Publications
2023
Scholarly publications
Hermens, J. M., & Kesmir, C. (2023). Role of T cells in severe COVID-19 disease, protection, and long term immunity. Immunogenetics, 75(3), 295-307. https://doi.org/10.1007/s00251-023-01294-9
2022
Scholarly publications
Pascoal Ramos, M. I., Keşmir, C., Stok, J. E., Geerdink, R., Satravelas, N., Westerlaken, G. H. A., Meyaard, L., & van der Vlist, M. (2022). CD200R1L is a functional evolutionary conserved activating receptor in human neutrophils. Journal of Leukocyte Biology, 111(2), 367-377. https://doi.org/10.1002/JLB.2A0520-334R
2021
Scholarly publications
Timmerman, L. M., De Graaf, J. F., Satravelas, N., Kesmir, Ç., Meyaard, L., & Van Der Vlist, M. (2021). Identification of a novel conserved signaling motif in CD200 receptor required for its inhibitory function. PLoS One, 16(3), 1-16. [e0244770]. https://doi.org/10.1371/journal.pone.0244770
Andeweg, S. P., Kesmir, C., & Dutilh, B. E. (2021). Quantifying The Impact Of Human Leukocyte Antigen On The Human Gut Microbiota. mSphere, 6(4), 1-12. https://doi.org/10.1128/mSphere.00476-21
2020
Scholarly publications
Ritmahan, W., Kesmir, C., & Vroomans, R. M. A. (2020). Revealing factors determining immunodominant responses against dominant epitopes. Immunogenetics, 72(1-2), 109-118. https://doi.org/10.1007/s00251-019-01134-9
Wortel, I. M. N., Keşmir, C., de Boer, R. J., Mandl, J. N., & Textor, J. (2020). Is T Cell Negative Selection a Learning Algorithm? Cells, 9(3), [690]. https://doi.org/10.3390/cells9030690
Bagaev, D. V., Vroomans, R. M. A., Samir, J., Stervbo, U., Rius, C., Dolton, G., Greenshields-Watson, A., Attaf, M., Egorov, E. S., Zvyagin, I. V., Babel, N., Cole, D. K., Godkin, A. J., Sewell, A. K., Kesmir, C., Chudakov, D. M., Luciani, F., & Shugay, M. (2020). VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium. Nucleic Acids Research, 48(D1), D1057–D1062. https://doi.org/10.1093/nar/gkz874
2019
Scholarly publications
Kesmir, C., & Bontrop, R. (2019). Immunogenetics special issue 2020: nomenclature, databases, and bioinformatics in immunogenetics. Immunogenetics, 72(1), 1-3. https://doi.org/10.1007/s00251-019-01150-9
Geneugelijk, K., Thus, K. A., Van Deutekom, H. W. M., Calis, J. J. A., Borst, E., Keşmir, C., Oudshoorn, M., Van Der Holt, B., Meijer, E., Zeerleder, S., De Groot, M. R., Von Dem Borne, P. A., Schaap, N., Cornelissen, J., Kuball, J., & Spierings, E. (2019). Exploratory study of predicted indirectly recognizable HLA epitopes in mismatched hematopoietic cell transplantations. Frontiers in Immunology, 10, [880]. https://doi.org/10.3389/fimmu.2019.00880
van Belzen, I. A. E. M., & Kesmir, C. (2019). Immune biomarkers for predicting response to adoptive cell transfer as cancer treatment. Immunogenetics, 71(2), 71-86. https://doi.org/10.1007/s00251-018-1083-1
2018
Scholarly publications
Shugay, M., Bagaev, D. V., Zvyagin, I. V., Vroomans, R. M., Crawford, J. C., Dolton, G., Komech, E. A., Sycheva, A. L., Koneva, A. E., Egorov, E. S., Eliseev, A. V., Van Dyk, E., Dash, P., Attaf, M., Rius, C., Ladell, K., McLaren, J. E., Matthews, K. K., Clemens, E. B., ... Chudakov, D. M. (2018). VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Research, 46(D1), D419–D427. https://doi.org/10.1093/nar/gkx760
Carrillo-Bustamante, P., de Boer, R. J., & Kesmir, C. (2018). Specificity of inhibitory KIRs enables NK cells to detect changes in an altered peptide environment. Immunogenetics, 70(2), 87-97. https://doi.org/10.1007/s00251-017-1019-1
2017
Scholarly publications
Thus, K. A., Geneugelijk, K., van Deutekom, H., Calis, J., Borst, E., Kesmir, C., Oudshoorn, M., van der Holt, B., Meijer, E., Zeerleder, S., de Groot, M. R., von dem Borne, P., Schaap, N., Cornelissen, J., Kuball, J., & Spierings, E. (2017). Identifying Permissible HLA-Mismatches in Unrelated-Donor Hematopoietic Stem-Cell Transplantation Using Predicted Indirectly Recognizable HLA Epitopes. Biology of Blood and Marrow Transplantation, 23(3), S107-S108. https://doi.org/10.1016/j.bbmt.2016.12.064
2016
Scholarly publications
Marriott, I., Van Baarle, D., De Wit, J., Borghans, J. A. M., & Kesmir, C. (2016). Editorial: Role of HLA and KIR in viral infections. Frontiers in Immunology, 7(7), [286]. https://doi.org/10.3389/fimmu.2016.00286
Woolthuis, R. G., van Dorp, C. H., Kesmir, C., de Boer, R. J., & van Boven, M. (2016). Long-term adaptation of the influenza A virus by escaping cytotoxic T-cell recognition. Scientific Reports, 6, [33334]. https://doi.org/10.1038/srep33334
Carrillo-Bustamante, P., Kesmir, C., & de Boer, R. J. (2016). The evolution of natural killer cell receptors. Immunogenetics, 68(1), 3-18. https://doi.org/10.1007/s00251-015-0869-7
2015
Scholarly publications
Geneugelijk, K., Hönger, G., van Deutekom, H. W. M., Thus, K. A., Kesmir, C., Hösli, I., Schaub, S., & Spierings, E. (2015). Predicted Indirectly Recognizable HLA Epitopes Presented by HLA-DRB1 Are Related to HLA Antibody Formation During Pregnancy. American Journal of Transplantation, 15(12), 3112-22. https://doi.org/10.1111/ajt.13508
Schellens, I. M., Meiring, H. D., Hoof, I., Spijkers, S. N., Poelen, M. C. M., Van Gaans-van den Brink, J. A. M., Costa, A. I., Vennema, H., Kesmir, C., Van Baarle, D., & Van Els, C. A. C. M. (2015). Measles virus epitope presentation by HLA: Novel insights into epitope selection, dominance, and microvariation. Frontiers in Immunology [E], 6(NOV), [546]. https://doi.org/10.3389/fimmu.2015.00546
Rao, X., Hoof, I., van Baarle, D., Kesmir, C., & Textor, J. (2015). HLA preferences for conserved epitopes: A potential mechanism for hepatitis C clearance. Frontiers in Immunology [E], 6(OCT), [552]. https://doi.org/10.3389/fimmu.2015.00552
Kløverpris, H. N., McGregor, R., McLaren, J. E., Ladell, K., Harndahl, M., Stryhn, A., Carlson, J. M., Koofhethile, C., Gerritsen, B., Kesmir, C., Chen, F., Riddell, L., Luzzi, G., Leslie, A., Walker, B. D., Ndung'u, T., Buus, S., Price, D. A., & Goulder, P. J. (2015). CD8+ TCR Bias and Immunodominance in HIV-1 Infection. Journal of Immunology, 194(11), 5329-5345. https://doi.org/10.4049/jimmunol.1400854
https://dspace.library.uu.nl/bitstream/handle/1874/321661/cd8.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/321661/cd8.pdf?sequence=1
Carrillo-Bustamante, P., Kesmir, C., & de Boer, R. J. (2015). A Coevolutionary Arms Race between Hosts and Viruses Drives Polymorphism and Polygenicity of NK Cell Receptors. Molecular Biology and Evolution, 32(8), 2149-2160. https://doi.org/10.1093/molbev/msv096
van Deutekom, H. W. M., & Kesmir, C. (2015). Zooming into the binding groove of HLA molecules: which positions and which substitutions change peptide binding most? Immunogenetics, 67(8), 425-36. https://doi.org/10.1007/s00251-015-0849-y
Carrillo-Bustamante, P., Kesmir, C., & de Boer, R. J. (2015). Can Selective MHC Downregulation Explain the Specificity and Genetic Diversity of NK Cell Receptors? Frontiers in Immunology [E], 6, 311. https://doi.org/10.3389/fimmu.2015.00311
Schellens, I. M. M., Hoof, I., Meiring, H. D., Spijkers, S. N. M., Poelen, M. C. M., van Gaans-van den Brink, J. A. M., van der Poel, K., Costa, A. I., van Els, C. A. C. M., van Baarle, D., & Kesmir, C. (2015). Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome. PLoS One, 10(9), e0136417. https://doi.org/10.1371/journal.pone.0136417
Schumacher, T. N., Kesmir, C., & van Buuren, M. M. (2015). Biomarkers in cancer immunotherapy. Cancer Cell, 27(1), 12-14. https://doi.org/10.1016/j.ccell.2014.12.004
https://dspace.library.uu.nl/bitstream/handle/1874/320977/biomarkers.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/320977/biomarkers.pdf?sequence=1
Costa, A. I., Koning, D., Ladell, K., McLaren, J. E., Grady, B. P. X., Schellens, I. M. M., van Ham, P., Nijhuis, M., Borghans, J. A. M., Kesmir, C., Price, D. A., & van Baarle, D. (2015). Complex T-Cell Receptor Repertoire Dynamics Underlie the CD8+ T-Cell Response to HIV-1. Journal of Virology, 89(1), 110-119. https://doi.org/10.1128/JVI.01765-14
Calis, J. J. A., Reinink, P., Keller, C., Kloetzel, P. M., & Kesmir, C. (2015). Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs. Immunogenetics, 67(2), 85-93. https://doi.org/10.1007/s00251-014-0815-0
2014
Scholarly publications
Thus, K. A., Furst, D., van Deutekom, H., Calis, J., Borst, E., Kesmir, C., Kuball, J., Mytilineos, J., & Spierings, E. (2014). A Universal Approach to Identify Permissible HLA-Mismatches in HSCT: Predicted Indirectly Recognizable HLA Epitopes. Biology of Blood and Marrow Transplantation, 20(2), S141-S142. https://doi.org/10.1016/j.bbmt.2013.12.218
Koning, D., Costa, A. I., Hasrat, R., Grady, B. P. X., Spijkers, S., Nanlohy, N., Keşmir, C., van Baarle, D., & Kesmir, C. (2014). In vitro expansion of antigen-specific CD8(+) T cells distorts the T-cell repertoire. Journal of Immunological Methods, 405, 199-203. https://doi.org/10.1016/j.jim.2014.01.013
Gold, M. C., McLaren, J. E., Reistetter, J. A., Smyk-Pearson, S., Ladell, K., Swarbrick, G. M., Yu, Y. Y. L., Hansen, T. H., Lund, O., Nielsen, M., Gerritsen, B., Kesmir, C., Miles, J. J., Lewinsohn, D. A., Price, D. A., & Lewinsohn, D. M. (2014). MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage. Journal of Experimental Medicine, 211(8), 1601-10. https://doi.org/10.1084/jem.20140507
Carrillo-Bustamante, P., Kesmir, C., & de Boer, R. J. (2014). Quantifying the Protection of Activating and Inhibiting NK Cell Receptors during Infection with a CMV-Like Virus. Frontiers in Immunology [E], 5, [20]. https://doi.org/10.3389/fimmu.2014.00020
2013
Scholarly publications
de Goede, A. L., van Deutekom, H. W. M., Vrancken, B., Schutten, M., Allard, S. D., Baalen, C. A., Osterhaus, A. D., Thielemans, K., Aerts, J. L., Kesmir, C., Lemey, P., & Gruters, R. A. (2013). HIV-1 evolution in patients undergoing immunotherapy with Tat, Rev, and Nef expressing dendritic cells followed by treatment interruption. AIDS, 27(17), 2679-2689. https://doi.org/10.1097/01.aids.0000433813.67662.92
Rao, X., de Boer, R. J., van Baarle, D., Maiers, M., & Kesmir, C. (2013). Complementarity of Binding Motifs is a General Property of HLA-A and HLA-B Molecules and Does Not Seem to Effect HLA Haplotype Composition. Frontiers in Immunology [E], 4, 374. https://doi.org/10.3389/fimmu.2013.00374
Otten, H. G., Calis, J. J., Kesmir, C., van Zuilen, A. D., & Spierings, E. (2013). Predicted indirectly recognizable HLA epitopes presented by HLA-DR correlate with the de novo development of donor-specific HLA IgG antibodies after kidney transplantation. Human Immunology, 74(3), 290-296. https://doi.org/10.1016/j.humimm.2012.12.004
Koning, D., Costa, A. I., Hoof, I., Miles, J. J., Nanlohy, N. M., Ladell, K., Matthews, K. K., Venturi, V., Schellens, I. M. M., Borghans, J. A. M., Kesmir, C., Price, D. A., & van Baarle, D. (2013). CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigen complex. Journal of Immunology, 190(3), 931-939. https://doi.org/10.4049/jimmunol.1202466
Calis, J. J., Maybeno, M., Greenbaum, J. A., Weiskopf, D., De Silva, A. D., Sette, A., Kesmir, C., & Peters, B. (2013). Properties of MHC class I presented peptides that enhance immunogenecity. PLoS Computational Biology, October(10), e1003266. https://doi.org/10.1371/journal.pcbi.1003266
van Rooij, N., van Buuren, M. M., Philips, D., Velds, A., Toebes, M., van Heemskerk, B., van Dijk, L. J., Behjati, S., Hilkmann, H., Atmioui, D., Nieuwland, M., Stratton, M. R., Kerkhoven, R. M., Kesmir, C., Haanen, J. B., Kvistborg, P., & Schumacher, T. N. (2013). Tumor exome analysis reveals neoantigen-specific T=cell reactivity in an ipilimumab-responsive melanoma. Journal of Clinical Oncology, 31(32), e439-e442. https://doi.org/10.1200/JCO.2012.47.7521
Carrillo Bustamante, N. P., Kesmir, C., & de Boer, R. J. (2013). Virus encoded MHC-like decoys diversity the inhibitory KIR repertoire. PLoS Computational Biology, 9(10), e1003264. https://doi.org/10.1371/journal.pcbi.1003264
2012
Scholarly publications
Mostowy, R., Kouyos, R. D., Hoof, I., Hinkley, T., Haddad, M., Whitcomb, J. M., Petropoulos, C. J., Kesmir, C., & Bonhoeffer, S. (2012). Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase. PLoS Computational Biology, 8(5), e1002525. https://doi.org/10.1371/journal.pcbi.1002525
Calis, J. J. A., de Boer, R. J., & Kesmir, C. (2012). Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire. PLoS Computational Biology, 8(3), e1002412.
Schipper, H. S., Nuboer, R., Prop, S., van den Ham, H. J., de Boer, F. K., Kesmir, C., Mombers, I. M., van Bekkum, K. A., Woudstra, J., Kieft, J. H., Hoefer, I. E., de Jager, W., Prakken, A. B. J., van Summeren, M. J. H., & Kalkhoven, E. (2012). Systemic inflammation in childhood obesity: circulating inflammatory mediators and activated CD14++ monocytes. Diabetologia, 55(10), 2800-2810. [22806355]. https://doi.org/10.1007/s00125-012-2641-y
Hoof, I., van Baarle, D., Hildebrand, W., & Kesmir, C. (2012). Proteome sampling by the HLA class I antigen processing pathway. PLoS Computational Biology, 8(5), e1002517. http://www.ncbi.nlm.nih.gov/pubmed/22615552
Mostomy, R., Kouyos, R. D., Hoof, I., Hinkley, T., Haddad, M., Whitcomb, J. M., Petropoulos, C. J., Kesmir, C., & Bonhoeffer, S. (2012). Estimating the fitness cost of escape from HA presentation in HIV-1 protease and reverse transcriptase. PLoS Computational Biology, 8, e1002525.
2011
Scholarly publications
Schellens, I. M. M., Navis, M., van Deutekom, H. W. M., Boeser-Nunnink, B., Berkhout, B., Kootstra, N., Miedema, F., Kesmir, C., Schuitemaker, H., van Baarle, D., & Borghans, J. A. M. (2011). Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic. AIDS, 25(14), 1691-700. https://doi.org/10.1097/QAD.0b013e32834981b3
Rao, X., Hoof, I., Fontaine Costa, A. I., van Baarle, D., & Kesmir, C. (2011). HLA class I allele promiscuity revisited. Immunogenetics, 63, 691-701.
Schellens, I. M. M., Navis, M., van Deutekom, H. W. M., Boeser-Nunnink, B., Berkhout, B., Kootstra, N., Miedema, F., Kesmir, C., Schuitemaker, H., van Baarle, D., & Borghans, J. A. M. (2011). Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted ty protective HLA-B alleles during the HIV-1 epidemic. AIDS, 25, 1691-1700.
van Deutekom, H. W. M., Hoof, I., Bontrop, R. E., & Kesmir, C. (2011). A comparative analysis of viral peptides presented by contemporary human and chimpanzee MHC class I molecules. Journal of Immunology, 187, 5995-6001.
2010
Scholarly publications
Costa, A. I., Rao, X., Lechenadec, E., van Baarle, D., & Kesmir, C. (2010). HLA-B molecules target more conserved regions of the HIV-1 proteome. AIDS, 24(2), 211-215.
Calis, J. J. A., Sanchez-Perez, G. F., & Kesmir, C. (2010). MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation. European Journal of Immunology, 40(DOI MEDLINE. DownLoad PDF), 2699-2709.
2009
Scholarly publications
Schmid, B. V., Kesmir, C., & de Boer, R. J. (2009). The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes. BMC Evolutionary Biology, 9, 184.
Rao, X., Costa, A. I., van Baarle, D., & Kesmir, C. (2009). A Comparative Study of HLA Binding Affinity and Ligand Diversity: Implications for Generating Immunodominant CD8+ T Cell Responses. Journal of Immunology, 182(3), 1526-1532. http://www.ncbi.nlm.nih.gov/pubmed/19155500?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=8
Rao, X., Costa, A. I., van Baarle, D., & Kesmir, C. (2009). A comparative study of HLA binding affinity and ligand diversity: implications for generating immunodominant CD8 T cell responses. Journal of Immunology, 182, 1526-1632.
2008
Scholarly publications
Schellens, I. M. M., Kesmir, C., Miedema, F., van Baarle, D., & Borghans, J. A. M. (2008). An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs. AIDS, 22(1), 33-37.
https://dspace.library.uu.nl/bitstream/handle/1874/32153/DvB%2520an%2520unanticipated.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/32153/DvB%2520an%2520unanticipated.pdf?sequence=1
Frankild, S., de Boer, R. J., Lund, O., Nielsen, M., & Kesmir, C. (2008). Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire. PLoS One, 3, e183.
Schmid, B. V., Kesmir, C., & de Boer, R. J. (2008). The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP. PLoS One, 3, e3525.
Hoof, I., Kesmir, C., Lund, O., & Nielsen, M. N. (2008). Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection. AIDS, 22, 1303-MEDLINE.
2007
Scholarly publications
Lundegaard, C., Lund, O., Kesmir, C., Brunak, S., & Nielsen, M. (2007). Modeling the adaptive immune system: predictions and simulations. Bioinformatics, 15, 3265-3275.
Borghans, J. A. M., Kesmir, C., & de Boer, R. J. (2007). MHC diversity in individuals and populations. In In: J. Silico Immunology (pp. 177-196). Springer (Flower, D. & Timmis, J., eds.).
Borghans, J. A. M., Mølgaard, A., de Boer, R. J., & Kesmir, C. (2007). HLA alleles associated with slow progression to AIDS truly prefer to present HIV-1 p24. PLoS One, 2(9), e920.
Frahm, N., Kaufmann, D. E., Yusim, K., Muldoon, M., Kesmir, C., Li, B., Miura, T., & Korber, B. T. (2007). Increased sequence diversity coverage improves detection of HIV-specific T cell responses. Journal of Immunology, 15, 6638-6650.
https://dspace.library.uu.nl/bitstream/handle/1874/27121/frahm%2520et%2520al.pdf?sequence=1
https://dspace.library.uu.nl/bitstream/handle/1874/27121/frahm%2520et%2520al.pdf?sequence=1
2006
Scholarly publications
Rapin, N., Kesmir, C., Frankild, S., Nielsen, M., Lundegaard, C., Brunak, S., & Lund, O. (2006). Modelling the human immune system by combining bioinformatics and systems biology approaches. Journal of Biological Physics, 32, 335-353.
2005
Scholarly publications
Luciani, F., Kesmir, C., Mishto, M., Or-Guil, M., & de Boer, R. J. (2005). A mathematical model of protein degradation by the proteasome. Biophysical Journal, 88, 2422-2432.
Nielsen, M. N., Lundegaard, C., Lund, O., & Kesmir, C. (2005). The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics, 2005, 33-41.
Lund, O., Nielsen, M., Lundegaard, C., Kesmir, C., & Brunak, S. (2005). Immunological Bioinformatics. MIT Press.
2004
Scholarly publications
Burroughs, N. J., de Boer, R. J., & Kesmir, C. (2004). Discriminating self from nonself with short peptides from large proteosomes. Immunogenetics, 56, 311-320.
de Boer, R. J., Borghans, J. A. M., Boven, M., Kesmir, C., & Weissing, F. J. (2004). Heterozygote advantage fails to explain the high degree of polymorphism of the MHC. Immunogenetics, 55, 725-731.
Saxova, P., Buus, S., & Kesmir, C. (2004). Integrating proteasome and MHC predictions for better identification of CTL epitopes. In HLA 2004: Immunobiology of the human MHC (pp. 45-51). IHWG Press.
Lund, O., Nielsen, M., Kesmir, C., Petersen, A. G., Lundedgaard, C., Worning, P., Sylvester-Hvid, C., Lamberth, K., Roder, G., Justesen, S., Buus, S., & Brunak, S. (2004). Definition of supertypes for HLA molecules using clustering of specificity matrices. Immunogenetics, 55, 797-810.
2003
Scholarly publications
Kesmir, C., & de Boer, R. J. (2003). Clonal exhaustion as a result of immune deviation. Bulletin of Mathematical Biology, 65, 359-374.
Kesmir, C., van Noort, V., de Boer, R. J., & Hogeweg, P. (2003). Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome. Immunogenetics, 55, 437-449.
Saxova, P., Buus, S., Brunak, S., & Kesmir, C. (2003). Predicting proteasomal cleavage sites: a comparison of available methods. International Immunology, 15, 781-787.
Kesmir, C., & de Boer, R. J. (2003). A spatial model of germinal center reactions: cellular adhesion based sorting of b cells results in efficient affinity maturation06. Journal of Theoretical Biology, 222, 9-22.
Buus, S., Lauemoller, S. L., Worning, P., Kesmir, C., Frimurer, T., Corbet, S., Fomsgaard, A., Hilden, J., Holm, A., & Brunak, S. (2003). Sensitive quantitative predictions of peptide-mhc binding by a 'query by committee' artificial neural network approach. Tissue Antigens, 62, 378-384.
2002
Scholarly publications
Yusim, K., Kesmir, C., Gaschen, B., Addo, M. M., Altfeld, M., Brunak, S., Chigaev, A., Detours, V., & Korber, B. T. (2002). Clustering patterns of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1 (HIV-1) proteins reveal imprints of immune evasion on HIV-1 global variation. Journal of Virology, 76, 8757-8768.
Sorensen, H. A., Sperotto, M. M., Petersen, M., Kesmir, C., Radzikowski, L., Jacobsen, S., & Sondergaard, I. (2002). Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis. Rapid Communications in Mass Spectrometry, 16, 1232-1237.
Kesmir, C., Nussbaum, A. K., Schild, H., Detours, V., & Brunak, S. (2002). Prediction of proteasome cleavage motifs by neural networks. Protein Engineering, 15, 287-296.
Jensen, L. J., Gupta, R., Blom, N., DeVos, D., Tamames, J., Kesmir, C., Nielsen, H., Staerfeldt, H. H., Rapacki, K., Workman, C., Andersen, C. A., Knudsen, S., Krogh, A., Valencia, A., & Brunak, S. (2002). Prediction of humanprotein function from post-translational modifications and localization features. Journal of Molecular Biology, 319, 1257-1265.
2001
Scholarly publications
Bloch, H. A., Petersen, M., Sperotto, M. M., Kesmir, C., Radzikowski, L., Jacobsen, S. E., & Sondergaard, I. (2001). Identification of barley and rye varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks. Rapid Communications in Mass Spectrometry, 15(6), 440-445.
Korber, B., Gaschen, B., Yusim, K., Thakallapally, R., Kesmir, C., & Detours, V. (2001). Evolutionary and immunological implications of contemporary HIV-1 variation. Review. British Medical Bulletin, 58, 19-42.
2000
Scholarly publications
Lauemøller, S. L., Kesmir, C., Corbet, S. L., Fomsgaard, A., Holm, A., Claesson, M. H., Brunak, S., & Buus, S. (2000). Identifying cytotoxic T cell epitopes from genomic and proteomic information: "The human MHC project". Reviews in Immunogenetics, 2(4), 477-491.
Kesmir, C., Borghans, J. A. M., & de Boer, R. J. (2000). Diversity of human alpha beta T cell receptors. Science, 288, 1135a-1135a.
1999
Scholarly publications
Bloch, H. A., Kesmir, C., Petersen, E. J., Jacobsen, R., Sondergaard, I., & Kesmir, C. (1999). Identification of wheat varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and an artificial neural network. Rapid Communications in Mass Spectrometry, 13(14), 1535-9. https://doi.org/10.1002/(SICI)1097-0231(19990730)13:14<1535::AID-RCM686>3.0.CO;2-U
Kesmir, C., & de Boer, R. J. (1999). A mathematical model on germinal center kinetics and termination. Journal of Immunology, 163, 2463-2469.
1998
Scholarly publications
Keşmir, C., De Boer, R. J., & Kesmir, C. (1998). How does cytopathicity affect the production of neutralizing antibody? Scandinavian Journal of Immunology, 48(4), 347-9.
1997
Scholarly publications
Jensen, K., Tygesen, T. K., Keşmir, C., Skovgaard, I. M., & Søndergaard, I. (1997). Classification of Potato Varieties Using Isoelectrophoretic Focusing Patterns, Neural Nets, and Statistical Methods. Journal of Agricultural and Food Chemistry, 45(1), 158-161. https://doi.org/10.1021/jf9602737
1996
Scholarly publications
Jensen, K., Keşmir, C., & Sendergaard, I. (1996). From image processing to classification: IV. Classification of electrophoretic patterns by neural networks and statistical methods enable quality assessment of wheat varieties for breadmaking. Electrophoresis, 17(4), 694-698. https://doi.org/10.1002/elps.1150170412
1995
Scholarly publications
Keşmir, C., Søndergaard, I., Jensen, K., & Kesmir, C. (1995). From image processing to classification: II. Classification of electrophoretic patterns using self-organizing feature maps and feed-forward neural networks. Electrophoresis, 16(6), 927-33.