{"id":"https://openalex.org/W4404092673","doi":"https://doi.org/10.1093/bioinformatics/btae637","title":"Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides","display_name":"Ranking antibody binding epitopes and proteins across samples from whole proteome tiled linear peptides","publication_year":2024,"publication_date":"2024-11-01","ids":{"openalex":"https://openalex.org/W4404092673","doi":"https://doi.org/10.1093/bioinformatics/btae637","pmid":"https://pubmed.ncbi.nlm.nih.gov/39499154"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae637","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btae637","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036323056","display_name":"Sean J. McIlwain","orcid":"https://orcid.org/0000-0002-3820-8400"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210103341","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/01e4byj08","country_code":"US","type":"funder","lineage":["https://openalex.org/I2799905417","https://openalex.org/I4210103341","https://openalex.org/I4210132596"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sean J McIlwain","raw_affiliation_strings":["Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison , Madison, WI, 53705,","University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , Madison, WI, 53705,","University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , WI","University of Wisconsin-Madison Department of Biostatistics and Medical Informatics, , WI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I4210103341"]},{"raw_affiliation_string":"University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , WI","institution_ids":["https://openalex.org/I135310074","https://openalex.org/I4210103341"]},{"raw_affiliation_string":"University of Wisconsin-Madison Department of Biostatistics and Medical Informatics, , WI","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042246572","display_name":"Anna Hoefges","orcid":"https://orcid.org/0000-0002-3712-4854"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anna Hoefges","raw_affiliation_strings":["Department of Human Oncology, University of Wisconsin-Madison , Madison, WI, 53705,","University of Wisconsin-Madison Department of Human Oncology, , WI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Oncology, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin-Madison Department of Human Oncology, , WI","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089532829","display_name":"Amy K. Erbe","orcid":"https://orcid.org/0000-0003-1175-4062"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amy K Erbe","raw_affiliation_strings":["Department of Human Oncology, University of Wisconsin-Madison , Madison, WI, 53705,","University of Wisconsin-Madison Department of Human Oncology, , WI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Oncology, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin-Madison Department of Human Oncology, , WI","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011569932","display_name":"Paul M. Sondel","orcid":"https://orcid.org/0000-0002-0981-8875"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210103341","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/01e4byj08","country_code":"US","type":"funder","lineage":["https://openalex.org/I2799905417","https://openalex.org/I4210103341","https://openalex.org/I4210132596"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul M Sondel","raw_affiliation_strings":["Department of Human Oncology, University of Wisconsin-Madison , Madison, WI, 53705,","Department of Pediatrics, University of Wisconsin-Madison , Madison, WI, 53705,","University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , Madison, WI, 53705,","University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , WI","University of Wisconsin-Madison Department of Human Oncology, , WI","University of Wisconsin-Madison Department of Pediatrics, , WI"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Human Oncology, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Pediatrics, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I4210103341"]},{"raw_affiliation_string":"University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , WI","institution_ids":["https://openalex.org/I135310074","https://openalex.org/I4210103341"]},{"raw_affiliation_string":"University of Wisconsin-Madison Department of Human Oncology, , WI","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin-Madison Department of Pediatrics, , WI","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019665472","display_name":"Irene M. Ong","orcid":"https://orcid.org/0000-0002-9353-6941"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]},{"id":"https://openalex.org/I4210103341","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/01e4byj08","country_code":"US","type":"funder","lineage":["https://openalex.org/I2799905417","https://openalex.org/I4210103341","https://openalex.org/I4210132596"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Irene M Ong","raw_affiliation_strings":["Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison , Madison, WI, 53705,","Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison , Madison, WI, 53705,","Department of Obstetrics and Gynecology, University of Wisconsin-Madison , Madison, WI, 53705,","University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , Madison, WI, 53705,","University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , WI","University of Wisconsin-Madison Center for Human Genomics and Precision Medicine, , WI","University of Wisconsin-Madison Department of Biostatistics and Medical Informatics, , WI","University of Wisconsin-Madison Department of Obstetrics and Gynecology, , WI"],"raw_orcid":"https://orcid.org/0000-0002-9353-6941","affiliations":[{"raw_affiliation_string":"Center for Human Genomics and Precision Medicine, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Obstetrics and Gynecology, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , Madison, WI, 53705,","institution_ids":["https://openalex.org/I4210103341"]},{"raw_affiliation_string":"University of Wisconsin Carbone Comprehensive Cancer Center, University of Wisconsin-Madison , WI","institution_ids":["https://openalex.org/I135310074","https://openalex.org/I4210103341"]},{"raw_affiliation_string":"University of Wisconsin-Madison Center for Human Genomics and Precision Medicine, , WI","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin-Madison Department of Biostatistics and Medical Informatics, , WI","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"University of Wisconsin-Madison Department of Obstetrics and Gynecology, , WI","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5019665472","https://openalex.org/A5036323056"],"corresponding_institution_ids":["https://openalex.org/I135310074","https://openalex.org/I4210103341"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.16,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.50399025,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"40","issue":"12","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":0.7269999980926514,"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":0.7269999980926514,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.19429999589920044,"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":0.043699998408555984,"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/epitope","display_name":"Epitope","score":0.8789520263671875},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.7197827100753784},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6667140126228333},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5250506401062012},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.5190559029579163},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.45117560029029846},{"id":"https://openalex.org/keywords/linear-epitope","display_name":"Linear epitope","score":0.4363902807235718},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.32550257444381714},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23878881335258484},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.20378488302230835},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17085504531860352},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07396590709686279}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.8789520263671875},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.7197827100753784},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6667140126228333},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5250506401062012},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.5190559029579163},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.45117560029029846},{"id":"https://openalex.org/C78598654","wikidata":"https://www.wikidata.org/wiki/Q17140316","display_name":"Linear epitope","level":4,"score":0.4363902807235718},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.32550257444381714},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23878881335258484},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.20378488302230835},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17085504531860352},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07396590709686279}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000906","descriptor_name":"Antibodies","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae637","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39499154","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39499154","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11631460","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11631460","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11631460/pdf/btae637.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae637","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae637","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G115506582","display_name":null,"funder_award_id":"UL1TR002373.","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G1217549976","display_name":null,"funder_award_id":"U19 AI104317","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G1332332826","display_name":null,"funder_award_id":"CA 014520","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1359571829","display_name":null,"funder_award_id":"P01CA250972","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1475746525","display_name":null,"funder_award_id":"R35 CA197078","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1501672413","display_name":"Institutional Career Development Core","funder_award_id":"2kl2tr002374-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1711654737","display_name":null,"funder_award_id":"P30 CA014520","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G1712026730","display_name":null,"funder_award_id":"CA014520","funder_id":"https://openalex.org/F4320310176","funder_display_name":"University of Wisconsin Carbone Cancer Center"},{"id":"https://openalex.org/G181383032","display_name":null,"funder_award_id":"U54 CA232568","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1901119385","display_name":null,"funder_award_id":"CA197078","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1959862837","display_name":"Flow Cytometry Laboratory","funder_award_id":"5p30ca014520-50","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2022595383","display_name":"Molecular Targeted Radionuclide Therapy for Tumor Immunomodulation and Enhancing Immunotherapy Response","funder_award_id":"3p01ca250972-05s1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2173499975","display_name":null,"funder_award_id":"UL1T R002373","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4004214011","display_name":null,"funder_award_id":"P30 CA 014520","funder_id":"https://openalex.org/F4320310176","funder_display_name":"University of Wisconsin Carbone Cancer Center"},{"id":"https://openalex.org/G42679306","display_name":null,"funder_award_id":"P30CA014520","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4667300268","display_name":null,"funder_award_id":"P30 CA014520","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G5171721139","display_name":null,"funder_award_id":"CA233102","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5265733349","display_name":"Enhancing Antibody-directed Innate Immunity to Improve Cancer Outcome","funder_award_id":"5r35ca197078-07","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5638354291","display_name":null,"funder_award_id":"Project 3","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G596254795","display_name":null,"funder_award_id":"KL2TR002374","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G7340370193","display_name":null,"funder_award_id":"U01-CA2331 02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7512500759","display_name":null,"funder_award_id":"UL1TR002373","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G8577699080","display_name":"Administrative and Statistical Core Resource","funder_award_id":"1u54ca232568-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8803782758","display_name":null,"funder_award_id":"P30 CA014520","funder_id":"https://openalex.org/F4320306155","funder_display_name":"Cancer Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306155","display_name":"Cancer Research Institute","ror":"https://ror.org/02f3xk561"},{"id":"https://openalex.org/F4320306589","display_name":"Alex's Lemonade Stand Foundation for Childhood Cancer","ror":"https://ror.org/038ja4880"},{"id":"https://openalex.org/F4320310176","display_name":"University of Wisconsin Carbone Cancer Center","ror":"https://ror.org/02mqqhj42"},{"id":"https://openalex.org/F4320316231","display_name":"Midwest Athletes Against Childhood Cancer","ror":null},{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337368","display_name":"Division of Graduate Education","ror":"https://ror.org/00whkrf32"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1549716303","https://openalex.org/W1973012451","https://openalex.org/W1983210486","https://openalex.org/W1985078733","https://openalex.org/W1994865855","https://openalex.org/W2038200783","https://openalex.org/W2082786279","https://openalex.org/W2087323922","https://openalex.org/W2089175718","https://openalex.org/W2092442974","https://openalex.org/W2122851743","https://openalex.org/W2170189627","https://openalex.org/W2339221558","https://openalex.org/W2346039915","https://openalex.org/W2406250479","https://openalex.org/W2511863223","https://openalex.org/W2754396261","https://openalex.org/W2883227601","https://openalex.org/W2889418962","https://openalex.org/W2907099021","https://openalex.org/W2949854354","https://openalex.org/W2964381629","https://openalex.org/W2970241796","https://openalex.org/W2972729032","https://openalex.org/W3098962209","https://openalex.org/W3170326106","https://openalex.org/W4206254216","https://openalex.org/W4210861522","https://openalex.org/W4289527519","https://openalex.org/W4290977073","https://openalex.org/W6651723475"],"related_works":["https://openalex.org/W3145510187","https://openalex.org/W2003116223","https://openalex.org/W1991572753","https://openalex.org/W1992575377","https://openalex.org/W3139969521","https://openalex.org/W4241031629","https://openalex.org/W1996102030","https://openalex.org/W2062700146","https://openalex.org/W2016943232","https://openalex.org/W2061599389"],"abstract_inverted_index":{"INTRODUCTION:":[0],"Ultradense":[1],"peptide":[2,57,158],"binding":[3,58,95],"arrays":[4,59],"that":[5,127],"can":[6,107,128],"probe":[7],"millions":[8],"of":[9,16,22,24,66,81,87,136,174,187,209],"linear":[10,62,157],"peptides":[11,101],"comprising":[12],"the":[13,31,61,85,139,156,172],"entire":[14,140],"proteomes":[15],"human":[17],"or":[18,20,78,148],"mouse,":[19],"hundreds":[21],"thousands":[23],"microbes,":[25],"are":[26,44],"powerful":[27],"tools":[28,46],"for":[29,47,55,83,146,168,211],"studying":[30],"antibody":[32,53,94,119,144,212],"repertoire":[33],"in":[34,198],"serum":[35],"samples":[36,137],"to":[37,117,142,164],"understand":[38],"adaptive":[39],"immune":[40,88],"responses.":[41,89],"MOTIVATION:":[42],"There":[43],"few":[45],"exploring":[48],"high-dimensional,":[49],"significant":[50],"and":[51,69,97,113,124,161,185,193,203,206],"reproducible":[52],"targets":[54,120],"ultradense":[56],"at":[60,121,155,223],"peptide,":[63],"epitope":[64,76,188],"(grouping":[65],"adjacent":[67],"peptides),":[68],"protein":[70,162],"level":[71,163],"across":[72,132],"multiple":[73],"samples/subjects":[74],"(i.e.":[75],"spread":[77],"immunogenic":[79,109],"regions":[80,208],"proteins)":[82],"understanding":[84],"heterogeneity":[86],"RESULTS:":[90],"We":[91,170],"developed":[92],"Hierarchical":[93],"Epitopes":[96],"pROteins":[98],"from":[99],"liNear":[100],"(HERON),":[102],"an":[103],"R":[104,219],"package,":[105],"which":[106],"identify":[108,165],"epitopes,":[110],"using":[111,180],"meta-analyses":[112],"spatial":[114],"clustering":[115],"techniques":[116],"explore":[118],"various":[122],"resolution":[123],"confidence":[125],"levels,":[126],"be":[129],"found":[130],"consistently":[131],"a":[133],"specified":[134],"number":[135],"through":[138],"proteome":[141],"study":[143],"responses":[145],"diagnostics":[147],"treatment.":[149],"Our":[150],"approach":[151],"estimates":[152],"significance":[153],"values":[154],"(probe),":[159],"epitope,":[160],"top":[166],"candidates":[167],"validation.":[169],"tested":[171],"performance":[173],"predictions":[175],"on":[176,190],"all":[177],"three":[178],"levels":[179],"correlation":[181],"between":[182],"technical":[183],"replicates":[184],"comparison":[186],"calls":[189],"two":[191],"datasets,":[192],"results":[194],"showed":[195],"HERON's":[196],"competitiveness":[197],"estimating":[199],"false":[200],"discovery":[201],"rates":[202],"finding":[204],"general":[205],"sample-level":[207],"interest":[210],"binding.":[213],"AVAILABILITY":[214],"AND":[215],"IMPLEMENTATION:":[216],"The":[217],"HERON":[218],"package":[220],"is":[221],"available":[222],"Bioconductor":[224],"https://bioconductor.org/packages/release/bioc/html/HERON.html.":[225]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
