org/W2951959160","https://openalex.org/W2966465234","https://openalex.org/W2981568805","https://openalex.org/W2991341799","https://openalex.org/W3047483639","https://openalex.org/W3116512470","https://openalex.org/W3163602801","https://openalex.org/W3184584468","https://openalex.org/W3196626346","https://openalex.org/W3198942356","https://openalex.org/W4200468913","https://openalex.org/W4206471589","https://openalex.org/W4210297691","https://openalex.org/W4224286034","https://openalex.org/W4281834364"],"related_works":["https://openalex.org/W2011835836","https://openalex.org/W2089872551","https://openalex.org/W1973836350","https://openalex.org/W2038509173","https://openalex.org/W2136036540","https://openalex.org/W2075125040","https://openalex.org/W2113488569","https://openalex.org/W3032468696","https://openalex.org/W2176905394","https://openalex.org/W2381567441"],"abstract_inverted_index":{"T":[0,5],"cells":[1],"rely":[2],"on":[3,158],"their":[4,159],"cell":[6],"receptors":[7],"(TCRs)":[8],"to":[9,38,122,124,153,199],"discern":[10],"foreign":[11],"antigens":[12],"presented":[13],"by":[14,114],"human":[15],"leukocyte":[16],"antigen":[17],"(HLA)":[18],"proteins.":[19],"The":[20,81],"TCRs":[21,59,73],"of":[22,28,78,84,90,149,169,218],"an":[23,112],"individual":[24],"contain":[25],"a":[26,75,95,107,141],"record":[27],"this":[29,99,137],"individual's":[30],"past":[31],"immune":[32,36,53,223],"activities,":[33],"such":[34],"as":[35,106],"response":[37],"infections":[39],"or":[40,50,56,110],"vaccines.":[41],"Mining":[42],"the":[43,64,88,125,132,179,182,188,201,215],"TCR":[44,183],"data":[45],"may":[46],"recover":[47],"useful":[48],"information":[49],"biomarkers":[51],"for":[52,98,173],"related":[54],"diseases":[55],"conditions.":[57],"Some":[58],"are":[60,128,212],"observed":[61],"only":[62],"in":[63,131,187],"individuals":[65],"with":[66,214],"certain":[67],"HLA":[68,85,92,105,113,180,205,210],"alleles,":[69,206],"and":[70,87,118,207],"thus":[71],"characterizing":[72],"requires":[74],"thorough":[76],"understanding":[77],"TCR-HLA":[79,150,155,174],"associations.":[80],"extensive":[82],"diversity":[83],"alleles":[86,93],"rareness":[89],"some":[91],"present":[94],"formidable":[96],"challenge":[97],"task.":[100],"Existing":[101],"methods":[102],"either":[103],"treat":[104],"categorical":[108],"variable":[109],"represent":[111],"its":[115],"alphanumeric":[116],"name,":[117],"have":[119,184],"limited":[120],"ability":[121],"generalize":[123],"HLAs":[126],"that":[127,165,194,208],"not":[129],"seen":[130],"training":[133,189],"process.":[134],"To":[135],"address":[136],"challenge,":[138],"we":[139,192],"propose":[140],"neural":[142],"network-based":[143],"method":[144],"named":[145],"Deep":[146],"learning":[147],"Prediction":[148],"association":[151],"(DePTH)":[152],"predict":[154],"associations":[156],"based":[157],"amino":[160],"acid":[161],"sequences.":[162],"We":[163],"demonstrate":[164],"DePTH":[166,195],"is":[167],"capable":[168],"making":[170],"reasonable":[171],"predictions":[172],"associations,":[175],"even":[176],"when":[177],"neither":[178],"nor":[181],"been":[185],"included":[186],"dataset.":[190],"Furthermore,":[191],"establish":[193],"can":[196],"be":[197],"used":[198],"quantify":[200],"functional":[202],"similarities":[203,211],"among":[204],"these":[209],"associated":[213],"survival":[216],"outcomes":[217],"cancer":[219],"patients":[220],"who":[221],"received":[222],"checkpoint":[224],"blockade":[225],"treatments.":[226]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}