{"id":"https://openalex.org/W4391758650","doi":"https://doi.org/10.1093/bib/bbae024","title":"ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction","display_name":"ImmuneMirror: A machine learning-based integrative pipeline and web server for neoantigen prediction","publication_year":2024,"publication_date":"2024-01-16","ids":{"openalex":"https://openalex.org/W4391758650","doi":"https://doi.org/10.1093/bib/bbae024","pmid":"https://pubmed.ncbi.nlm.nih.gov/38343325"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae024","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae024/56657535/bbae024.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/25/2/bbae024/56657535/bbae024.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114046305","display_name":"Gulam Sarwar Chuwdhury","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]},{"id":"https://openalex.org/I4210087348","display_name":"National Cancer Centre Japan","ror":"https://ror.org/0025ww868","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210087348"]},{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK","JP"],"is_corresponding":false,"raw_author_name":"Gulam Sarwar Chuwdhury","raw_affiliation_strings":["Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I4210087348"]},{"raw_affiliation_string":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071779537","display_name":"Yunshan Guo","orcid":"https://orcid.org/0000-0001-6671-3300"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yunshan Guo","raw_affiliation_strings":["Department of Biostatistics, Yale School of Public Health , New Haven, Connecticut , USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Yale School of Public Health , New Haven, Connecticut , USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055682207","display_name":"Chi\u2010Leung Chiang","orcid":"https://orcid.org/0000-0002-9836-6478"},"institutions":[{"id":"https://openalex.org/I4210087348","display_name":"National Cancer Centre Japan","ror":"https://ror.org/0025ww868","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210087348"]},{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK","JP"],"is_corresponding":false,"raw_author_name":"Chi-Leung Chiang","raw_affiliation_strings":["Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I4210087348"]},{"raw_affiliation_string":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108833252","display_name":"Ka-On Lam","orcid":null},"institutions":[{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]},{"id":"https://openalex.org/I4210087348","display_name":"National Cancer Centre Japan","ror":"https://ror.org/0025ww868","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210087348"]},{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK","JP"],"is_corresponding":false,"raw_author_name":"Ka-On Lam","raw_affiliation_strings":["Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I4210087348"]},{"raw_affiliation_string":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036436064","display_name":"Ngar\u2010Woon Kam","orcid":"https://orcid.org/0000-0002-4053-6040"},"institutions":[{"id":"https://openalex.org/I4210087348","display_name":"National Cancer Centre Japan","ror":"https://ror.org/0025ww868","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210087348"]},{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]},{"id":"https://openalex.org/I4210130449","display_name":"State Key Laboratory of Synthetic Chemistry","ror":"https://ror.org/038ey3e97","country_code":"CN","type":"facility","lineage":["https://openalex.org/I177725633","https://openalex.org/I19820366","https://openalex.org/I4210112946","https://openalex.org/I4210130449","https://openalex.org/I889458895"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK","JP"],"is_corresponding":false,"raw_author_name":"Ngar-Woon Kam","raw_affiliation_strings":["Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park , Shatin , Hong Kong","University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I4210087348"]},{"raw_affiliation_string":"Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park , Shatin , Hong Kong","institution_ids":["https://openalex.org/I4210130449"]},{"raw_affiliation_string":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100413280","display_name":"Zhonghua Liu","orcid":"https://orcid.org/0000-0003-3048-9823"},"institutions":[{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhonghua Liu","raw_affiliation_strings":["Department of Biostatistics, Columbia University , New York, NY , USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Columbia University , New York, NY , USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100671163","display_name":"Wei Dai","orcid":"https://orcid.org/0000-0002-5558-0685"},"institutions":[{"id":"https://openalex.org/I4210141719","display_name":"University of Hong Kong - Shenzhen Hospital","ror":"https://ror.org/047w7d678","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210141719"]},{"id":"https://openalex.org/I4210087348","display_name":"National Cancer Centre Japan","ror":"https://ror.org/0025ww868","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210087348"]},{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["CN","HK","JP"],"is_corresponding":true,"raw_author_name":"Wei Dai","raw_affiliation_strings":["Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","University of Hong Kong-Shenzhen Hospital , Shenzhen , P. R. China","Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China"],"affiliations":[{"raw_affiliation_string":"Department of Clinical Oncology , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I4210087348"]},{"raw_affiliation_string":"University of Hong Kong , Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, , Hong Kong (SAR) , P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]},{"raw_affiliation_string":"University of Hong Kong-Shenzhen Hospital , Shenzhen , P. R. China","institution_ids":["https://openalex.org/I4210141719","https://openalex.org/I889458895"]},{"raw_affiliation_string":"Department of Clinical Oncology, Center of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (SAR), P. R. China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5100413280","https://openalex.org/A5100671163"],"corresponding_institution_ids":["https://openalex.org/I177725633","https://openalex.org/I4210087348","https://openalex.org/I4210141719","https://openalex.org/I78577930","https://openalex.org/I889458895"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.7782,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.9380303,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"25","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9994000196456909,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.9991999864578247,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/microsatellite-instability","display_name":"Microsatellite instability","score":0.734975278377533},{"id":"https://openalex.org/keywords/arid1a","display_name":"ARID1A","score":0.5941757559776306},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.5443174839019775},{"id":"https://openalex.org/keywords/immune-checkpoint","display_name":"Immune checkpoint","score":0.4653435945510864},{"id":"https://openalex.org/keywords/exome","display_name":"Exome","score":0.4343253970146179},{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.4340170919895172},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.4270898401737213},{"id":"https://openalex.org/keywords/colorectal-cancer","display_name":"Colorectal cancer","score":0.41176721453666687},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.41060927510261536},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.3936017155647278},{"id":"https://openalex.org/keywords/immunotherapy","display_name":"Immunotherapy","score":0.37238574028015137},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3707610070705414},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.3675413727760315},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.3571242690086365},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.3476264476776123},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.33049947023391724},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.25066548585891724},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.21642884612083435},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12579822540283203},{"id":"https://openalex.org/keywords/microsatellite","display_name":"Microsatellite","score":0.10305291414260864},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09346896409988403}],"concepts":[{"id":"https://openalex.org/C2779767149","wikidata":"https://www.wikidata.org/wiki/Q488212","display_name":"Microsatellite instability","level":5,"score":0.734975278377533},{"id":"https://openalex.org/C2781273526","wikidata":"https://www.wikidata.org/wiki/Q18032797","display_name":"ARID1A","level":4,"score":0.5941757559776306},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.5443174839019775},{"id":"https://openalex.org/C2780851360","wikidata":"https://www.wikidata.org/wiki/Q21686041","display_name":"Immune checkpoint","level":4,"score":0.4653435945510864},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.4343253970146179},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.4340170919895172},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.4270898401737213},{"id":"https://openalex.org/C526805850","wikidata":"https://www.wikidata.org/wiki/Q188874","display_name":"Colorectal cancer","level":3,"score":0.41176721453666687},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41060927510261536},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.3936017155647278},{"id":"https://openalex.org/C2777701055","wikidata":"https://www.wikidata.org/wiki/Q1427096","display_name":"Immunotherapy","level":3,"score":0.37238574028015137},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3707610070705414},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.3675413727760315},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.3571242690086365},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.3476264476776123},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.33049947023391724},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.25066548585891724},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.21642884612083435},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12579822540283203},{"id":"https://openalex.org/C61320498","wikidata":"https://www.wikidata.org/wiki/Q265193","display_name":"Microsatellite","level":4,"score":0.10305291414260864},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09346896409988403},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.0}],"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":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077277","descriptor_name":"Esophageal Squamous Cell Carcinoma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077277","descriptor_name":"Esophageal Squamous Cell Carcinoma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077277","descriptor_name":"Esophageal Squamous Cell Carcinoma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077277","descriptor_name":"Esophageal Squamous Cell Carcinoma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077277","descriptor_name":"Esophageal Squamous Cell Carcinoma","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000951","descriptor_name":"Antigens, Neoplasm","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004938","descriptor_name":"Esophageal Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004938","descriptor_name":"Esophageal Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004938","descriptor_name":"Esophageal Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004938","descriptor_name":"Esophageal Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004938","descriptor_name":"Esophageal Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053842","descriptor_name":"Microsatellite Instability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053842","descriptor_name":"Microsatellite Instability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053842","descriptor_name":"Microsatellite Instability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053842","descriptor_name":"Microsatellite Instability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053842","descriptor_name":"Microsatellite Instability","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbae024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae024","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae024/56657535/bbae024.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:38343325","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38343325","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:10859690","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10859690","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10859690/pdf/bbae024.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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"},{"id":"pmh:oai:hub.hku.hk:10722/344364","is_oa":true,"landing_page_url":"https://hub.hku.hk/handle/10722/344364","pdf_url":null,"source":{"id":"https://openalex.org/S4377196271","display_name":"The HKU Scholars Hub (University of Hong Kong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I889458895","host_organization_name":"University of Hong Kong","host_organization_lineage":["https://openalex.org/I889458895"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae024","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae024/56657535/bbae024.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":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.6899999976158142}],"awards":[{"id":"https://openalex.org/G1859322275","display_name":null,"funder_award_id":"InnoHK","funder_id":"https://openalex.org/F4320321920","funder_display_name":"Innovation and Technology Commission"},{"id":"https://openalex.org/G5728806482","display_name":null,"funder_award_id":"InnoHK","funder_id":"https://openalex.org/F4320329815","funder_display_name":"Hong Kong Government"},{"id":"https://openalex.org/G6029191517","display_name":null,"funder_award_id":"Health@InnoHK","funder_id":"https://openalex.org/F4320321920","funder_display_name":"Innovation and Technology Commission"}],"funders":[{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"},{"id":"https://openalex.org/F4320329815","display_name":"Hong Kong Government","ror":"https://ror.org/034179816"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391758650.pdf"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1831050183","https://openalex.org/W1950829641","https://openalex.org/W2020534880","https://openalex.org/W2054606083","https://openalex.org/W2080303593","https://openalex.org/W2104471998","https://openalex.org/W2119180969","https://openalex.org/W2120399005","https://openalex.org/W2124662474","https://openalex.org/W2140235037","https://openalex.org/W2148143831","https://openalex.org/W2149441684","https://openalex.org/W2168688111","https://openalex.org/W2256496883","https://openalex.org/W2299181842","https://openalex.org/W2326870000","https://openalex.org/W2487770199","https://openalex.org/W2587048937","https://openalex.org/W2591378383","https://openalex.org/W2607497548","https://openalex.org/W2614443510","https://openalex.org/W2620563544","https://openalex.org/W2622499649","https://openalex.org/W2625427953","https://openalex.org/W2739132742","https://openalex.org/W2743893844","https://openalex.org/W2766564423","https://openalex.org/W2767298971","https://openalex.org/W2767699537","https://openalex.org/W2767891987","https://openalex.org/W2790516087","https://openalex.org/W2796153225","https://openalex.org/W2953065444","https://openalex.org/W2972864093","https://openalex.org/W2979330780","https://openalex.org/W3009999407","https://openalex.org/W3091991776","https://openalex.org/W3183864458","https://openalex.org/W4210388887","https://openalex.org/W4319939997","https://openalex.org/W4391758650","https://openalex.org/W6738337739"],"related_works":["https://openalex.org/W2082685488","https://openalex.org/W2093932542","https://openalex.org/W2043256480","https://openalex.org/W2172231381","https://openalex.org/W1983406990","https://openalex.org/W2106924416","https://openalex.org/W2772505697","https://openalex.org/W3083501552","https://openalex.org/W2400191746","https://openalex.org/W3167069925"],"abstract_inverted_index":{"Neoantigens":[0],"are":[1,10,29],"derived":[2,206],"from":[3,68,100,107,180,207],"somatic":[4],"mutations":[5,143],"in":[6,12,155,221],"the":[7,75,85,92,147,203,227,243],"tumors":[8,106],"but":[9,135],"absent":[11],"normal":[13],"tissues.":[14],"Emerging":[15],"evidence":[16],"suggests":[17],"that":[18],"neoantigens":[19],"can":[20],"stimulate":[21],"tumor-specific":[22],"T-cell-mediated":[23],"antitumor":[24],"immune":[25],"responses,":[26],"and":[27,41,54,61,95,116,195,245],"therefore":[28],"potential":[30,218],"immunotherapeutic":[31],"targets.":[32],"We":[33,88,120],"developed":[34],"ImmuneMirror":[35,90,248],"as":[36,216],"a":[37,42,46,122,131,136,171,208,217],"stand-alone":[38],"open-source":[39],"pipeline":[40],"web":[43],"server":[44],"incorporating":[45],"balanced":[47],"random":[48],"forest":[49],"model":[50,58,80],"for":[51,187,249],"neoantigen":[52,133,185,233,250],"prediction":[53,57,234],"prioritization.":[55],"The":[56,72],"was":[59,81,214],"trained":[60,79],"tested":[62],"using":[63,236],"known":[64],"immunogenic":[65],"neopeptides":[66],"collected":[67],"19":[69],"published":[70],"studies.":[71],"area":[73],"under":[74],"curve":[76],"of":[77,124,149,161,173,247],"our":[78],"0.87":[82],"based":[83],"on":[84],"testing":[86],"data.":[87],"applied":[89],"to":[91,230],"whole-exome":[93],"sequencing":[94,97],"RNA":[96],"data":[98],"obtained":[99],"gastrointestinal":[101],"tract":[102],"cancers":[103],"including":[104],"805":[105],"colorectal":[108],"cancer":[109],"(CRC),":[110],"esophageal":[111],"squamous":[112],"cell":[113],"carcinoma":[114,118],"(ESCC)":[115],"hepatocellular":[117],"patients.":[119],"discovered":[121],"subgroup":[123],"microsatellite":[125],"instability-high":[126],"(MSI-H)":[127],"CRC":[128],"patients":[129,163,175],"with":[130,183],"low":[132],"load":[134,186],"high":[137],"tumor":[138],"mutation":[139,210],"burden":[140],"(>":[141],"10":[142],"per":[144],"Mbp).":[145],"Although":[146],"efficacy":[148],"PD-1":[150],"blockade":[151],"has":[152],"been":[153],"demonstrated":[154],"advanced":[156],"MSI-H":[157,174],"patients,":[158],"almost":[159],"half":[160],"such":[162],"do":[164],"not":[165,178],"respond":[166],"well.":[167],"Our":[168,240],"study":[169,229],"identified":[170,215],"subset":[172],"who":[176],"may":[177],"benefit":[179],"this":[181],"treatment":[182],"lower":[184],"major":[188],"histocompatibility":[189],"complex":[190],"I":[191],"(P":[192,197],"<":[193],"0.0001)":[194],"II":[196],"=":[198],"0.0008)":[199],"molecules,":[200],"respectively.":[201],"Additionally,":[202],"neopeptide":[204],"YMCNSSCMGV-TP53G245V,":[205],"hotspot":[209],"restricted":[211],"by":[212],"HLA-A02,":[213],"actionable":[219],"target":[220],"ESCC.":[222],"This":[223],"is":[224],"so":[225],"far":[226],"largest":[228],"comprehensively":[231],"evaluate":[232],"models":[235],"experimentally":[237],"validated":[238],"neopeptides.":[239],"results":[241],"demonstrate":[242],"reliability":[244],"effectiveness":[246],"prediction.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":3}],"updated_date":"2026-03-25T14:56:36.534964","created_date":"2025-10-10T00:00:00"}