{"id":"https://openalex.org/W3125209804","doi":"https://doi.org/10.1093/bioinformatics/btaa1064","title":"bbeaR: an R package and framework for epitope-specific antibody profiling","display_name":"bbeaR: an R package and framework for epitope-specific antibody profiling","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3125209804","doi":"https://doi.org/10.1093/bioinformatics/btaa1064","mag":"3125209804","pmid":"https://pubmed.ncbi.nlm.nih.gov/33471075"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa1064","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1064","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/1/131/37005941/btaa1064.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/1/131/37005941/btaa1064.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051648553","display_name":"Maria Suprun","orcid":"https://orcid.org/0000-0001-9161-4021"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maria Suprun","raw_affiliation_strings":["Department of Pediatrics, Allergy and Immunology, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA"],"raw_orcid":"https://orcid.org/0000-0001-9161-4021","affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Allergy and Immunology, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012155836","display_name":"Randall J. Ellis","orcid":"https://orcid.org/0000-0003-3862-0881"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Randall J Ellis","raw_affiliation_strings":["Departments of Neuroscience and Psychiatry, Addiction Institute of Mount Sinai, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Departments of Neuroscience and Psychiatry, Addiction Institute of Mount Sinai, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015552885","display_name":"Hugh A. Sampson","orcid":"https://orcid.org/0000-0003-1613-8875"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hugh A Sampson","raw_affiliation_strings":["Department of Pediatrics, Allergy and Immunology, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Allergy and Immunology, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074081568","display_name":"Mayte Su\u00e1rez\u2010Fari\u00f1as","orcid":"https://orcid.org/0000-0001-8712-3553"},"institutions":[{"id":"https://openalex.org/I98704320","display_name":"Icahn School of Medicine at Mount Sinai","ror":"https://ror.org/04a9tmd77","country_code":"US","type":"education","lineage":["https://openalex.org/I1320796813","https://openalex.org/I98704320"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mayte Su\u00e1rez-Fari\u00f1as","raw_affiliation_strings":["Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA","Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]},{"raw_affiliation_string":"Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai , New York, NY 10029, USA","institution_ids":["https://openalex.org/I98704320"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5074081568"],"corresponding_institution_ids":["https://openalex.org/I98704320"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2867,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.55197234,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"37","issue":"1","first_page":"131","last_page":"133"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.2167000025510788,"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"}},"topics":[{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.2167000025510788,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10877","display_name":"Allergic Rhinitis and Sensitization","score":0.19670000672340393,"subfield":{"id":"https://openalex.org/subfields/2723","display_name":"Immunology and Allergy"},"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.18610000610351562,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.9391264915466309},{"id":"https://openalex.org/keywords/multiplex","display_name":"Multiplex","score":0.6692060828208923},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5912630558013916},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.5740986466407776},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5501837730407715},{"id":"https://openalex.org/keywords/immunoglobulin-d","display_name":"Immunoglobulin D","score":0.549383282661438},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5048604607582092},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.4945628345012665},{"id":"https://openalex.org/keywords/epitope-mapping","display_name":"Epitope mapping","score":0.46293845772743225},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26126575469970703},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22877833247184753},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.22122499346733093},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.1234181821346283},{"id":"https://openalex.org/keywords/b-cell","display_name":"B cell","score":0.11504027247428894},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10006240010261536}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.9391264915466309},{"id":"https://openalex.org/C2781188995","wikidata":"https://www.wikidata.org/wiki/Q6934982","display_name":"Multiplex","level":2,"score":0.6692060828208923},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5912630558013916},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.5740986466407776},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5501837730407715},{"id":"https://openalex.org/C48010095","wikidata":"https://www.wikidata.org/wiki/Q79447","display_name":"Immunoglobulin D","level":4,"score":0.549383282661438},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5048604607582092},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.4945628345012665},{"id":"https://openalex.org/C2781241564","wikidata":"https://www.wikidata.org/wiki/Q1347450","display_name":"Epitope mapping","level":4,"score":0.46293845772743225},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26126575469970703},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22877833247184753},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.22122499346733093},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.1234181821346283},{"id":"https://openalex.org/C2778453870","wikidata":"https://www.wikidata.org/wiki/Q188930","display_name":"B cell","level":3,"score":0.11504027247428894},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10006240010261536}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa1064","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1064","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/1/131/37005941/btaa1064.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:33471075","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33471075","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:8034521","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8034521","pdf_url":null,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa1064","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa1064","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/1/131/37005941/btaa1064.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.4699999988079071,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G2360587265","display_name":null,"funder_award_id":"T32GM062754","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4008171572","display_name":null,"funder_award_id":"UM1 AI109565","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6156573265","display_name":null,"funder_award_id":"T32GM062754","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7310101195","display_name":null,"funder_award_id":"T32 GM062754","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8956336593","display_name":null,"funder_award_id":"UM1 AI109565","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3125209804.pdf","grobid_xml":"https://content.openalex.org/works/W3125209804.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1588943321","https://openalex.org/W1942586809","https://openalex.org/W1977292892","https://openalex.org/W2017956110","https://openalex.org/W2081098333","https://openalex.org/W2099079147","https://openalex.org/W2106840507","https://openalex.org/W2168360445","https://openalex.org/W2169353806","https://openalex.org/W2233727091","https://openalex.org/W2725957738","https://openalex.org/W2766842037","https://openalex.org/W2885092805","https://openalex.org/W2897877332","https://openalex.org/W2903681664","https://openalex.org/W2906935111","https://openalex.org/W2993471499","https://openalex.org/W3012758763","https://openalex.org/W6757793730"],"related_works":["https://openalex.org/W4224037588","https://openalex.org/W1481419192","https://openalex.org/W2086226498","https://openalex.org/W2807990694","https://openalex.org/W2007511503","https://openalex.org/W1567266611","https://openalex.org/W1600929005","https://openalex.org/W2048515479","https://openalex.org/W3172430216","https://openalex.org/W3080200277"],"abstract_inverted_index":{"SUMMARY:":[0],"Analysis":[1],"of":[2,13,32,100],"epitope-specific":[3,33,101],"antibody":[4,102],"repertoires":[5],"has":[6],"provided":[7],"novel":[8,19],"insights":[9],"into":[10],"the":[11,50,65],"pathogenesis":[12],"inflammatory":[14],"disorders,":[15],"especially":[16],"allergies.":[17],"A":[18],"multiplex":[20],"immunoassay,":[21],"termed":[22],"Bead-Based":[23],"Epitope":[24],"Assay":[25],"(BBEA),":[26],"was":[27],"developed":[28,48],"to":[29,55,88],"quantify":[30],"levels":[31],"immunoglobulins,":[34],"including":[35],"IgE,":[36],"IgG,":[37],"IgA":[38],"and":[39,58,82,97,110],"IgD":[40],"isotypes.":[41],"bbeaR":[42,94,107],"is":[43,108],"an":[44,116],"open-source":[45,109],"R":[46,117],"package,":[47],"for":[49],"BBEA,":[51],"provides":[52],"a":[53],"framework":[54],"import,":[56],"process":[57],"normalize":[59],".csv":[60],"data":[61,125],"files":[62],"exported":[63],"from":[64,113],"Luminex":[66],"reader,":[67],"evaluate":[68],"various":[69],"quality":[70],"control":[71],"metrics,":[72],"analyze":[73],"differential":[74],"epitope-binding":[75],"antibodies":[76],"with":[77],"linear":[78],"modeling,":[79],"visualize":[80],"results":[81],"map":[83],"epitopes'":[84],"amino":[85],"acid":[86],"sequences":[87],"their":[89],"respective":[90],"primary":[91],"protein":[92],"structures.":[93],"enables":[95],"streamlined":[96],"reproducible":[98],"analysis":[99],"profiles.":[103],"AVAILABILITY":[104],"AND":[105],"IMPLEMENTATION:":[106],"freely":[111],"available":[112,127],"GitHub":[114],"as":[115],"package:":[118],"https://github.com/msuprun/bbeaR;":[119],"vignettes":[120],"included.":[121],"SUPPLEMENTARY":[122],"INFORMATION:":[123],"Supplementary":[124],"are":[126],"at":[128],"Bioinformatics":[129],"online.":[130]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
