{"id":"https://openalex.org/W4414161554","doi":"https://doi.org/10.1371/journal.pcbi.1013050","title":"THLANet: A deep learning framework for predicting TCR-pHLA binding in immunotherapy applications","display_name":"THLANet: A deep learning framework for predicting TCR-pHLA binding in immunotherapy applications","publication_year":2025,"publication_date":"2025-09-12","ids":{"openalex":"https://openalex.org/W4414161554","doi":"https://doi.org/10.1371/journal.pcbi.1013050","pmid":"https://pubmed.ncbi.nlm.nih.gov/40939018"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013050","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013050","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1013050","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100713766","display_name":"Long Xu","orcid":"https://orcid.org/0000-0003-4952-9178"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xu Long","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China"],"raw_orcid":"https://orcid.org/0000-0003-4952-9178","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101648196","display_name":"Qiang Yang","orcid":"https://orcid.org/0000-0002-6524-9443"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qiang Yang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038137938","display_name":"Weihe Dong","orcid":"https://orcid.org/0000-0001-8022-9793"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Weihe Dong","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100628723","display_name":"Xiaokun Li","orcid":"https://orcid.org/0000-0002-6645-6890"},"institutions":[{"id":"https://openalex.org/I1300757298","display_name":"Heilongjiang University of Science and Technology","ror":"https://ror.org/030xwyx96","country_code":"CN","type":"education","lineage":["https://openalex.org/I1300757298"]},{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]},{"id":"https://openalex.org/I4210140537","display_name":"Education Department of Heilongjiang Province","ror":"https://ror.org/04rn1rm44","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210140537"]},{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaokun Li","raw_affiliation_strings":["Postdoctoral Program of Heilongjiang Hengxun Technology Co., Ltd., Harbin, China","School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","School of Computer Science and Technology, Heilongjiang University, Harbin, China","Shandong Hengxun Technology Co., Ltd., Qingdao, China"],"raw_orcid":"https://orcid.org/0000-0002-6645-6890","affiliations":[{"raw_affiliation_string":"Postdoctoral Program of Heilongjiang Hengxun Technology Co., Ltd., Harbin, China","institution_ids":["https://openalex.org/I4210140537"]},{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]},{"raw_affiliation_string":"School of Computer Science and Technology, Heilongjiang University, Harbin, China","institution_ids":["https://openalex.org/I1300757298"]},{"raw_affiliation_string":"Shandong Hengxun Technology Co., Ltd., Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049558861","display_name":"Kuanquan Wang","orcid":"https://orcid.org/0000-0003-1347-3491"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Kuanquan Wang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024430250","display_name":"Suyu Dong","orcid":"https://orcid.org/0000-0001-7521-8782"},"institutions":[{"id":"https://openalex.org/I47689461","display_name":"Northeast Forestry University","ror":"https://ror.org/02yxnh564","country_code":"CN","type":"education","lineage":["https://openalex.org/I47689461"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Suyu Dong","raw_affiliation_strings":["College of Computer and Control Engineering, Northeast Forestry University, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer and Control Engineering, Northeast Forestry University, Harbin, China","institution_ids":["https://openalex.org/I47689461"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091843570","display_name":"Gongning Luo","orcid":"https://orcid.org/0000-0003-3662-0335"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Gongning Luo","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041630373","display_name":"Xianyu Zhang","orcid":"https://orcid.org/0000-0002-9738-2361"},"institutions":[{"id":"https://openalex.org/I156144747","display_name":"Harbin Medical University","ror":"https://ror.org/05jscf583","country_code":"CN","type":"education","lineage":["https://openalex.org/I156144747"]},{"id":"https://openalex.org/I4210103956","display_name":"Third Affiliated Hospital of Harbin Medical University","ror":"https://ror.org/01f77gp95","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210103956"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xianyu Zhang","raw_affiliation_strings":["Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China","institution_ids":["https://openalex.org/I156144747","https://openalex.org/I4210103956"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090875515","display_name":"Tiansong Yang","orcid":"https://orcid.org/0000-0002-4008-702X"},"institutions":[{"id":"https://openalex.org/I4210102855","display_name":"First Affiliated Hospital of Heilongjiang University of Chinese Medicine","ror":"https://ror.org/01c0exk17","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210102855"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tiansong Yang","raw_affiliation_strings":["Department of Rehabilitation, The First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Rehabilitation, The First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, China","institution_ids":["https://openalex.org/I4210102855"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100618900","display_name":"Xin Gao","orcid":"https://orcid.org/0000-0002-7108-3574"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Xin Gao","raw_affiliation_strings":["Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia","Computer Science Program, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Excellence for Smart Health (KCSH), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"Computer Science Program, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100649978","display_name":"Guohua Wang","orcid":"https://orcid.org/0000-0001-7381-2374"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guohua Wang","raw_affiliation_strings":["School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China","institution_ids":["https://openalex.org/I204983213"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5024430250","https://openalex.org/A5038137938","https://openalex.org/A5041630373","https://openalex.org/A5049558861","https://openalex.org/A5090875515","https://openalex.org/A5091843570","https://openalex.org/A5100618900","https://openalex.org/A5100628723","https://openalex.org/A5100649978","https://openalex.org/A5100713766","https://openalex.org/A5101648196"],"corresponding_institution_ids":["https://openalex.org/I1300757298","https://openalex.org/I156144747","https://openalex.org/I204983213","https://openalex.org/I4210102855","https://openalex.org/I4210103956","https://openalex.org/I4210140537","https://openalex.org/I47689461","https://openalex.org/I71920554","https://openalex.org/I80143920"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.3991,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.8976968,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"21","issue":"9","first_page":"e1013050","last_page":"e1013050"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9997000098228455,"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":0.9995999932289124,"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":0.6700000166893005},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.5699999928474426},{"id":"https://openalex.org/keywords/acquired-immune-system","display_name":"Acquired immune system","score":0.5450000166893005},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.5435000061988831},{"id":"https://openalex.org/keywords/repertoire","display_name":"Repertoire","score":0.501800000667572},{"id":"https://openalex.org/keywords/immunotherapy","display_name":"Immunotherapy","score":0.4966000020503998},{"id":"https://openalex.org/keywords/cancer-immunotherapy","display_name":"Cancer immunotherapy","score":0.46480000019073486},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.42250001430511475},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.3479999899864197}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.6700000166893005},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6363999843597412},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.5699999928474426},{"id":"https://openalex.org/C193419808","wikidata":"https://www.wikidata.org/wiki/Q1645075","display_name":"Acquired immune system","level":3,"score":0.5450000166893005},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.5435000061988831},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.501800000667572},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.4966000020503998},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.47609999775886536},{"id":"https://openalex.org/C2780674031","wikidata":"https://www.wikidata.org/wiki/Q2012719","display_name":"Cancer immunotherapy","level":4,"score":0.46480000019073486},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4577000141143799},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4449000060558319},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.42250001430511475},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.3479999899864197},{"id":"https://openalex.org/C2778827112","wikidata":"https://www.wikidata.org/wiki/Q22245680","display_name":"Feature engineering","level":3,"score":0.32820001244544983},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.3255000114440918},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.31520000100135803},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.31029999256134033},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.30869999527931213},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3005000054836273},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.29330000281333923},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.29179999232292175},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.2913999855518341},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.28380000591278076},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.27900001406669617},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.26649999618530273},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26499998569488525},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.26440000534057617},{"id":"https://openalex.org/C136449434","wikidata":"https://www.wikidata.org/wiki/Q428253","display_name":"Innate immune system","level":3,"score":0.2637999951839447},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.26030001044273376},{"id":"https://openalex.org/C2776662205","wikidata":"https://www.wikidata.org/wiki/Q2459684","display_name":"Tumor antigen","level":4,"score":0.2533000111579895}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006680","descriptor_name":"HLA Antigens","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D007167","descriptor_name":"Immunotherapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007167","descriptor_name":"Immunotherapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D007167","descriptor_name":"Immunotherapy","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000628","qualifier_name":"therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000628","qualifier_name":"therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000628","qualifier_name":"therapy","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":"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":"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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1013050","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013050","pdf_url":null,"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:40939018","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40939018","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:doaj.org/article:1b08985368c643469c3821722b37dc39","is_oa":true,"landing_page_url":"https://doaj.org/article/1b08985368c643469c3821722b37dc39","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 21, Iss 9, p e1013050 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11258427","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12449017","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12449017","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12449017/","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":"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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013050","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013050","pdf_url":null,"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":[],"awards":[{"id":"https://openalex.org/G1745487217","display_name":null,"funder_award_id":"62372135","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5644938599","display_name":null,"funder_award_id":"62202092","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G777547140","display_name":null,"funder_award_id":"62450122","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G870551797","display_name":null,"funder_award_id":"62225109","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320315911","display_name":"Center of Excellence for Stress and Mental Health","ror":null},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W193169599","https://openalex.org/W1532828658","https://openalex.org/W1938515409","https://openalex.org/W2011458181","https://openalex.org/W2043995349","https://openalex.org/W2068046103","https://openalex.org/W2142739377","https://openalex.org/W2201214180","https://openalex.org/W2360792712","https://openalex.org/W2410863870","https://openalex.org/W2488156821","https://openalex.org/W2530695400","https://openalex.org/W2607497548","https://openalex.org/W2613978126","https://openalex.org/W2728365508","https://openalex.org/W2774113098","https://openalex.org/W2791512052","https://openalex.org/W2887577080","https://openalex.org/W2898389621","https://openalex.org/W2899327929","https://openalex.org/W2911644242","https://openalex.org/W2963521239","https://openalex.org/W2990308980","https://openalex.org/W2995997429","https://openalex.org/W3020331344","https://openalex.org/W3037875124","https://openalex.org/W3087683890","https://openalex.org/W3124720941","https://openalex.org/W3134443156","https://openalex.org/W3135351475","https://openalex.org/W3138156743","https://openalex.org/W3160420762","https://openalex.org/W3161479873","https://openalex.org/W3176460341","https://openalex.org/W3179304282","https://openalex.org/W3185560091","https://openalex.org/W3187834303","https://openalex.org/W3196225703","https://openalex.org/W3196626346","https://openalex.org/W3198942356","https://openalex.org/W3216334900","https://openalex.org/W4206384730","https://openalex.org/W4210388887","https://openalex.org/W4226199741","https://openalex.org/W4291624945","https://openalex.org/W4310945495","https://openalex.org/W4313547267","https://openalex.org/W4318981550","https://openalex.org/W4319455163","https://openalex.org/W4323320132","https://openalex.org/W4327550249","https://openalex.org/W4383371650","https://openalex.org/W4385235597","https://openalex.org/W4389262331","https://openalex.org/W4400060956","https://openalex.org/W4405229840"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W3031052312","https://openalex.org/W4389568370","https://openalex.org/W3032375762","https://openalex.org/W1995515455","https://openalex.org/W2080531066","https://openalex.org/W3108674512","https://openalex.org/W1506200166","https://openalex.org/W1489783725"],"abstract_inverted_index":{"Adaptive":[0],"immunity":[1],"is":[2],"a":[3,18,61,88,134,189],"targeted":[4],"immune":[5,24,130],"response":[6],"that":[7],"enables":[8],"the":[9,22,32,40,95,114,128,177,200],"body":[10],"to":[11,55,72,93,100,118,138],"identify":[12],"and":[13,132,165,183,206],"eliminate":[14],"foreign":[15],"pathogens,":[16],"playing":[17],"critical":[19],"role":[20],"in":[21,82,192],"anti-tumor":[23],"response.":[25,38],"Tumor":[26],"cell":[27],"expression":[28],"of":[29,46,65,98,169,181],"antigens":[30,43,47],"forms":[31],"foundation":[33],"for":[34,77],"inducing":[35],"this":[36],"adaptive":[37],"However,":[39],"human":[41],"leukocyte":[42],"(HLA)-restricted":[44],"recognition":[45],"by":[48,103,158],"T-cell":[49],"receptors":[50],"(TCR)":[51],"limits":[52],"their":[53,79],"ability":[54],"detect":[56],"all":[57],"neoantigens,":[58],"with":[59],"only":[60,199],"small":[62],"subset":[63],"capable":[64],"activating":[66],"T-cells.":[67],"Accurately":[68],"predicting":[69],"neoantigen":[70],"binding":[71,96,136,179],"TCR":[73,99,129,201],"is,":[74],"therefore,":[75],"crucial":[76],"assessing":[78],"immunogenic":[80],"potential":[81],"clinical":[83,141,150],"settings.":[84],"We":[85],"present":[86],"THLANet,":[87],"deep":[89],"learning":[90],"model":[91],"designed":[92],"predict":[94],"specificity":[97],"neoantigens":[101],"presented":[102],"class":[104,207],"I":[105,208],"HLAs.":[106],"THLANet":[107,194],"employs":[108],"evolutionary":[109],"scale":[110],"modeling-2":[111],"(ESM-2),":[112],"replacing":[113],"traditional":[115],"embedding":[116],"methods":[117],"enhance":[119],"sequence":[120,202],"feature":[121],"representation.":[122],"Using":[123],"scTCR-seq":[124],"data,":[125],"we":[126,172],"obtained":[127],"repertoire":[131],"constructed":[133],"TCR-pHLA":[135],"database":[137],"validate":[139],"THLANet's":[140],"potential.":[142],"The":[143],"model's":[144],"performance":[145],"was":[146],"further":[147],"evaluated":[148],"using":[149,198],"cancer":[151,155],"data":[152],"across":[153],"various":[154],"types.":[156],"Additionally,":[157],"analyzing":[159],"divided":[160],"complementarity-determining":[161],"region":[162],"(CDR3)":[163],"sequences":[164],"simulating":[166],"alanine":[167],"scanning":[168],"antigen":[170,204],"sequences,":[171],"provided":[173],"new":[174],"insights":[175,212],"into":[176,213],"3D":[178],"interactions":[180],"TCRs":[182],"antigens.":[184],"Predicting":[185],"TCR-neoantigen":[186],"pairing":[187],"remains":[188],"significant":[190],"challenge":[191],"immunology,":[193],"provides":[195],"accurate":[196],"predictions":[197],"(CDR3\u03b2),":[203],"sequence,":[205],"HLA,":[209],"offering":[210],"novel":[211],"TCR-antigen":[214],"interactions.":[215]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2}],"updated_date":"2026-07-14T08:27:34.040176","created_date":"2025-10-10T00:00:00"}
