{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:51:34Z","timestamp":1792788694020,"version":"4.5.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005725","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,9,5]],"date-time":"2017-09-05T00:00:00Z","timestamp":1504569600000}}],"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2017,8,23]],"date-time":"2017-08-23T00:00:00Z","timestamp":1503446400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"CADMOS"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005725","type":"journal-article","created":{"date-parts":[[2017,8,23]],"date-time":"2017-08-23T13:50:13Z","timestamp":1503496213000},"page":"e1005725","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":261,"title":["Deciphering HLA-I motifs across HLA peptidomes improves neo-antigen predictions and identifies allostery regulating HLA specificity"],"prefix":"10.1371","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1934-954X","authenticated-orcid":true,"given":"Michal","family":"Bassani-Sternberg","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chlo\u00e9","family":"Chong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Guillaume","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marthe","family":"Solleder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"HuiSong","family":"Pak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3263-3999","authenticated-orcid":true,"given":"Philippe O.","family":"Gannon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lana E.","family":"Kandalaft","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George","family":"Coukos","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3952-0930","authenticated-orcid":true,"given":"David","family":"Gfeller","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2017,8,23]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1038\/nri3084","article-title":"Towards a systems understanding of MHC class I and MHC class II antigen presentation","volume":"11","author":"J Neefjes","year":"2011","journal-title":"Nat Rev Immunol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1126\/science.aaa4971","article-title":"Neoantigens in cancer immunotherapy","volume":"348","author":"TN Schumacher","year":"2015","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"D423","DOI":"10.1093\/nar\/gku1161","article-title":"The IPD and IMGT\/HLA database: allele variant databases","volume":"43","author":"J Robinson","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"D405","DOI":"10.1093\/nar\/gku938","article-title":"The immune epitope database (IEDB) 3.0","volume":"43","author":"R Vita","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"ref5","first-page":"278","article-title":"The Immune Epitope Database and Analysis Resource in Epitope Discovery and Synthetic Vaccine Design","volume":"8","author":"W Fleri","year":"2017","journal-title":"Front Immunol. Frontiers"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/1471-2105-6-132","article-title":"Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method","volume":"6","author":"B Peters","year":"2005","journal-title":"BMC Bioinformatics. BioMed Central"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1110\/ps.0239403","article-title":"Reliable prediction of T-cell epitopes using neural networks with novel sequence representations","volume":"12","author":"M Nielsen","year":"2003","journal-title":"Protein Sci"},{"key":"ref8","article-title":"Gapped sequence alignment using artificial neural networks: application to the MHC class I system","author":"M Andreatta","year":"2015","journal-title":"Bioinformatics"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1007\/s00251-011-0579-8","article-title":"NetMHCcons: a consensus method for the major histocompatibility complex class I predictions","volume":"64","author":"E Karosiene","year":"2012","journal-title":"Immunogenetics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1745-7580-4-2","article-title":"Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries","volume":"4","author":"J Sidney","year":"2008","journal-title":"Immunome Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"e1177691","DOI":"10.1080\/2162402X.2016.1177691","article-title":"Current tools for predicting cancer-specific T cell immunity","author":"D Gfeller","year":"2016","journal-title":"Oncoimmunology. Taylor & Francis"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/s13073-016-0288-x","article-title":"NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets","volume":"8","author":"M Nielsen","year":"2016","journal-title":"Genome Med. BioMed Central"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"572","DOI":"10.1038\/nature14001","article-title":"Predicting immunogenic tumour mutations by combining mass spectrometry and exome sequencing","volume":"515","author":"M Yadav","year":"2014","journal-title":"Nature"},{"key":"ref14","first-page":"12992","article-title":"Direct interrogation of viral peptides presented by the class I HLA of HIV-infected T cells","volume":"88","author":"JC Yaciuk","year":"2014","journal-title":"J Virol. American Society for Microbiology"},{"key":"ref15","first-page":"246","article-title":"Toxoplasma gondii peptide ligands open the gate of the HLA class I binding groove","volume":"5","author":"C McMurtrey","year":"2016","journal-title":"Elife. eLife Sciences Publications Limited"},{"key":"ref16","article-title":"A dendritic cell vaccine increases the breadth and diversity of melanoma neoantigen-specific T cells","author":"BM Carreno","year":"2015","journal-title":"Science"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"13404","DOI":"10.1038\/ncomms13404","article-title":"Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry","volume":"7","author":"M Bassani-Sternberg","year":"2016","journal-title":"Nat Commun. Nature Publishing Group"},{"key":"ref18","first-page":"3058","article-title":"Human Leukocyte Antigen (HLA) Peptides Derived from Tumor Antigens Induced by Inhibition of DNA Methylation for Development of Drug-facilitated Immunotherapy","volume":"15","author":"B Shraibman","year":"2016","journal-title":"Mol Cell Proteomics. American Society for Biochemistry and Molecular Biology"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.coi.2016.04.005","article-title":"Mass spectrometry-based antigen discovery for cancer immunotherapy","volume":"41","author":"M Bassani-Sternberg","year":"2016","journal-title":"Curr Opin Immunol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"5110","DOI":"10.18632\/oncotarget.6960","article-title":"Use of HLA peptidomics and whole exome sequencing to identify human immunogenic neo-antigens","volume":"7","author":"S Kalaora","year":"2016","journal-title":"Oncotarget. Impact Journals"},{"key":"ref21","first-page":"O111.011833","article-title":"An open-source computational and data resource to analyze digital maps of immunopeptidomes","volume":"4","author":"E Caron","year":"2015","journal-title":"Elife. eLife Sciences Publications Limited"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"658","DOI":"10.1074\/mcp.M114.042812","article-title":"Mass spectrometry of human leukocyte antigen class I peptidomes reveals strong effects of protein abundance and turnover on antigen presentation","volume":"14","author":"M Bassani-Sternberg","year":"2015","journal-title":"Mol Cell Proteomics"},{"key":"ref23","first-page":"n\/a","article-title":"High-sensitivity HLA class I peptidome analysis enables a precise definition of peptide motifs and the identification of peptides from cell lines and patients&apos; sera","author":"D Ritz","year":"2016","journal-title":"Proteomics"},{"key":"ref24","first-page":"2492","article-title":"Unsupervised HLA Peptidome Deconvolution Improves Ligand Prediction Accuracy and Predicts Cooperative Effects in Peptide-HLA Interactions","volume":"197","author":"M Bassani-Sternberg","year":"2016","journal-title":"J Immunol. American Association of Immunologists"},{"key":"ref25","article-title":"GibbsCluster: unsupervised clustering and alignment of peptide sequences","author":"M Andreatta","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"4507","DOI":"10.1073\/pnas.1321458111","article-title":"Expanding the detectable HLA peptide repertoire using electron-transfer\/higher-energy collision dissociation (EThcD)","volume":"111","author":"GPM Mommen","year":"2014","journal-title":"Proc Natl Acad Sci USA. National Acad Sciences"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1377","DOI":"10.1007\/s00262-016-1897-3","article-title":"Mass spectrometric analysis of the HLA class I peptidome of melanoma cell lines as a promising tool for the identification of putative tumor-associated HLA epitopes","volume":"65","author":"A Gloger","year":"2016","journal-title":"Cancer Immunol Immunother"},{"key":"ref28","article-title":"MHC class I-associated peptides derive from selective regions of the human genome","volume":"126","author":"H Pearson","year":"2016","journal-title":"J Clin Invest. American Society for Clinical Investigation"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"484","DOI":"10.1038\/msb.2011.18","article-title":"The multiple-specificity landscape of modular peptide recognition domains","volume":"7","author":"D Gfeller","year":"2011","journal-title":"Mol Syst Biol. EMBO Press"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkr1294","article-title":"MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets","volume":"40","author":"T Kim","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1016\/j.immuni.2017.02.007","article-title":"Mass Spectrometry Profiling of HLA-Associated Peptidomes in Mono-allelic Cells Enables More Accurate Epitope Prediction","volume":"46","author":"JG Abelin","year":"2017","journal-title":"Immunity"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1111\/j.1399-0039.1994.tb02327.x","article-title":"HLA-B15: a widespread and diverse family of HLA-B alleles","volume":"43","author":"WH Hildebrand","year":"1994","journal-title":"Tissue Antigens"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e1000010","DOI":"10.1371\/journal.pcbi.1000010","article-title":"A novel Bayesian DNA motif comparison method for clustering and retrieval","volume":"4","author":"N Habib","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"492","DOI":"10.1111\/tan.12565","article-title":"A comprehensive analysis of peptides presented by HLA-A1","volume":"85","author":"K Giam","year":"2015","journal-title":"Tissue Antigens. Blackwell Publishing Ltd"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1111\/tan.12282","article-title":"A comprehensive analysis of constitutive naturally processed and presented HLA-C*04:01 (Cw4)-specific peptides","volume":"83","author":"RB Schittenhelm","year":"2014","journal-title":"Tissue Antigens. Blackwell Publishing Ltd"},{"key":"ref36","first-page":"1517","article-title":"Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity","volume":"197","author":"M Rasmussen","year":"2016","journal-title":"J Immunol. American Association of Immunologists"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1038\/nbt.3662","article-title":"Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes","volume":"34","author":"AK Bentzen","year":"2016","journal-title":"Nat Biotechnol. Nature Research"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"D816","DOI":"10.1093\/nar\/gkn673","article-title":"CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens","volume":"37","author":"LG Almeida","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"J Cox","year":"2008","journal-title":"Nat Biotechnol. Nature Publishing Group"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"2459","DOI":"10.4049\/jimmunol.175.4.2459","article-title":"Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression","volume":"175","author":"GBE Stewart-Jones","year":"2005","journal-title":"J Immunol"},{"key":"ref41","first-page":"1243","article-title":"Structural and kinetic basis for heightened immunogenicity of T cell vaccines","volume":"201","author":"J-L Chen","year":"2005","journal-title":"J Exp Med. Rockefeller University Press"},{"key":"ref42","first-page":"29784","article-title":"Structural basis for T cell alloreactivity among three HLA-B14 and HLA-B27 antigens","volume":"284","author":"P Kumar","year":"2009","journal-title":"J Biol Chem. American Society for Biochemistry and Molecular Biology"},{"key":"ref43","first-page":"1601157","article-title":"The MHC Class II Immunopeptidome of Lymph Nodes in Health and in Chemically Induced Colitis","author":"T Fugmann","year":"2016","journal-title":"J Immunol"},{"key":"ref44","article-title":"NetMHCpan 4.0: Improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data","author":"VI Jurtz","year":"2017","journal-title":"bioRxiv"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s002510050595","article-title":"SYFPEITHI: database for MHC ligands and peptide motifs","volume":"50","author":"H Rammensee","year":"1999","journal-title":"Immunogenetics"},{"key":"ref46","first-page":"8","article-title":"Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach","volume":"29","author":"M Andreatta","year":"2013","journal-title":"Bioinformatics. Oxford University Press"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"4790","DOI":"10.4049\/jimmunol.1401689","article-title":"Uncovering the peptide-binding specificities of HLA-C: a general strategy to determine the specificity of any MHC class I molecule","volume":"193","author":"M Rasmussen","year":"2014","journal-title":"J Immunol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s13073-016-0264-5","article-title":"pVAC-Seq: A genome-guided in silico approach to identifying tumor neoantigens","volume":"8","author":"J Hundal","year":"2016","journal-title":"Genome Med. BioMed Central"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1007\/s00018-011-0659-9","article-title":"Insights into MHC class I antigen processing gained from large-scale analysis of class I ligands","volume":"68","author":"G Mester","year":"2011","journal-title":"Cell Mol Life Sci"},{"key":"ref50","first-page":"1480","article-title":"The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference","volume":"196","author":"T Trolle","year":"2016","journal-title":"J Immunol. American Association of Immunologists"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"6122","DOI":"10.1158\/1078-0432.CCR-10-1297","article-title":"CD8+ enriched \u201cyoung\u201d tumor infiltrating lymphocytes can mediate regression of metastatic melanoma","volume":"16","author":"ME Dudley","year":"2010","journal-title":"Clin Cancer Res. American Association for Cancer Research"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1016\/j.jcyt.2014.02.004","article-title":"Simplified protocol for clinical-grade tumor-infiltrating lymphocyte manufacturing with use of the Wave bioreactor","volume":"16","author":"M Donia","year":"2014","journal-title":"Cytotherapy"},{"key":"ref53","first-page":"246","article-title":"Molecular characterisation of the monocytic cell line THP-1 demonstrates a discrepancy with the documented HLA type","volume":"132","author":"R Battle","year":"2013","journal-title":"Int J Cancer. Wiley Subscription Services, Inc., A Wiley Company"},{"key":"ref54","first-page":"1388","article-title":"Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach","volume":"20","author":"M Nielsen","year":"2004","journal-title":"Bioinformatics. Oxford University Press"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005725","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,9,5]],"date-time":"2017-09-05T00:00:00Z","timestamp":1504569600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005725","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,2]],"date-time":"2019-10-02T14:33:40Z","timestamp":1570026820000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005725"}},"subtitle":[],"editor":[{"given":"Tomer","family":"Hertz","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,8,23]]},"references-count":54,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2017,8,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005725","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/098780","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,8,23]]}}}