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Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire.
Calis JJ, de Boer RJ, Keşmir C. Calis JJ, et al. PLoS Comput Biol. 2012;8(3):e1002412. doi: 10.1371/journal.pcbi.1002412. Epub 2012 Mar 1. PLoS Comput Biol. 2012. PMID: 22396638 Free PMC article.
MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation.
Calis JJ, Sanchez-Perez GF, Keşmir C. Calis JJ, et al. Eur J Immunol. 2010 Oct;40(10):2699-709. doi: 10.1002/eji.201040339. Eur J Immunol. 2010. PMID: 21038467
Predicted indirectly recognizable HLA epitopes presented by HLA-DR correlate with the de novo development of donor-specific HLA IgG antibodies after kidney transplantation.
Otten HG, Calis JJ, Keşmir C, van Zuilen AD, Spierings E. Otten HG, et al. Among authors: calis jj. Hum Immunol. 2013 Mar;74(3):290-6. doi: 10.1016/j.humimm.2012.12.004. Epub 2012 Dec 8. Hum Immunol. 2013. PMID: 23232063
Properties of MHC class I presented peptides that enhance immunogenicity.
Calis JJ, Maybeno M, Greenbaum JA, Weiskopf D, De Silva AD, Sette A, Keşmir C, Peters B. Calis JJ, et al. PLoS Comput Biol. 2013 Oct;9(10):e1003266. doi: 10.1371/journal.pcbi.1003266. Epub 2013 Oct 24. PLoS Comput Biol. 2013. PMID: 24204222 Free PMC article.
Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs.
Calis JJ, Reinink P, Keller C, Kloetzel PM, Keşmir C. Calis JJ, et al. Immunogenetics. 2015 Feb;67(2):85-93. doi: 10.1007/s00251-014-0815-0. Epub 2014 Dec 6. Immunogenetics. 2015. PMID: 25475908 Free PMC article.
Exploratory Study of Predicted Indirectly ReCognizable HLA Epitopes in Mismatched Hematopoietic Cell Transplantations.
Geneugelijk K, Thus KA, van Deutekom HWM, Calis JJA, Borst E, Keşmir C, Oudshoorn M, van der Holt B, Meijer E, Zeerleder S, de Groot MR, von dem Borne PA, Schaap N, Cornelissen J, Kuball J, Spierings E. Geneugelijk K, et al. Among authors: calis jja. Front Immunol. 2019 Apr 24;10:880. doi: 10.3389/fimmu.2019.00880. eCollection 2019. Front Immunol. 2019. PMID: 31068946 Free PMC article.
High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma.
Linnemann C, van Buuren MM, Bies L, Verdegaal EM, Schotte R, Calis JJ, Behjati S, Velds A, Hilkmann H, Atmioui DE, Visser M, Stratton MR, Haanen JB, Spits H, van der Burg SH, Schumacher TN. Linnemann C, et al. Among authors: calis jj. Nat Med. 2015 Jan;21(1):81-5. doi: 10.1038/nm.3773. Epub 2014 Dec 22. Nat Med. 2015. PMID: 25531942
Corrigendum: High-throughput epitope discovery reveals frequent recognition of neo-antigens by CD4+ T cells in human melanoma.
Linnemann C, van Buuren MM, Bies L, Verdegaal EM, Schotte R, Calis JJ, Behjati S, Velds A, Hilkmann H, El Atmioui D, Visser M, Stratton MR, Haanen JB, Spits H, van der Burg SH, Schumacher TN. Linnemann C, et al. Among authors: calis jj. Nat Med. 2016 Oct 6;22(10):1192. doi: 10.1038/nm1016-1192d. Nat Med. 2016. PMID: 27711057 No abstract available.
High sensitivity of cancer exome-based CD8 T cell neo-antigen identification.
van Buuren MM, Calis JJ, Schumacher TN. van Buuren MM, et al. Among authors: calis jj. Oncoimmunology. 2014 May 14;3:e28836. doi: 10.4161/onci.28836. eCollection 2014. Oncoimmunology. 2014. PMID: 25083320 Free PMC article.
Transcriptome of airway neutrophils reveals an interferon response in life-threatening respiratory syncytial virus infection.
Besteman SB, Callaghan A, Langedijk AC, Hennus MP, Meyaard L, Mokry M, Bont LJ, Calis JJA. Besteman SB, et al. Among authors: calis jja. Clin Immunol. 2020 Nov;220:108593. doi: 10.1016/j.clim.2020.108593. Epub 2020 Sep 11. Clin Immunol. 2020. PMID: 32920212 Free article.
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