{"id":"https://openalex.org/W4386412401","doi":"https://doi.org/10.1109/tcbb.2023.3311444","title":"Family-Specific Training Improves Linear B Cell Epitope Prediction for Emerging Viruses","display_name":"Family-Specific Training Improves Linear B Cell Epitope Prediction for Emerging Viruses","publication_year":2023,"publication_date":"2023-09-04","ids":{"openalex":"https://openalex.org/W4386412401","doi":"https://doi.org/10.1109/tcbb.2023.3311444","pmid":"https://pubmed.ncbi.nlm.nih.gov/37665713"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3311444","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3311444","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062630559","display_name":"Ran Liu","orcid":"https://orcid.org/0000-0003-3627-3994"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Ran Liu","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong, Hong Kong, SAR, China"],"raw_orcid":"https://orcid.org/0000-0003-3627-3994","affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong, SAR, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021719279","display_name":"Ye\u2010Fan Hu","orcid":"https://orcid.org/0000-0002-7834-1476"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Ye-Fan Hu","raw_affiliation_strings":["Li Ka Shing Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China"],"raw_orcid":"https://orcid.org/0000-0002-7834-1476","affiliations":[{"raw_affiliation_string":"Li Ka Shing Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong, SAR, China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100761227","display_name":"Jin Du","orcid":"https://orcid.org/0009-0006-0456-3988"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Jin Du","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong, Hong Kong, SAR, China"],"raw_orcid":"https://orcid.org/0009-0006-0456-3988","affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong, SAR, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100664720","display_name":"Bao\u2010Zhong Zhang","orcid":"https://orcid.org/0000-0002-8716-2306"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Bao-Zhong Zhang","raw_affiliation_strings":["School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China"],"raw_orcid":"https://orcid.org/0000-0002-8716-2306","affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089328049","display_name":"Thomas Yau","orcid":"https://orcid.org/0000-0002-7114-0305"},"institutions":[{"id":"https://openalex.org/I2800810863","display_name":"Queen Mary Hospital","ror":"https://ror.org/02xkx3e48","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I1294586568","https://openalex.org/I2800810863"]},{"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"],"is_corresponding":false,"raw_author_name":"Thomas Yau","raw_affiliation_strings":["Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, SAR, China"],"raw_orcid":"https://orcid.org/0000-0002-7114-0305","affiliations":[{"raw_affiliation_string":"Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, SAR, China","institution_ids":["https://openalex.org/I2800810863","https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060018541","display_name":"Xiaodan Fan","orcid":"https://orcid.org/0000-0002-2744-9030"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Xiaodan Fan","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong, Hong Kong, SAR, China"],"raw_orcid":"https://orcid.org/0000-0002-2744-9030","affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong, Hong Kong, SAR, China","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113217968","display_name":"Jian\u2010Dong Huang","orcid":"https://orcid.org/0000-0001-7531-2816"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Jian-Dong Huang","raw_affiliation_strings":["School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China"],"raw_orcid":"https://orcid.org/0000-0001-7531-2816","affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China","institution_ids":["https://openalex.org/I177725633","https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.5644,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.69460151,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"20","issue":"6","first_page":"3669","last_page":"3680"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10340","display_name":"Hepatitis B Virus Studies","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.9173704981803894},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4855353832244873},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.4733158349990845},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.4728311002254486},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46065354347229004},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4254143238067627},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37445133924484253},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36137402057647705},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.3583197593688965},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.28644633293151855},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.26630938053131104},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20970728993415833},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.13376104831695557}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9173704981803894},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4855353832244873},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.4733158349990845},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.4728311002254486},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46065354347229004},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4254143238067627},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37445133924484253},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36137402057647705},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.3583197593688965},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.28644633293151855},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.26630938053131104},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20970728993415833},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.13376104831695557},{"id":"https://openalex.org/C99454951","wikidata":"https://www.wikidata.org/wiki/Q932068","display_name":"Environmental health","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014612","descriptor_name":"Vaccines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018985","descriptor_name":"Epitopes, B-Lymphocyte","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2023.3311444","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3311444","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37665713","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37665713","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5400000214576721}],"awards":[{"id":"https://openalex.org/G4133620392","display_name":null,"funder_award_id":"2020B1212030004","funder_id":"https://openalex.org/F4320324202","funder_display_name":"Guangdong Science and Technology Department"}],"funders":[{"id":"https://openalex.org/F4320323291","display_name":"Food and Health Bureau","ror":"https://ror.org/03qh32912"},{"id":"https://openalex.org/F4320324202","display_name":"Guangdong Science and Technology Department","ror":"https://ror.org/00tjzgn92"},{"id":"https://openalex.org/F4320335055","display_name":"Health and Medical Research Fund","ror":"https://ror.org/03qh32912"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1900892538","https://openalex.org/W1971713783","https://openalex.org/W1991599908","https://openalex.org/W1993568862","https://openalex.org/W1994413971","https://openalex.org/W2017519756","https://openalex.org/W2051112468","https://openalex.org/W2087064593","https://openalex.org/W2100316154","https://openalex.org/W2100878787","https://openalex.org/W2110298304","https://openalex.org/W2118943119","https://openalex.org/W2123339893","https://openalex.org/W2131005359","https://openalex.org/W2148882270","https://openalex.org/W2149984099","https://openalex.org/W2151539653","https://openalex.org/W2160397907","https://openalex.org/W2181263624","https://openalex.org/W2211925278","https://openalex.org/W2256933318","https://openalex.org/W2466982071","https://openalex.org/W2544105246","https://openalex.org/W2611314002","https://openalex.org/W2613878747","https://openalex.org/W2799524357","https://openalex.org/W2805857020","https://openalex.org/W2898389621","https://openalex.org/W2903899730","https://openalex.org/W2964753092","https://openalex.org/W3008366910","https://openalex.org/W3011488280","https://openalex.org/W3023251337","https://openalex.org/W3038233058","https://openalex.org/W3094514351","https://openalex.org/W3095205894","https://openalex.org/W3112376646","https://openalex.org/W3115254893","https://openalex.org/W3137649039","https://openalex.org/W3139099049","https://openalex.org/W3150505176","https://openalex.org/W4251386234","https://openalex.org/W4283754535","https://openalex.org/W4290975501","https://openalex.org/W4311342303","https://openalex.org/W6688384279"],"related_works":["https://openalex.org/W2021824670","https://openalex.org/W2009867644","https://openalex.org/W2363997565","https://openalex.org/W1981120125","https://openalex.org/W3036615648","https://openalex.org/W2408448169","https://openalex.org/W2182598264","https://openalex.org/W2075879923","https://openalex.org/W1978626146","https://openalex.org/W2205639271"],"abstract_inverted_index":{"The":[0],"rational":[1,187],"design":[2,188],"of":[3,24,65,89,113,147,177,189],"vaccines":[4,190],"and":[5,131,191],"antibody-based":[6,192],"therapeutics":[7,193],"against":[8],"newly":[9,178],"emerging":[10,179],"viruses":[11,91,97,149,180],"relies":[12],"on":[13,39,58,106,143],"B":[14,21,44,86,174],"cell":[15,22,45,87,175],"epitopes":[16,23,46,88],"mainly.":[17],"To":[18,124],"predict":[19,120],"the":[20,62,111,117,121,144,165,186,195],"a":[25,40,80,157,161,168],"novel":[26,81,90,169],"virus,":[27],"several":[28],"algorithms":[29,36],"have":[30],"been":[31],"developed.":[32],"While":[33],"most":[34],"existing":[35,141],"are":[37,47,110],"trained":[38],"dataset":[41,163],"in":[42,72,160,194],"which":[43,109,183],"classified":[48],"as":[49],"'Positive'":[50],"or":[51],"'Negative'.":[52],"However,":[53],"we":[54,78,128],"found":[55],"that":[56],"training":[57,99],"such":[59],"data":[60,146],"contaminates":[61],"target":[63],"pattern":[64],"specific":[66],"viruses,":[67],"leading":[68],"to":[69,119],"inaccurate":[70],"predictions":[71],"some":[73],"cases.":[74],"In":[75],"this":[76],"paper,":[77],"introduce":[79],"framework":[82,170],"for":[83,98],"predicting":[84],"linear":[85,173],"by":[92],"exclusively":[93],"using":[94],"highly":[95],"similar":[96],"data.":[100],"We":[101],"employed":[102],"kernel":[103],"regression":[104],"based":[105],"seropositive":[107,114,151],"rates,":[108],"percentages":[112],"samples":[115],"among":[116],"population,":[118],"potential":[122],"epitopes.":[123],"assess":[125],"our":[126,154],"method,":[127],"conducted":[129],"simulations":[130],"utilized":[132],"two":[133],"real-world":[134],"datasets.":[135],"Our":[136],"method":[137],"significantly":[138],"outperformed":[139],"other":[140],"methods":[142],"testing":[145],"four":[148],"with":[150],"rates.":[152],"Also,":[153],"strategy":[155],"showed":[156],"better":[158,172],"prediction":[159,176],"larger":[162],"from":[164],"IEDB.":[166],"Thus,":[167],"providing":[171],"is":[181],"established,":[182],"will":[184],"benefit":[185],"future.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-23T13:55:30.953635","created_date":"2025-10-10T00:00:00"}
