{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,4]],"date-time":"2025-12-04T14:37:31Z","timestamp":1764859051268,"version":"3.37.3"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2018,6,7]],"date-time":"2018-06-07T00:00:00Z","timestamp":1528329600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Health","award":["HHSN272201200010C"],"award-info":[{"award-number":["HHSN272201200010C"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Datasets that are derived from different studies (e.g. MHC ligand elution, MHC binding, B\/T cell epitope screening etc.) often vary in terms of experimental approaches, sizes of peptides tested, including partial and or nested overlapping peptides and in the number of donors tested.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a customized application of the Immune Epitope Database\u2019s ImmunomeBrowser tool, which can be used to effectively aggregate and visualize heterogeneous immunological data. User provided peptide sets and associated response data is mapped to a user-provided protein reference sequence. The output consists of tables and figures representing the aggregated data represented by a Response Frequency score and associated estimated confidence interval. This allows the user to visualizing regions associated with dominant responses and their boundaries. The results are presented both as a user interactive javascript based web interface and a tabular format in a selected reference sequence.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The \u2018ImmunomeBrowser\u2019 has been a longstanding feature of the IEDB (http:\/\/www.iedb.org). The present application extends the use of this tool to work with user-provided datasets, rather than the output of IEDB queries. This new server version of the ImmunomeBrowser is freely accessible at http:\/\/tools.iedb.org\/immunomebrowser\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty463","type":"journal-article","created":{"date-parts":[[2018,6,6]],"date-time":"2018-06-06T19:10:40Z","timestamp":1528312240000},"page":"3931-3933","source":"Crossref","is-referenced-by-count":46,"title":["ImmunomeBrowser: a tool to aggregate and visualize complex and heterogeneous epitopes in reference proteins"],"prefix":"10.1093","volume":"34","author":[{"given":"Sandeep Kumar","family":"Dhanda","sequence":"first","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA"}]},{"given":"Randi","family":"Vita","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA"}]},{"given":"Brendan","family":"Ha","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA"}]},{"given":"Alba","family":"Grifoni","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA"}]},{"given":"Bjoern","family":"Peters","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA"},{"name":"Department of Medicine, University of California, San Diego, CA, USA"}]},{"given":"Alessandro","family":"Sette","sequence":"additional","affiliation":[{"name":"Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA"},{"name":"Department of Medicine, University of California, San Diego, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,6,7]]},"reference":[{"key":"2023012712335371800_bty463-B1","doi-asserted-by":"crossref","DOI":"10.1002\/pmic.201700252","article-title":"Computational tools for the identification and interpretation of sequence motifs in immunopeptidomes","author":"Alvarez","year":"2018","journal-title":"Proteomics"},{"key":"2023012712335371800_bty463-B2","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/j.biologicals.2015.07.008","article-title":"Rational design of stable and functional hirudin III mutants with lower antigenicity","volume":"43","author":"Asgari","year":"2015","journal-title":"Biologicals"},{"key":"2023012712335371800_bty463-B3","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1111\/imm.12816","article-title":"Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity","volume":"153","author":"Dhanda","year":"2018","journal-title":"Immunology"},{"key":"2023012712335371800_bty463-B4","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1016\/j.clim.2013.09.006","article-title":"T-cell dependent immunogenicity of protein therapeutics: preclinical assessment and mitigation","volume":"149","author":"Jawa","year":"2013","journal-title":"Clin. 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USA"},{"key":"2023012712335371800_bty463-B8","doi-asserted-by":"crossref","first-page":"e0136417","DOI":"10.1371\/journal.pone.0136417","article-title":"Comprehensive analysis of the naturally processed peptide repertoire: differences between HLA-A and B in the immunopeptidome","volume":"10","author":"Schellens","year":"2015","journal-title":"PLoS One"},{"key":"2023012712335371800_bty463-B9","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1146\/annurev.immunol.20.100301.064819","article-title":"Producing nature\u2019s gene-chips: the generation of peptides for display by MHC class I molecules","volume":"20","author":"Shastri","year":"2002","journal-title":"Annu. Rev. Immunol"},{"key":"2023012712335371800_bty463-B10","doi-asserted-by":"crossref","first-page":"729","DOI":"10.1080\/14789450.2017.1361825","article-title":"Deciphering the MHC-associated peptidome: a review of naturally processed ligand data","volume":"14","author":"Vaughan","year":"2017","journal-title":"Expert. 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Proteomics"},{"key":"2023012712335371800_bty463-B11","doi-asserted-by":"crossref","first-page":"D405","DOI":"10.1093\/nar\/gku938","article-title":"The immune epitope database (IEDB) 3.0","volume":"43","author":"Vita","year":"2015","journal-title":"Nucleic Acids Res"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/22\/3931\/48920038\/bioinformatics_34_22_3931.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/22\/3931\/48920038\/bioinformatics_34_22_3931.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:22:59Z","timestamp":1674825779000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/22\/3931\/5034429"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,7]]},"references-count":11,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2018,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty463","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,11,15]]},"published":{"date-parts":[[2018,6,7]]}}}