{"id":"https://openalex.org/W4402170901","doi":"https://doi.org/10.1093/bib/bbae431","title":"Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors","display_name":"Robust detection of infectious disease, autoimmunity, and cancer from the paratope networks of adaptive immune receptors","publication_year":2024,"publication_date":"2024-07-25","ids":{"openalex":"https://openalex.org/W4402170901","doi":"https://doi.org/10.1093/bib/bbae431","pmid":"https://pubmed.ncbi.nlm.nih.gov/39226888"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae431","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae431/59002501/bbae431.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae431/59002501/bbae431.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5008390028","display_name":"Zichang Xu","orcid":"https://orcid.org/0000-0003-1940-6898"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Zichang Xu","raw_affiliation_strings":["Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027659401","display_name":"Hendra S. Ismanto","orcid":"https://orcid.org/0000-0001-9543-6998"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hendra S Ismanto","raw_affiliation_strings":["Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034890365","display_name":"Dianita S. Saputri","orcid":"https://orcid.org/0000-0002-5538-0499"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Dianita S Saputri","raw_affiliation_strings":["Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007376415","display_name":"Soichiro Haruna","orcid":null},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Soichiro Haruna","raw_affiliation_strings":["Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100690608","display_name":"Guanqun Sun","orcid":"https://orcid.org/0009-0008-4704-7072"},"institutions":[{"id":"https://openalex.org/I177738480","display_name":"Japan Advanced Institute of Science and Technology","ror":"https://ror.org/03frj4r98","country_code":"JP","type":"education","lineage":["https://openalex.org/I177738480"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Guanqun Sun","raw_affiliation_strings":["School of information Science , Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 , Japan"],"raw_orcid":"https://orcid.org/0009-0008-4704-7072","affiliations":[{"raw_affiliation_string":"School of information Science , Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292 , Japan","institution_ids":["https://openalex.org/I177738480"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036385963","display_name":"Jan Wilamowski","orcid":"https://orcid.org/0000-0002-8522-4825"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Jan Wilamowski","raw_affiliation_strings":["Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003805192","display_name":"Shunsuke Teraguchi","orcid":"https://orcid.org/0000-0002-5104-0227"},"institutions":[{"id":"https://openalex.org/I171494771","display_name":"Shiga University","ror":"https://ror.org/01vvhy971","country_code":"JP","type":"education","lineage":["https://openalex.org/I171494771"]},{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shunsuke Teraguchi","raw_affiliation_strings":["Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Faculty of Data Science , Shiga University 1-1-1 Banba, Hikone, Shiga 522-8522 , Japan","Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Faculty of Data Science , Shiga University 1-1-1 Banba, Hikone, Shiga 522-8522 , Japan","institution_ids":["https://openalex.org/I171494771"]},{"raw_affiliation_string":"Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102585614","display_name":"Ayan Sengupta","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ayan Sengupta","raw_affiliation_strings":["Cogent Labs , 3-2-1 Roppongi, Minato-ku, Tokyo 106-6122 , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cogent Labs , 3-2-1 Roppongi, Minato-ku, Tokyo 106-6122 , Japan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088092930","display_name":"Songling Li","orcid":"https://orcid.org/0000-0001-9554-2248"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Songling Li","raw_affiliation_strings":["Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003461562","display_name":"Daron M. Standley","orcid":"https://orcid.org/0000-0003-4078-0817"},"institutions":[{"id":"https://openalex.org/I98285908","display_name":"The University of Osaka","ror":"https://ror.org/035t8zc32","country_code":"JP","type":"education","lineage":["https://openalex.org/I98285908"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Daron M Standley","raw_affiliation_strings":["Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan"],"raw_orcid":"https://orcid.org/0000-0003-4078-0817","affiliations":[{"raw_affiliation_string":"Department of Genome Informatics , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Department of Systems Immunology , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":[]},{"raw_affiliation_string":"Osaka University , Immunology Frontier Research Institute (IFReC), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]},{"raw_affiliation_string":"Osaka University , Research Institute for Microbial Diseases (RIMD), , 3-1 Yamadaoka, Suita 565-0871 , Japan","institution_ids":["https://openalex.org/I98285908"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.5598,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.65900618,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"25","issue":"5","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":0.9994999766349792,"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":0.9994999766349792,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9884999990463257,"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/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.9857000112533569,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.611494779586792},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.5558267831802368},{"id":"https://openalex.org/keywords/paratope","display_name":"Paratope","score":0.5457273721694946},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.5017426013946533},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4869893491268158},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.4224843978881836},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.4182332158088684},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.26533859968185425},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.25547391176223755}],"concepts":[{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.611494779586792},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.5558267831802368},{"id":"https://openalex.org/C9086966","wikidata":"https://www.wikidata.org/wiki/Q489135","display_name":"Paratope","level":4,"score":0.5457273721694946},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.5017426013946533},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4869893491268158},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4224843978881836},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.4182332158088684},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.26533859968185425},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.25547391176223755}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D001327","descriptor_name":"Autoimmune Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D003141","descriptor_name":"Communicable Diseases","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":"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011971","descriptor_name":"Receptors, Immunologic","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015551","descriptor_name":"Autoimmunity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015551","descriptor_name":"Autoimmunity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015551","descriptor_name":"Autoimmunity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015551","descriptor_name":"Autoimmunity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae431","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae431/59002501/bbae431.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39226888","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39226888","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11370640","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11370640","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11370640/pdf/bbae431.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae431","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae431","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae431/59002501/bbae431.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7300000190734863,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G5658992440","display_name":null,"funder_award_id":"JP20am0101108","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G8940805373","display_name":"Machine Learning of Disease Biomarkers from B and T cell Receptor Repertoires","funder_award_id":"23K28188","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402170901.pdf","grobid_xml":"https://content.openalex.org/works/W4402170901.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W1989223689","https://openalex.org/W2091596054","https://openalex.org/W2104662981","https://openalex.org/W2147268908","https://openalex.org/W2170747616","https://openalex.org/W2570205435","https://openalex.org/W2613978126","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2752126733","https://openalex.org/W2769070560","https://openalex.org/W2905884391","https://openalex.org/W2910384850","https://openalex.org/W2911980279","https://openalex.org/W2924247059","https://openalex.org/W2946830989","https://openalex.org/W2950954328","https://openalex.org/W2952647092","https://openalex.org/W2963981387","https://openalex.org/W3002599793","https://openalex.org/W3012544261","https://openalex.org/W3095906425","https://openalex.org/W3100486620","https://openalex.org/W3103855458","https://openalex.org/W3107488047","https://openalex.org/W3120317537","https://openalex.org/W3122882833","https://openalex.org/W3182376523","https://openalex.org/W3184997006","https://openalex.org/W3211434666","https://openalex.org/W4205608584","https://openalex.org/W4220764901","https://openalex.org/W4282935197","https://openalex.org/W4285141972","https://openalex.org/W4285405545","https://openalex.org/W4317565748","https://openalex.org/W4319314995","https://openalex.org/W4321765744","https://openalex.org/W4323793457","https://openalex.org/W4366824173","https://openalex.org/W4385223093","https://openalex.org/W4387954034","https://openalex.org/W4388762308","https://openalex.org/W4389495228","https://openalex.org/W4393246014","https://openalex.org/W6805383208"],"related_works":["https://openalex.org/W2093006382","https://openalex.org/W3094563030","https://openalex.org/W4285597652","https://openalex.org/W2917097596","https://openalex.org/W3130759820","https://openalex.org/W4229020575","https://openalex.org/W3167731532","https://openalex.org/W4396954701","https://openalex.org/W2972990938","https://openalex.org/W3138783506"],"abstract_inverted_index":{"Liquid":[0],"biopsies":[1,14],"based":[2,125,136],"on":[3,45,55,126,137,163],"peripheral":[4],"blood":[5],"offer":[6],"a":[7,34,86,120,166,213],"minimally":[8],"invasive":[9],"alternative":[10],"to":[11,60,104,173,200],"solid":[12],"tissue":[13],"for":[15,150,190],"the":[16,28,77,96,106,183],"detection":[17],"of":[18,31,38,82,98,108,123,169,222],"diseases,":[19],"primarily":[20],"cancers.":[21],"However,":[22,74],"such":[23],"tests":[24],"currently":[25],"consider":[26],"only":[27,64],"serum":[29],"component":[30],"blood,":[32],"overlooking":[33],"potentially":[35],"rich":[36],"source":[37],"biomarkers:":[39],"adaptive":[40],"immune":[41,224],"receptors":[42],"(AIRs)":[43],"expressed":[44],"circulating":[46,113],"B":[47,114],"and":[48,69,155,182],"T":[49,116],"cells.":[50],"Machine":[51],"learning-based":[52],"classifiers":[53,161,179],"trained":[54,162],"AIRs":[56,124,197,211],"have":[57],"been":[58],"reported":[59],"accurately":[61],"identify":[62],"not":[63],"cancers":[65],"but":[66],"also":[67],"autoimmune":[68,153],"infectious":[70,151],"diseases":[71,111],"as":[72,212],"well.":[73],"when":[75,171],"using":[76],"conventional":[78],"\"clonotype":[79],"cluster\"":[80],"representation":[81,122],"AIRs,":[83],"individuals":[84],"within":[85],"disease":[87,147],"or":[88,115],"healthy":[89,210],"cohort":[90],"exhibit":[91],"vastly":[92],"different":[93],"features,":[94],"limiting":[95],"generalizability":[97],"these":[99],"classifiers.":[100],"This":[101],"study":[102],"aimed":[103],"address":[105],"challenge":[107],"classifying":[109],"specific":[110],"from":[112,130],"cells":[117,225],"by":[118,230],"developing":[119],"novel":[121,139],"similarity":[127],"networks":[128],"constructed":[129],"their":[131],"antigen-binding":[132],"regions":[133],"(paratopes).":[134],"Features":[135],"this":[138],"representation,":[140],"paratope":[141],"cluster":[142],"occupancies":[143],"(PCOs),":[144],"significantly":[145],"improved":[146],"classification":[148],"performance":[149],"disease,":[152,154],"cancer.":[156],"Under":[157],"identical":[158],"methodological":[159],"conditions,":[160],"PCOs":[164],"achieved":[165],"mean":[167],"AUC":[168],"0.893":[170],"applied":[172],"new":[174],"individuals,":[175],"outperforming":[176],"clonotype":[177],"cluster-based":[178],"(AUC":[180,187],"0.714)":[181],"best-performing":[184],"published":[185],"classifier":[186],"0.777).":[188],"Surprisingly,":[189],"cancer":[191],"patients,":[192],"we":[193],"observed":[194],"that":[195,226],"\"healthy-biased\"":[196],"were":[198],"predicted":[199],"target":[201],"known":[202],"cancer-associated":[203],"antigens":[204],"at":[205],"dramatically":[206],"higher":[207],"rates":[208],"than":[209],"whole":[214],"(Z":[215],"scores":[216],">75),":[217],"suggesting":[218],"an":[219],"overlooked":[220],"reservoir":[221],"cancer-targeting":[223],"could":[227],"be":[228],"identified":[229],"PCOs.":[231]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
