{"id":"https://openalex.org/W4415728502","doi":"https://doi.org/10.1186/s13040-025-00490-5","title":"Deep learning-driven TCR$$\\beta$$ repertoire analysis enhances diagnosis and enables mining of immunological biomarkers in systemic lupus erythematosus","display_name":"Deep learning-driven TCR$$\\beta$$ repertoire analysis enhances diagnosis and enables mining of immunological biomarkers in systemic lupus erythematosus","publication_year":2025,"publication_date":"2025-10-31","ids":{"openalex":"https://openalex.org/W4415728502","doi":"https://doi.org/10.1186/s13040-025-00490-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/41174657"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-025-00490-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00490-5","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00490-5","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00490-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046146934","display_name":"Tongfei Shen","orcid":"https://orcid.org/0009-0008-7621-8125"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Tongfei Shen","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052210770","display_name":"Yifei Sheng","orcid":"https://orcid.org/0000-0002-4431-8382"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yifei Sheng","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078522162","display_name":"Wan Nie","orcid":"https://orcid.org/0000-0002-0590-6608"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Wan Nie","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087559347","display_name":"Shuo Yang","orcid":"https://orcid.org/0000-0003-4164-4438"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Shuo Yang","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078425505","display_name":"K.K. Li","orcid":"https://orcid.org/0000-0001-5467-763X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Kaiqi Li","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101964409","display_name":"Ziwei Ma","orcid":"https://orcid.org/0000-0001-9833-8568"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Ziwei Ma","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101067202","display_name":"Zhao Ling","orcid":"https://orcid.org/0000-0003-0512-6369"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Zhao Ling","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026166032","display_name":"Bowen Tan","orcid":"https://orcid.org/0000-0003-1522-988X"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Bowen Tan","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100599551","display_name":"Xikang Feng","orcid":"https://orcid.org/0000-0003-4029-3795"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xikang Feng","raw_affiliation_strings":["School of Software, Northwestern Polytechnical University, Xi'an, Shaanxi, China. fxk@nwpu.edu.cn","School of Software, Northwestern Polytechnical University, Xi'an, Shaanxi, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software, Northwestern Polytechnical University, Xi'an, Shaanxi, China. fxk@nwpu.edu.cn","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Software, Northwestern Polytechnical University, Xi'an, Shaanxi, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067964641","display_name":"Miaozhe Huo","orcid":"https://orcid.org/0000-0002-3891-3812"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Miaozhe Huo","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China. miaozhhuo2-c@my.cityu.edu.hk","Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China. miaozhhuo2-c@my.cityu.edu.hk","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5100599551"],"corresponding_institution_ids":["https://openalex.org/I17145004"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.40476373,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"18","issue":"1","first_page":"76","last_page":"76"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.8914999961853027,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10308","display_name":"Systemic Lupus Erythematosus Research","score":0.8914999961853027,"subfield":{"id":"https://openalex.org/subfields/2745","display_name":"Rheumatology"},"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/T11157","display_name":"Chronic Lymphocytic Leukemia Research","score":0.014399999752640724,"subfield":{"id":"https://openalex.org/subfields/2716","display_name":"Genetics"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.012199999764561653,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"Biomarker discovery","score":0.6761999726295471},{"id":"https://openalex.org/keywords/repertoire","display_name":"Repertoire","score":0.6438999772071838},{"id":"https://openalex.org/keywords/personalized-medicine","display_name":"Personalized medicine","score":0.5670999884605408},{"id":"https://openalex.org/keywords/biomarker","display_name":"Biomarker","score":0.5622000098228455},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5611000061035156},{"id":"https://openalex.org/keywords/autoimmune-disease","display_name":"Autoimmune disease","score":0.5569000244140625},{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.4927000105381012},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.4553000032901764}],"concepts":[{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.6761999726295471},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.6545000076293945},{"id":"https://openalex.org/C2778473898","wikidata":"https://www.wikidata.org/wiki/Q2145110","display_name":"Repertoire","level":2,"score":0.6438999772071838},{"id":"https://openalex.org/C32220436","wikidata":"https://www.wikidata.org/wiki/Q2072214","display_name":"Personalized medicine","level":2,"score":0.5670999884605408},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.5622000098228455},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5611000061035156},{"id":"https://openalex.org/C2779075594","wikidata":"https://www.wikidata.org/wiki/Q8084905","display_name":"Autoimmune disease","level":3,"score":0.5569000244140625},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.5098000168800354},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.4927000105381012},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4812000095844269},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.4553000032901764},{"id":"https://openalex.org/C2775915377","wikidata":"https://www.wikidata.org/wiki/Q188297","display_name":"Lupus erythematosus","level":3,"score":0.42660000920295715},{"id":"https://openalex.org/C3018877446","wikidata":"https://www.wikidata.org/wiki/Q1421432","display_name":"Disease monitoring","level":3,"score":0.40950000286102295},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37940001487731934},{"id":"https://openalex.org/C2780130043","wikidata":"https://www.wikidata.org/wiki/Q192360","display_name":"Autoimmunity","level":3,"score":0.3560999929904938},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35519999265670776},{"id":"https://openalex.org/C177713679","wikidata":"https://www.wikidata.org/wiki/Q679690","display_name":"Intensive care medicine","level":1,"score":0.3456999957561493},{"id":"https://openalex.org/C2776912625","wikidata":"https://www.wikidata.org/wiki/Q1485","display_name":"Systemic lupus erythematosus","level":3,"score":0.34360000491142273},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.28949999809265137},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.2718999981880188},{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.25679999589920044},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.2540000081062317},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.25290000438690186}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13040-025-00490-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00490-5","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00490-5","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:41174657","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41174657","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":"BioData mining","raw_type":null},{"id":"pmh:oai:pure.atira.dk:publications/c3ad53f2-1070-47a2-9a07-ba1995467c10","is_oa":true,"landing_page_url":"https://hdl.handle.net/2031/c3ad53f2-1070-47a2-9a07-ba1995467c10","pdf_url":"https://scholars.cityu.edu.hk/files/401325200/362365974.pdf","source":{"id":"https://openalex.org/S7407055387","display_name":"CityU Scholars","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Shen, T, Sheng, Y, Nie, W, Yang, S, Li, K, Ma, Z, Ling, Z, Tan, B, Feng, X & Huo, M 2025, 'Deep learning-driven TCR \u03b2 repertoire analysis enhances diagnosis and enables mining of immunological biomarkers in systemic lupus erythematosus', BioData Mining, vol. 18, 76. https://doi.org/10.1186/s13040-025-00490-5","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:630437c8623c413ba3f2bcf9ee8d4191","is_oa":true,"landing_page_url":"https://doaj.org/article/630437c8623c413ba3f2bcf9ee8d4191","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":"BioData Mining, Vol 18, Iss 1, Pp 1-21 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11386519","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12577242","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"}],"best_oa_location":{"id":"doi:10.1186/s13040-025-00490-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-025-00490-5","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-025-00490-5","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8979388604","display_name":null,"funder_award_id":"2023YFC3403200","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415728502.pdf","grobid_xml":"https://content.openalex.org/works/W4415728502.grobid-xml"},"referenced_works_count":69,"referenced_works":["https://openalex.org/W968228412","https://openalex.org/W1601328537","https://openalex.org/W1887232166","https://openalex.org/W1921808050","https://openalex.org/W2025240311","https://openalex.org/W2029995436","https://openalex.org/W2046545994","https://openalex.org/W2052685738","https://openalex.org/W2064999867","https://openalex.org/W2079763590","https://openalex.org/W2083910835","https://openalex.org/W2084965322","https://openalex.org/W2087815747","https://openalex.org/W2098157239","https://openalex.org/W2123249056","https://openalex.org/W2136049573","https://openalex.org/W2173411263","https://openalex.org/W2229765919","https://openalex.org/W2326758788","https://openalex.org/W2331514369","https://openalex.org/W2467933133","https://openalex.org/W2547625098","https://openalex.org/W2605177850","https://openalex.org/W2670890989","https://openalex.org/W2768172834","https://openalex.org/W2802773414","https://openalex.org/W2889089680","https://openalex.org/W2901509748","https://openalex.org/W2910913933","https://openalex.org/W2946830989","https://openalex.org/W2971147032","https://openalex.org/W3005836320","https://openalex.org/W3026679694","https://openalex.org/W3028149335","https://openalex.org/W3036825926","https://openalex.org/W3063526921","https://openalex.org/W3116512470","https://openalex.org/W3120248484","https://openalex.org/W3120717168","https://openalex.org/W3172422681","https://openalex.org/W3200585592","https://openalex.org/W3213449307","https://openalex.org/W3216791550","https://openalex.org/W4200218124","https://openalex.org/W4206370840","https://openalex.org/W4220721882","https://openalex.org/W4225693858","https://openalex.org/W4228998244","https://openalex.org/W4234670376","https://openalex.org/W4237192272","https://openalex.org/W4292232933","https://openalex.org/W4292774549","https://openalex.org/W4311677551","https://openalex.org/W4320896710","https://openalex.org/W4322623421","https://openalex.org/W4362508400","https://openalex.org/W4375843252","https://openalex.org/W4376112749","https://openalex.org/W4387569385","https://openalex.org/W4390545744","https://openalex.org/W4392055622","https://openalex.org/W4395961834","https://openalex.org/W4400111091","https://openalex.org/W4400503324","https://openalex.org/W4400503348","https://openalex.org/W4403792929","https://openalex.org/W4406271212","https://openalex.org/W4406628023","https://openalex.org/W4409955377"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Systemic":[1],"Lupus":[2],"Erythematosus":[3],"(SLE)":[4],"is":[5,46],"a":[6,55,80,106,113,141,160,168,187,267,299],"complex":[7],"autoimmune":[8,147,309],"disorder":[9],"involving":[10],"dysregulation":[11],"of":[12,28,42,132,152,190,225,264,287,330],"multiple":[13],"immune":[14,26,191],"components,":[15],"including":[16,204],"T":[17],"cells.":[18],"Aberrant":[19],"T-cell":[20,49],"activity":[21],"contributes":[22],"significantly":[23,228],"to":[24,89,116],"the":[25,43,99,130,178,201,222,252,256,262,288,316,328],"pathology":[27],"SLE,":[29,75,295],"for":[30,48,58,94,129,270,301,318],"instance,":[31],"by":[32,102],"facilitating":[33],"autoantibody":[34],"production.":[35],"The":[36],"Complementarity":[37],"Determining":[38],"Region":[39],"3":[40],"(CDR3)":[41],"TCR\u03b2":[44],"chain":[45],"pivotal":[47],"specificity,":[50],"thereby":[51,227],"positioning":[52],"it":[53],"as":[54,137,167,177,243,266],"promising":[56],"target":[57],"enhancing":[59],"diagnostic":[60,72,83,108,281],"accuracy":[61],"and":[62,207,240,245,273,291,305,322],"gaining":[63],"deeper":[64],"mechanistic":[65],"insights":[66,250],"into":[67,251],"SLE.":[68,95,331],"To":[69],"address":[70],"these":[71],"limitations":[73],"in":[74,215,308,327],"our":[76,234,285,312],"team":[77],"developed":[78],"DeepTAPE,":[79,103],"deep":[81,126],"learning-based":[82],"framework":[84],"that":[85,110,135,172],"utilizes":[86],"CDR3":[87,202],"sequences":[88],"achieve":[90],"robust":[91],"classification":[92],"performance":[93],"RESULTS:":[96],"Building":[97],"upon":[98],"foundation":[100,300],"established":[101],"we":[104,194],"devised":[105],"novel":[107],"approach":[109,144],"effectively":[111],"integrates":[112],"TCR":[114],"classifier":[115],"quantify":[117],"SLE":[118,153,179,216,275],"disease":[119,164,276],"activity.":[120],"Furthermore,":[121],"this":[122,143,156,296],"methodology":[123],"employs":[124],"advanced":[125],"learning":[127],"models":[128],"bio-mining":[131],"disease-associated":[133],"motifs":[134,199,211],"serve":[136],"potential":[138,237,263],"biomarkers.":[139,232],"As":[140],"result,":[142],"generates":[145],"an":[146,219],"risk":[148],"score":[149],"(ARS)":[150],"indicative":[151],"probability.":[154],"Notably,":[155],"ARS":[157],"metric":[158],"exhibited":[159],"strong":[161],"correlation":[162],"with":[163,294],"activity,":[165,277],"functioning":[166],"quantitative":[169],"clinical":[170],"marker":[171],"complements":[173,279],"traditional":[174,280],"indices":[175],"such":[176,242],"Disease":[180],"Activity":[181],"Index":[182],"(SLEDAI).":[183],"In":[184],"addition,":[185],"through":[186],"comprehensive":[188],"analysis":[189],"repertoire":[192],"data,":[193],"identified":[195],"SLE-specific":[196],"amino":[197],"acid":[198],"within":[200],"sequences,":[203],"critical":[205],"3-mer":[206],"gapped-mer":[208],"oligopeptides.":[209],"These":[210],"demonstrated":[212],"high":[213],"efficacy":[214],"classification,":[217],"achieving":[218],"area":[220],"under":[221],"curve":[223],"(AUC)":[224],"0.908,":[226],"outperforming":[229],"other":[230],"candidate":[231],"Moreover,":[233],"model":[235],"revealed":[236],"SLE-associated":[238],"antigens":[239],"genes,":[241],"CD109":[244],"INS,":[246],"which":[247,278],"provide":[248],"new":[249],"immunological":[253,289],"mechanisms":[254,292],"underlying":[255],"disease.":[257],"CONCLUSION:":[258],"This":[259],"study":[260],"highlights":[261],"DeepTAPE":[265],"supportive":[268],"tool":[269],"biomarker":[271],"discovery":[272],"assessing":[274],"approaches.":[282],"By":[283],"deepening":[284],"understanding":[286],"characteristics":[290],"associated":[293],"work":[297],"lays":[298],"advancing":[302],"targeted":[303],"therapies":[304],"personalized":[306],"medicine":[307],"diseases.":[310],"Consequently,":[311],"findings":[313],"may":[314],"pave":[315],"way":[317],"improved":[319],"patient":[320],"outcomes":[321],"more":[323],"effective":[324],"treatment":[325],"strategies":[326],"management":[329]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-31T00:00:00"}