{"id":"https://openalex.org/W4410841061","doi":"https://doi.org/10.1093/bib/bbaf246","title":"LightCTL: lightweight contrastive TCR-pMHC specificity learning with context-aware prompt","display_name":"LightCTL: lightweight contrastive TCR-pMHC specificity learning with context-aware prompt","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4410841061","doi":"https://doi.org/10.1093/bib/bbaf246","pmid":"https://pubmed.ncbi.nlm.nih.gov/40439672"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf246","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf246/63398247/bbaf246.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/26/3/bbaf246/63398247/bbaf246.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100357209","display_name":"Fei Ye","orcid":"https://orcid.org/0000-0001-9512-3625"},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Ye","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":"https://orcid.org/0000-0001-9512-3625","affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Mao Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mao Chen","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114763064","display_name":"Yixuan Huang","orcid":"https://orcid.org/0000-0001-5204-5866"},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yixuan Huang","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101548217","display_name":"Ruihao Zhang","orcid":"https://orcid.org/0000-0002-0497-2566"},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruihao Zhang","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040611892","display_name":"Xuqi Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuqi Li","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051082655","display_name":"Xiuyuan Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiuyuan Wang","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020235901","display_name":"Sanyang Han","orcid":"https://orcid.org/0000-0001-7414-7193"},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Sanyang Han","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100699242","display_name":"Lan Ma","orcid":"https://orcid.org/0000-0003-3593-5626"},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lan Ma","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049736356","display_name":"Xiao Liu","orcid":"https://orcid.org/0009-0000-9541-0560"},"institutions":[{"id":"https://openalex.org/I4210114105","display_name":"Tsinghua\u2013Berkeley Shenzhen Institute","ror":"https://ror.org/02hhwwz98","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210114105","https://openalex.org/I95457486","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Liu","raw_affiliation_strings":["Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Biopharmaceutical and Health Engineering , Tsinghua ShenZhen International Graduate School, Tsinghua University, Lishui Road, Nanshan District, Shenzhen, Guangdong Province 518055,","institution_ids":["https://openalex.org/I4210114105","https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"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":1.7148,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.83598412,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"26","issue":"3","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":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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9959999918937683,"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.9940999746322632,"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":0.8427524566650391},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6393643021583557},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6300973892211914},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5985860228538513},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5283753871917725},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.47759437561035156},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.4751717448234558},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.42248648405075073},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.30102062225341797},{"id":"https://openalex.org/keywords/t-cell","display_name":"T cell","score":0.3000433146953583},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.2433561086654663},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.163619726896286},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13319042325019836},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.12916868925094604},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09923350811004639},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09704622626304626}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.8427524566650391},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6393643021583557},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6300973892211914},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5985860228538513},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5283753871917725},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.47759437561035156},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.4751717448234558},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.42248648405075073},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30102062225341797},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.3000433146953583},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.2433561086654663},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.163619726896286},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13319042325019836},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.12916868925094604},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09923350811004639},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09704622626304626},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"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":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf246","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf246/63398247/bbaf246.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40439672","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40439672","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:12121355","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12121355","pdf_url":null,"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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf246","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf246","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf246/63398247/bbaf246.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410841061.pdf","grobid_xml":"https://content.openalex.org/works/W4410841061.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1969500780","https://openalex.org/W2064675550","https://openalex.org/W2067069532","https://openalex.org/W2120518061","https://openalex.org/W2140323624","https://openalex.org/W2142739377","https://openalex.org/W2145831493","https://openalex.org/W2157384708","https://openalex.org/W2560674852","https://openalex.org/W2605177850","https://openalex.org/W2613978126","https://openalex.org/W2670890989","https://openalex.org/W2766169371","https://openalex.org/W2797380951","https://openalex.org/W2803170063","https://openalex.org/W2894849296","https://openalex.org/W2899327929","https://openalex.org/W2950230115","https://openalex.org/W2965921152","https://openalex.org/W2968849363","https://openalex.org/W2978329087","https://openalex.org/W3120050808","https://openalex.org/W3138156743","https://openalex.org/W3160420762","https://openalex.org/W3164277106","https://openalex.org/W3185225911","https://openalex.org/W3196225703","https://openalex.org/W3198942356","https://openalex.org/W3214452197","https://openalex.org/W4281690344","https://openalex.org/W4291624945","https://openalex.org/W4292566556","https://openalex.org/W4295242625","https://openalex.org/W4313527346","https://openalex.org/W4317532687","https://openalex.org/W4321191020","https://openalex.org/W4323320132","https://openalex.org/W4360819550","https://openalex.org/W4360999048","https://openalex.org/W4366816229","https://openalex.org/W4368357399","https://openalex.org/W4377093052","https://openalex.org/W4378781450","https://openalex.org/W4385693120","https://openalex.org/W4389262331","https://openalex.org/W4390971344","https://openalex.org/W4393931635","https://openalex.org/W4394786758","https://openalex.org/W4402926399","https://openalex.org/W4403339106","https://openalex.org/W4403650346","https://openalex.org/W4404511368","https://openalex.org/W4405498739","https://openalex.org/W4405577048","https://openalex.org/W6739901393","https://openalex.org/W6791353385","https://openalex.org/W6803859318","https://openalex.org/W6844493046"],"related_works":["https://openalex.org/W2167883292","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"],"abstract_inverted_index":{"Identification":[0],"of":[1,40,59,66,125,159,172,188],"T":[2],"cell":[3],"receptor":[4],"(TCR)":[5],"specificities":[6],"for":[7,193,237,246],"antigens":[8],"from":[9,222],"large-scale":[10],"single-cell":[11],"or":[12],"bulk":[13],"TCR":[14,67,91,98,142,205,217,224],"repertoire":[15,225],"data":[16,61],"plays":[17],"a":[18,74,97,102,115,149,233],"vital":[19],"role":[20],"in":[21,32,47],"disease":[22,247],"diagnosis":[23],"and":[24,38,62,92,101,137,143,147,208,219,242],"immunotherapy.":[25],"In":[26,69],"silico":[27],"prediction":[28,129],"models":[29,43],"have":[30],"emerged":[31],"recent":[33],"years.":[34],"However,":[35],"the":[36,56,63,122,132,141,156,170,185],"generalizability":[37],"transferability":[39],"current":[41],"computational":[42],"remain":[44],"significant":[45],"hurdles":[46],"accurately":[48],"predicting":[49,173,194],"TCR-pMHC":[50,77,86,117,126,136,174,196],"binding":[51,87,127,175],"specificity,":[52],"primarily":[53],"due":[54],"to":[55,84,106,120,154],"limited":[57],"availability":[58],"experimental":[60],"vast":[64],"diversity":[65,218],"sequences.":[68],"this":[70],"paper,":[71],"we":[72,95,113,199],"propose":[73],"lightweight":[75],"contrastive":[76,116],"learning":[78,118,131],"with":[79,164],"context-aware":[80,151],"prompts,":[81],"named":[82],"LightCTL,":[83,189],"infer":[85],"specificity.":[88,176],"For":[89],"each":[90],"peptide-MHC":[93],"sequence,":[94],"utilize":[96],"encoding":[99,104],"module":[100,105,153],"pMHC":[103,144],"transform":[107],"them":[108],"into":[109],"latent":[110,145],"representations.":[111],"Specifically,":[112],"introduce":[114],"paradigm":[119],"enhance":[121],"generalization":[123,186],"ability":[124,187],"specificity":[128],"by":[130],"matching":[133],"relationship":[134],"between":[135],"MHC-peptide.":[138],"We":[139],"fuse":[140],"representations":[146],"employ":[148],"novel":[150,239,244],"prompt":[152],"consider":[155],"varying":[157],"importance":[158],"different":[160,204],"feature":[161],"maps.":[162],"Compared":[163],"existing":[165],"methods,":[166],"LightCTL":[167,231],"substantially":[168],"improves":[169],"accuracy":[171],"Moreover,":[177],"comparative":[178],"experiments":[179],"across":[180,203],"eight":[181],"independent":[182],"datasets":[183],"demonstrate":[184],"showing":[190],"superior":[191],"performance":[192],"unknown":[195],"pairs.":[197],"Finally,":[198],"assess":[200],"LightCTL's":[201],"efficacy":[202],"sequence":[206],"lengths":[207],"distinct":[209],"unseen":[210],"epitopes,":[211],"as":[212,214,232],"well":[213],"estimate":[215],"cytomegalovirus-specific":[216],"clone":[220],"frequency":[221],"peripheral":[223],"data.":[226],"Overall,":[227],"our":[228],"findings":[229],"highlight":[230],"versatile":[234],"analytical":[235],"method":[236],"advancing":[238],"T-cell":[240],"therapies":[241],"identifying":[243],"biomarkers":[245],"diagnosis.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-18T07:39:51.176621","created_date":"2025-10-10T00:00:00"}