{"id":"https://openalex.org/W4394748422","doi":"https://doi.org/10.7554/elife.94658","title":"The T cell receptor \u03b2 chain repertoire of tumor infiltrating lymphocytes improves neoantigen prediction and prioritization","display_name":"The T cell receptor \u03b2 chain repertoire of tumor infiltrating lymphocytes improves neoantigen prediction and prioritization","publication_year":2024,"publication_date":"2024-04-12","ids":{"openalex":"https://openalex.org/W4394748422","doi":"https://doi.org/10.7554/elife.94658","pmid":"https://pubmed.ncbi.nlm.nih.gov/39466298","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/11517254"},"language":"en","primary_location":{"id":"doi:10.7554/elife.94658","doi":"https://doi.org/10.7554/elife.94658","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.94658","pdf_url":"https://elifesciences.org/reviewed-preprints/94658.pdf","source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"journal-article"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://elifesciences.org/reviewed-preprints/94658.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072921044","display_name":"Thi Mong Quynh Pham","orcid":"https://orcid.org/0000-0002-6977-6064","observed_orcids":["https://orcid.org/0000-0002-6977-6064"]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Thi Mong Quynh Pham","raw_affiliation_strings":["Medical Genetics Institute","University Medical Center Ho Chi Minh City"],"raw_orcid":"https://orcid.org/0000-0002-6977-6064","affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]},{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101774669","display_name":"Th\u00e0nh Nh\u00e2n Nguy\u1ec5n","orcid":"https://orcid.org/0000-0001-6338-3473","observed_orcids":["https://orcid.org/0000-0001-6338-3473"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thanh Nhan Nguyen","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086358236","display_name":"Bui Que Tran Nguyen","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bui Que Tran Nguyen","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Thi Phuong Diem Tran","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Thi Phuong Diem Tran","raw_affiliation_strings":["Medical Genetics Institute","University Medical Center Ho Chi Minh City"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]},{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104279683","display_name":"Nguyen My Diem Pham","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nguyen My Diem Pham","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101335546","display_name":"Hoang Thien Phuc Nguyen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Hoang Thien Phuc Nguyen","raw_affiliation_strings":["Medical Genetics Institute","University Medical Center Ho Chi Minh City"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]},{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106394799","display_name":"Thi Kim Cuong Ho","orcid":"https://orcid.org/0009-0002-8877-1207","observed_orcids":["https://orcid.org/0009-0002-8877-1207"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thi Kim Cuong Ho","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113378573","display_name":"Dinh Viet Linh Nguyen","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dinh Viet Linh Nguyen","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101790224","display_name":"Huu Thinh Nguyen","orcid":"https://orcid.org/0000-0002-0981-7274","observed_orcids":["https://orcid.org/0000-0002-0981-7274"]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Huu Thinh Nguyen","raw_affiliation_strings":["Medical Genetics Institute","University Medical Center Ho Chi Minh City"],"raw_orcid":"https://orcid.org/0000-0002-0981-7274","affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]},{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103219095","display_name":"Duc Huy Tran","orcid":"https://orcid.org/0000-0003-4830-2334","observed_orcids":["https://orcid.org/0000-0003-4830-2334"]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Duc Huy Tran","raw_affiliation_strings":["University Medical Center Ho Chi Minh City"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108878669","display_name":"Thanh Sang Tran","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Thanh Sang Tran","raw_affiliation_strings":["Medical Genetics Institute","University Medical Center Ho Chi Minh City"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]},{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006996565","display_name":"Truong-Vinh Ngoc Pham","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Truong Vinh Ngoc Pham","raw_affiliation_strings":["Medical Genetics Institute","University Medical Center Ho Chi Minh City"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]},{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026628678","display_name":"Minh-Triet Le","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":false,"raw_author_name":"Minh Triet Le","raw_affiliation_strings":["University Medical Center Ho Chi Minh City"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006269866","display_name":"Vy Nguyen","orcid":"https://orcid.org/0000-0003-3436-3662","observed_orcids":["https://orcid.org/0000-0003-3436-3662"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thi Tuong Vy Nguyen","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":"https://orcid.org/0000-0003-3436-3662","affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039569828","display_name":"Minh\u2010Duy Phan","orcid":"https://orcid.org/0000-0002-3426-1044","observed_orcids":["https://orcid.org/0000-0002-3426-1044"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Minh-Duy Phan","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030243137","display_name":"Hoa Giang","orcid":"https://orcid.org/0000-0001-6549-8012","observed_orcids":["https://orcid.org/0000-0001-6549-8012"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hoa Giang","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002677430","display_name":"Hoai\u2010Nghia Nguyen","orcid":"https://orcid.org/0000-0002-1542-1874","observed_orcids":["https://orcid.org/0000-0002-1542-1874"]},"institutions":[{"id":"https://openalex.org/I4210100991","display_name":"University Medical Center HCMC","ror":"https://ror.org/0154qvp54","country_code":"VN","type":"healthcare","lineage":["https://openalex.org/I4210100991"]}],"countries":["VN"],"is_corresponding":true,"raw_author_name":"Hoai-Nghia Nguyen","raw_affiliation_strings":["Medical Genetics Institute","University Medical Center Ho Chi Minh City"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]},{"raw_affiliation_string":"University Medical Center Ho Chi Minh City","institution_ids":["https://openalex.org/I4210100991"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004276773","display_name":"Le Son Tran","orcid":"https://orcid.org/0000-0002-5382-3903","observed_orcids":["https://orcid.org/0000-0002-5382-3903"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Le Son Tran","raw_affiliation_strings":["Medical Genetics Institute"],"raw_orcid":"https://orcid.org/0000-0002-5382-3903","affiliations":[{"raw_affiliation_string":"Medical Genetics Institute","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5002677430","https://openalex.org/A5004276773"],"corresponding_institution_ids":["https://openalex.org/I4210100991"],"apc_list":{"value":3000,"currency":"USD","value_usd":2500},"apc_paid":{"value":3000,"currency":"USD","value_usd":2500},"fwci":null,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"13","issue":null,"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":0.586899995803833,"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":0.586899995803833,"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.3174000084400177,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.07890000194311142,"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-beta-chain-repertoire","display_name":"T cell receptor beta chain repertoire","score":0.7990000247955322},{"id":"https://openalex.org/keywords/tumor-infiltrating-lymphocytes","display_name":"tumor-infiltrating lymphocytes","score":0.9480000138282776},{"id":"https://openalex.org/keywords/neoantigen-prioritization","display_name":"neoantigen prioritization","score":0.8730000257492065},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"colorectal cancer","score":0.7630000114440918},{"id":"https://openalex.org/keywords/personalized-cancer-immunotherapy","display_name":"personalized cancer immunotherapy","score":0.7429999709129333},{"id":"https://openalex.org/keywords/machine-learning-prediction-models","display_name":"machine learning prediction models","score":0.8009999990463257}],"concepts":[{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.9016985297203064},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.582749605178833},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.5512517094612122},{"id":"https://openalex.org/C2779053233","wikidata":"https://www.wikidata.org/wiki/Q731235","display_name":"ELISPOT","level":4,"score":0.509589672088623},{"id":"https://openalex.org/C2780674031","wikidata":"https://www.wikidata.org/wiki/Q2012719","display_name":"Cancer immunotherapy","level":4,"score":0.49735668301582336},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.48357006907463074},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.48216718435287476},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.47920212149620056},{"id":"https://openalex.org/C2778326572","wikidata":"https://www.wikidata.org/wiki/Q7852668","display_name":"Tumor-infiltrating lymphocytes","level":4,"score":0.46076181530952454},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.43118277192115784},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.4285440146923065},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39233386516571045},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.38974612951278687},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D016246","descriptor_name":"Lymphocytes, Tumor-Infiltrating","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D016693","descriptor_name":"Receptors, Antigen, T-Cell, alpha-beta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.7554/elife.94658","doi":"https://doi.org/10.7554/elife.94658","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.94658","pdf_url":"https://elifesciences.org/reviewed-preprints/94658.pdf","source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11517254","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11517254","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11517254/pdf/elife-94658.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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"Text"},{"id":"pmid:39466298","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39466298","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,"listed_in":[],"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":"eLife","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:66c3188ec28b4f9fbcec629602810ad9","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/66c3188ec28b4f9fbcec629602810ad9","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,"listed_in":[],"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":"eLife, Vol 13 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.7554/elife.94658","doi":"https://doi.org/10.7554/elife.94658","is_oa":true,"landing_page_url":"https://doi.org/10.7554/elife.94658","pdf_url":"https://elifesciences.org/reviewed-preprints/94658.pdf","source":{"id":"https://openalex.org/S1336409049","display_name":"eLife","issn_l":"2050-084X","issn":["2050-084X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","dongbi-a","jufo-2","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311710","host_organization_name":"eLife Sciences Publications Ltd","host_organization_lineage":["https://openalex.org/P4310311710"],"host_organization_lineage_names":["eLife Sciences Publications Ltd"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"eLife","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.98580002784729,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4394748422.pdf","grobid_xml":"https://content.openalex.org/works/W4394748422.grobid-xml"},"referenced_works_count":65,"referenced_works":["https://openalex.org/W1940241680","https://openalex.org/W1965235372","https://openalex.org/W2011458181","https://openalex.org/W2022990363","https://openalex.org/W2076536002","https://openalex.org/W2089488561","https://openalex.org/W2108234281","https://openalex.org/W2114380126","https://openalex.org/W2124555673","https://openalex.org/W2131271579","https://openalex.org/W2150056019","https://openalex.org/W2155943701","https://openalex.org/W2169456326","https://openalex.org/W2256496883","https://openalex.org/W2287918349","https://openalex.org/W2417483443","https://openalex.org/W2573152477","https://openalex.org/W2613978126","https://openalex.org/W2622499649","https://openalex.org/W2728919089","https://openalex.org/W2739132742","https://openalex.org/W2752126733","https://openalex.org/W2755102409","https://openalex.org/W2773406691","https://openalex.org/W2779221466","https://openalex.org/W2782183686","https://openalex.org/W2890085191","https://openalex.org/W2898389621","https://openalex.org/W2899518508","https://openalex.org/W2900704161","https://openalex.org/W2905817704","https://openalex.org/W2918815995","https://openalex.org/W2920863623","https://openalex.org/W2965921152","https://openalex.org/W2978203211","https://openalex.org/W2982476296","https://openalex.org/W2996488853","https://openalex.org/W2998313390","https://openalex.org/W3004398085","https://openalex.org/W3008682585","https://openalex.org/W3023007494","https://openalex.org/W3024570138","https://openalex.org/W3107548995","https://openalex.org/W3111191926","https://openalex.org/W3116512470","https://openalex.org/W3124720941","https://openalex.org/W3127841695","https://openalex.org/W3133573631","https://openalex.org/W3154423121","https://openalex.org/W3156419307","https://openalex.org/W3165846104","https://openalex.org/W3185017058","https://openalex.org/W3196626346","https://openalex.org/W3198942356","https://openalex.org/W4214923508","https://openalex.org/W4244583790","https://openalex.org/W4289519538","https://openalex.org/W4312190528","https://openalex.org/W4313547267","https://openalex.org/W4376278433","https://openalex.org/W4386420808","https://openalex.org/W4387452812","https://openalex.org/W4390938319","https://openalex.org/W6794406980","https://openalex.org/W6958751180"],"related_works":["https://openalex.org/W4389279810","https://openalex.org/W7167224736","https://openalex.org/W4414161554","https://openalex.org/W4414440963","https://openalex.org/W3010839140","https://openalex.org/W3198942356","https://openalex.org/W7130319993","https://openalex.org/W4391091304","https://openalex.org/W3133573631","https://openalex.org/W2953999486"],"abstract_inverted_index":{"In":[0,52],"the":[1,6,28,42,49,94,114,123,196,204],"realm":[2],"of":[3,9,30,97,117,126,164,206],"cancer":[4,79],"immunotherapy,":[5],"meticulous":[7],"selection":[8,21],"neoantigens":[10],"plays":[11],"a":[12,83],"fundamental":[13],"role":[14],"in":[15,65,113,131,150],"enhancing":[16],"personalized":[17],"treatments.":[18],"Traditionally,":[19],"this":[20,38,55],"process":[22],"has":[23],"heavily":[24],"relied":[25],"on":[26,173,177],"predicting":[27],"binding":[29,141,145,209,212],"peptides":[31],"to":[32,54,92,133,146,156],"human":[33],"leukocyte":[34],"antigens":[35],"(pHLA).":[36],"Nevertheless,":[37],"approach":[39],"often":[40],"overlooks":[41],"dynamic":[43],"interaction":[44],"between":[45],"tumor":[46],"cells":[47],"and":[48,110,128,153],"immune":[50],"system.":[51],"response":[53,132],"limitation,":[56],"we":[57],"have":[58],"developed":[59],"an":[60],"innovative":[61],"prediction":[62],"algorithm":[63],"rooted":[64],"machine":[66],"learning,":[67],"integrating":[68,207],"T":[69],"cell":[70],"receptor":[71],"\u03b2":[72],"chain":[73],"(TCR\u03b2)":[74],"profiling":[75],"data":[76,106],"from":[77,101,122],"colorectal":[78],"(CRC)":[80],"patients":[81],"for":[82,214],"more":[84,215],"precise":[85],"neoantigen":[86,185],"prioritization.":[87],"TCR\u03b2":[88,115],"sequencing":[89],"was":[90,168],"conducted":[91],"profile":[93],"TCR":[95],"repertoire":[96],"tumor-infiltrating":[98],"lymphocytes":[99],"(TILs)":[100],"28":[102],"CRC":[103,118,179],"patients.":[104,180],"The":[105,162],"unveiled":[107],"both":[108],"intra-tumor":[109],"inter-patient":[111],"heterogeneity":[112],"repertoires":[116],"patients,":[119],"likely":[120],"resulting":[121,149],"stochastic":[124],"utilization":[125],"V":[127],"J":[129],"segments":[130],"neoantigens.":[134],"Our":[135],"novel":[136],"combined":[137,190],"model":[138,167,191],"integrates":[139],"pHLA":[140,208],"information":[142],"with":[143,210],"pHLA-TCR":[144,211],"prioritize":[147],"neoantigens,":[148],"heightened":[151],"specificity":[152],"sensitivity":[154],"compared":[155],"models":[157],"using":[158],"individual":[159],"features":[160],"alone.":[161],"efficacy":[163],"our":[165,189],"proposed":[166],"corroborated":[169],"through":[170],"ELISpot":[171],"assays":[172,182],"long":[174],"peptides,":[175],"performed":[176],"four":[178],"These":[181],"demonstrated":[183],"that":[184],"candidates":[186],"prioritized":[187],"by":[188,195],"outperformed":[192],"predictions":[193],"made":[194],"established":[197],"tool":[198],"NetMHCpan.":[199],"This":[200],"comprehensive":[201],"assessment":[202],"underscores":[203],"significance":[205],"analysis":[213],"effective":[216],"immunotherapeutic":[217],"strategies.":[218]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-11-12T12:28:57.059296","created_date":"2024-04-13T00:00:00"}