{"id":"https://openalex.org/W2748343486","doi":"https://doi.org/10.1371/journal.pcbi.1005725","title":"Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity","display_name":"Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity","publication_year":2017,"publication_date":"2017-08-23","ids":{"openalex":"https://openalex.org/W2748343486","doi":"https://doi.org/10.1371/journal.pcbi.1005725","mag":"2748343486","pmid":"https://pubmed.ncbi.nlm.nih.gov/28832583"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005725","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005725","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005725&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005725&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087479651","display_name":"Michal Bassani\u2010Sternberg","orcid":"https://orcid.org/0000-0002-1934-954X"},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"University Hospital of Lausanne","ror":"https://ror.org/05a353079","country_code":"CH","type":"funder","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Michal Bassani-Sternberg","raw_affiliation_strings":["Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882"]},{"raw_affiliation_string":"Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046828383","display_name":"Chlo\u00e9 Chong","orcid":null},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"University Hospital of Lausanne","ror":"https://ror.org/05a353079","country_code":"CH","type":"funder","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Chlo\u00e9 Chong","raw_affiliation_strings":["Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882"]},{"raw_affiliation_string":"Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001841343","display_name":"Philippe Guillaume","orcid":"https://orcid.org/0000-0002-6340-0963"},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"University Hospital of Lausanne","ror":"https://ror.org/05a353079","country_code":"CH","type":"funder","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philippe Guillaume","raw_affiliation_strings":["Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882"]},{"raw_affiliation_string":"Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089293907","display_name":"Marthe Solleder","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Marthe Solleder","raw_affiliation_strings":["Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066269629","display_name":"HuiSong Pak","orcid":"https://orcid.org/0009-0001-4362-699X"},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"University Hospital of Lausanne","ror":"https://ror.org/05a353079","country_code":"CH","type":"funder","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"HuiSong Pak","raw_affiliation_strings":["Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882"]},{"raw_affiliation_string":"Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005580505","display_name":"Philippe O. Gannon","orcid":"https://orcid.org/0000-0003-3263-3999"},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"University Hospital of Lausanne","ror":"https://ror.org/05a353079","country_code":"CH","type":"funder","lineage":["https://openalex.org/I2802229882"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Philippe O. Gannon","raw_affiliation_strings":["Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007749781","display_name":"Lana E. Kandalaft","orcid":"https://orcid.org/0000-0002-1575-6674"},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"University Hospital of Lausanne","ror":"https://ror.org/05a353079","country_code":"CH","type":"funder","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Lana E. Kandalaft","raw_affiliation_strings":["Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882"]},{"raw_affiliation_string":"Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017724230","display_name":"George Coukos","orcid":"https://orcid.org/0000-0001-8813-7367"},"institutions":[{"id":"https://openalex.org/I2802229882","display_name":"University Hospital of Lausanne","ror":"https://ror.org/05a353079","country_code":"CH","type":"funder","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"George Coukos","raw_affiliation_strings":["Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882"]},{"raw_affiliation_string":"Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017097104","display_name":"David Gfeller","orcid":"https://orcid.org/0000-0002-3952-0930"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I2802229882","display_name":"University Hospital of Lausanne","ror":"https://ror.org/05a353079","country_code":"CH","type":"funder","lineage":["https://openalex.org/I2802229882"]},{"id":"https://openalex.org/I4210117758","display_name":"Ludwig Cancer Research","ror":"https://ror.org/02cn3rm21","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I4210117758","https://openalex.org/I4210150094"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"David Gfeller","raw_affiliation_strings":["Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Fundamental Oncology, University Hospital of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I2802229882"]},{"raw_affiliation_string":"Ludwig Centre for Cancer Research, University of Lausanne, Epalinges, Switzerland","institution_ids":["https://openalex.org/I4210117758","https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5017097104","https://openalex.org/A5087479651"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I2802229882","https://openalex.org/I4210117758","https://openalex.org/I97565354"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":11.2265,"has_fulltext":true,"cited_by_count":268,"citation_normalized_percentile":{"value":0.99005014,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"13","issue":"8","first_page":"e1005725","last_page":"e1005725"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":1.0,"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":1.0,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.9988999962806702,"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"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9972000122070312,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/human-leukocyte-antigen","display_name":"Human leukocyte antigen","score":0.800727128982544},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6842426061630249},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.6386191844940186},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5633491277694702},{"id":"https://openalex.org/keywords/exome-sequencing","display_name":"Exome sequencing","score":0.5355697870254517},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5337342619895935},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.5225933790206909},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.4831382930278778},{"id":"https://openalex.org/keywords/exome","display_name":"Exome","score":0.4235844612121582},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.41920557618141174},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.2724141478538513},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16675209999084473}],"concepts":[{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.800727128982544},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6842426061630249},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.6386191844940186},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5633491277694702},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.5355697870254517},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5337342619895935},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.5225933790206909},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.4831382930278778},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.4235844612121582},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.41920557618141174},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.2724141478538513},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16675209999084473}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D015395","descriptor_name":"Histocompatibility Antigens Class I","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1005725","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005725","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005725&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:28832583","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28832583","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:serval.unil.ch:BIB_0F969601F848","is_oa":true,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_0F969601F848","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology, vol. 13, no. 8, pp. e1005725","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:RePEc:plo:pcbi00:1005725","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005725","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:85de754f22664449b0d218f3f61e9293","is_oa":true,"landing_page_url":"https://doaj.org/article/85de754f22664449b0d218f3f61e9293","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 13, Iss 8, p e1005725 (2017)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/5339317","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Deciphering_HLA-I_motifs_across_HLA_peptidomes_improves_neo-antigen_predictions_and_identifies_allostery_regulating_HLA_specificity/5339317","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:pubmedcentral.nih.gov:5584980","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5584980","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005725","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005725","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005725&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.7900000214576721,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G5929225917","display_name":null,"funder_award_id":"CADMOS","funder_id":"https://openalex.org/F4320323831","funder_display_name":"Universit\u00e9 de Lausanne"}],"funders":[{"id":"https://openalex.org/F4320323831","display_name":"Universit\u00e9 de Lausanne","ror":"https://ror.org/019whta54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2748343486.pdf","grobid_xml":"https://content.openalex.org/works/W2748343486.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W1954852590","https://openalex.org/W1981106544","https://openalex.org/W1981811253","https://openalex.org/W1986215428","https://openalex.org/W1994048581","https://openalex.org/W1996371910","https://openalex.org/W1998713127","https://openalex.org/W2000305183","https://openalex.org/W2006759360","https://openalex.org/W2007026865","https://openalex.org/W2011458181","https://openalex.org/W2028524752","https://openalex.org/W2043503180","https://openalex.org/W2053707749","https://openalex.org/W2073621589","https://openalex.org/W2080752012","https://openalex.org/W2098357256","https://openalex.org/W2098849902","https://openalex.org/W2101231992","https://openalex.org/W2101553545","https://openalex.org/W2103498243","https://openalex.org/W2105003357","https://openalex.org/W2105353410","https://openalex.org/W2110574412","https://openalex.org/W2112752664","https://openalex.org/W2117252247","https://openalex.org/W2125732073","https://openalex.org/W2141609931","https://openalex.org/W2143558133","https://openalex.org/W2147087392","https://openalex.org/W2150991884","https://openalex.org/W2153590293","https://openalex.org/W2159959024","https://openalex.org/W2256481604","https://openalex.org/W2256496883","https://openalex.org/W2267653167","https://openalex.org/W2271526964","https://openalex.org/W2271914738","https://openalex.org/W2299728699","https://openalex.org/W2326870000","https://openalex.org/W2344922370","https://openalex.org/W2345351072","https://openalex.org/W2464113003","https://openalex.org/W2471645096","https://openalex.org/W2507608410","https://openalex.org/W2509527114","https://openalex.org/W2518214177","https://openalex.org/W2552513321","https://openalex.org/W2555228033","https://openalex.org/W2561554887","https://openalex.org/W2589139221","https://openalex.org/W2605830019","https://openalex.org/W2607286972","https://openalex.org/W2626253213","https://openalex.org/W2953065444"],"related_works":["https://openalex.org/W2093932542","https://openalex.org/W2043256480","https://openalex.org/W2772505697","https://openalex.org/W3083501552","https://openalex.org/W2400191746","https://openalex.org/W2094815267","https://openalex.org/W1983406990","https://openalex.org/W2484239316","https://openalex.org/W3024198590","https://openalex.org/W4367844067"],"abstract_inverted_index":{"The":[0,128,157],"precise":[1],"identification":[2],"of":[3,34,80,93,150,164,183],"Human":[4],"Leukocyte":[5],"Antigen":[6],"class":[7],"I":[8],"(HLA-I)":[9],"binding":[10,66,82,166,179,200],"motifs":[11,67,90,100,130,159],"plays":[12],"a":[13,77,116],"central":[14],"role":[15],"in":[16,25,125,147,176,198],"our":[17],"ability":[18],"to":[19,71,106,119],"understand":[20],"and":[21,28,61,68,87,114,133,186,197],"predict":[22],"(neo-)antigen":[23],"presentation":[24],"infectious":[26],"diseases":[27],"cancer.":[29],"Here,":[30],"by":[31,174,192],"exploiting":[32],"co-occurrence":[33],"HLA-I":[35,65,81,172,178],"alleles":[36,74,103,173],"across":[37],"ten":[38],"newly":[39],"generated":[40],"as":[41,43],"well":[42],"forty":[44],"public":[45],"HLA":[46,122,141],"peptidomics":[47,123,142],"datasets":[48],"comprising":[49],"more":[50],"than":[51,110],"115,000":[52],"unique":[53],"peptides,":[54],"we":[55,58,187],"show":[56],"that":[57,104,139],"can":[59],"rapidly":[60],"accurately":[62],"identify":[63],"many":[64],"map":[69],"them":[70],"their":[72],"corresponding":[73],"without":[75],"any":[76],"priori":[78],"knowledge":[79],"specificity.":[83],"Our":[84],"approach":[85],"recapitulates":[86],"refines":[88],"known":[89,112],"for":[91,101,146,170],"43":[92],"the":[94,126,165,177,184,189],"most":[95],"frequent":[96],"alleles,":[97],"uncovers":[98],"new":[99,158],"9":[102],"up":[105],"now":[107],"had":[108],"less":[109],"five":[111],"ligands":[113],"provides":[115],"scalable":[117],"framework":[118],"incorporate":[120],"additional":[121],"studies":[124],"future.":[127],"refined":[129],"improve":[131],"neo-antigen":[132],"cancer":[134],"testis":[135],"antigen":[136],"predictions,":[137],"indicating":[138],"unbiased":[140],"data":[143],"are":[144],"ideal":[145],"silico":[148],"predictions":[149],"neo-antigens":[151],"from":[152],"tumor":[153],"exome":[154],"sequencing":[155],"data.":[156],"further":[160],"reveal":[161],"distant":[162],"modulation":[163],"specificity":[167],"at":[168],"P2":[169],"some":[171],"residues":[175],"site":[180],"but":[181],"outside":[182],"B-pocket":[185],"unravel":[188],"underlying":[190],"mechanisms":[191],"protein":[193],"structure":[194],"analysis,":[195],"mutagenesis":[196],"vitro":[199],"assays.":[201]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":29},{"year":2024,"cited_by_count":32},{"year":2023,"cited_by_count":42},{"year":2022,"cited_by_count":41},{"year":2021,"cited_by_count":27},{"year":2020,"cited_by_count":31},{"year":2019,"cited_by_count":30},{"year":2018,"cited_by_count":23},{"year":2017,"cited_by_count":7}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
