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Items: 1 to 50 of 72

1.

VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium.

Bagaev DV, Vroomans RMA, Samir J, Stervbo U, Rius C, Dolton G, Greenshields-Watson A, Attaf M, Egorov ES, Zvyagin IV, Babel N, Cole DK, Godkin AJ, Sewell AK, Kesmir C, Chudakov DM, Luciani F, Shugay M.

Nucleic Acids Res. 2019 Oct 7. pii: gkz874. doi: 10.1093/nar/gkz874. [Epub ahead of print]

PMID:
31588507
2.

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.

Front Immunol. 2019 Apr 24;10:880. doi: 10.3389/fimmu.2019.00880. eCollection 2019.

3.

Immune biomarkers for predicting response to adoptive cell transfer as cancer treatment.

van Belzen IAEM, Kesmir C.

Immunogenetics. 2019 Feb;71(2):71-86. doi: 10.1007/s00251-018-1083-1. Epub 2018 Sep 20. Review.

4.

VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.

Shugay M, Bagaev DV, Zvyagin IV, Vroomans RM, Crawford JC, Dolton G, Komech EA, Sycheva AL, Koneva AE, Egorov ES, Eliseev AV, Van Dyk E, Dash P, Attaf M, Rius C, Ladell K, McLaren JE, Matthews KK, Clemens EB, Douek DC, Luciani F, van Baarle D, Kedzierska K, Kesmir C, Thomas PG, Price DA, Sewell AK, Chudakov DM.

Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427. doi: 10.1093/nar/gkx760.

5.

Specificity of inhibitory KIRs enables NK cells to detect changes in an altered peptide environment.

Carrillo-Bustamante P, de Boer RJ, Keşmir C.

Immunogenetics. 2018 Feb;70(2):87-97. doi: 10.1007/s00251-017-1019-1. Epub 2017 Jul 10.

6.

Long-term adaptation of the influenza A virus by escaping cytotoxic T-cell recognition.

Woolthuis RG, van Dorp CH, Keşmir C, de Boer RJ, van Boven M.

Sci Rep. 2016 Sep 15;6:33334. doi: 10.1038/srep33334.

7.

Editorial: Role of HLA and KIR in Viral Infections.

de Wit J, Borghans JA, Kesmir C, van Baarle D.

Front Immunol. 2016 Jul 27;7:286. doi: 10.3389/fimmu.2016.00286. eCollection 2016. No abstract available.

8.

HLA Preferences for Conserved Epitopes: A Potential Mechanism for Hepatitis C Clearance.

Rao X, Hoof I, van Baarle D, Keşmir C, Textor J.

Front Immunol. 2015 Oct 29;6:552. doi: 10.3389/fimmu.2015.00552. eCollection 2015.

9.

Measles Virus Epitope Presentation by HLA: Novel Insights into Epitope Selection, Dominance, and Microvariation.

Schellens IM, Meiring HD, Hoof I, Spijkers SN, Poelen MC, van Gaans-van den Brink JA, Costa AI, Vennema H, Keşmir C, van Baarle D, van Els CA.

Front Immunol. 2015 Nov 2;6:546. doi: 10.3389/fimmu.2015.00546. eCollection 2015.

10.

Predicted Indirectly Recognizable HLA Epitopes Presented by HLA-DRB1 Are Related to HLA Antibody Formation During Pregnancy.

Geneugelijk K, Hönger G, van Deutekom HW, Thus KA, Keşmir C, Hösli I, Schaub S, Spierings E.

Am J Transplant. 2015 Dec;15(12):3112-22. doi: 10.1111/ajt.13508. Epub 2015 Oct 29.

11.

The evolution of natural killer cell receptors.

Carrillo-Bustamante P, Keşmir C, de Boer RJ.

Immunogenetics. 2016 Jan;68(1):3-18. doi: 10.1007/s00251-015-0869-7. Epub 2015 Sep 21. Review.

12.

Comprehensive Analysis of the Naturally Processed Peptide Repertoire: Differences between HLA-A and B in the Immunopeptidome.

Schellens IM, Hoof I, Meiring HD, Spijkers SN, Poelen MC, van Gaans-van den Brink JA, van der Poel K, Costa AI, van Els CA, van Baarle D, Kesmir C.

PLoS One. 2015 Sep 16;10(9):e0136417. doi: 10.1371/journal.pone.0136417. eCollection 2015.

13.

Can Selective MHC Downregulation Explain the Specificity and Genetic Diversity of NK Cell Receptors?

Carrillo-Bustamante P, Kesmir C, de Boer RJ.

Front Immunol. 2015 Jun 16;6:311. doi: 10.3389/fimmu.2015.00311. eCollection 2015.

14.

Zooming into the binding groove of HLA molecules: which positions and which substitutions change peptide binding most?

van Deutekom HW, Keşmir C.

Immunogenetics. 2015 Aug;67(8):425-36. doi: 10.1007/s00251-015-0849-y. Epub 2015 Jun 4.

15.

CD8+ TCR Bias and Immunodominance in HIV-1 Infection.

Kløverpris HN, McGregor R, McLaren JE, Ladell K, Harndahl M, Stryhn A, Carlson JM, Koofhethile C, Gerritsen B, Keşmir C, Chen F, Riddell L, Luzzi G, Leslie A, Walker BD, Ndung'u T, Buus S, Price DA, Goulder PJ.

J Immunol. 2015 Jun 1;194(11):5329-45. doi: 10.4049/jimmunol.1400854. Epub 2015 Apr 24.

16.

A Coevolutionary Arms Race between Hosts and Viruses Drives Polymorphism and Polygenicity of NK Cell Receptors.

Carrillo-Bustamante P, Keşmir C, de Boer RJ.

Mol Biol Evol. 2015 Aug;32(8):2149-60. doi: 10.1093/molbev/msv096. Epub 2015 Apr 23.

17.

Corrigendum: Quantifying the Protection of Activating and Inhibiting NK Cell Receptors during Infection with a CMV-Like Virus.

Carrillo-Bustamante P, Keşmir C, De Boer RJ.

Front Immunol. 2015 Jan 5;5:663. doi: 10.3389/fimmu.2014.00663. eCollection 2014.

18.

Biomarkers in cancer immunotherapy.

Schumacher TN, Kesmir C, van Buuren MM.

Cancer Cell. 2015 Jan 12;27(1):12-4. doi: 10.1016/j.ccell.2014.12.004.

19.

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.

Immunogenetics. 2015 Feb;67(2):85-93. doi: 10.1007/s00251-014-0815-0. Epub 2014 Dec 6.

20.

Complex T-cell receptor repertoire dynamics underlie the CD8+ T-cell response to HIV-1.

Costa AI, Koning D, Ladell K, McLaren JE, Grady BP, Schellens IM, van Ham P, Nijhuis M, Borghans JA, Keşmir C, Price DA, van Baarle D.

J Virol. 2015 Jan;89(1):110-9. doi: 10.1128/JVI.01765-14. Epub 2014 Oct 15.

21.

MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage.

Gold MC, McLaren JE, Reistetter JA, Smyk-Pearson S, Ladell K, Swarbrick GM, Yu YY, Hansen TH, Lund O, Nielsen M, Gerritsen B, Kesmir C, Miles JJ, Lewinsohn DA, Price DA, Lewinsohn DM.

J Exp Med. 2014 Jul 28;211(8):1601-10. doi: 10.1084/jem.20140507. Epub 2014 Jul 21.

22.

Quantifying the Protection of Activating and Inhibiting NK Cell Receptors during Infection with a CMV-Like Virus.

Carrillo-Bustamante P, Keşmir C, de Boer RJ.

Front Immunol. 2014 Jan 30;5:20. doi: 10.3389/fimmu.2014.00020. eCollection 2014. Review. Erratum in: Front Immunol. 2014;5:663.

23.

In vitro expansion of antigen-specific CD8(+) T cells distorts the T-cell repertoire.

Koning D, Costa AI, Hasrat R, Grady BP, Spijkers S, Nanlohy N, Keşmir C, van Baarle D.

J Immunol Methods. 2014 Mar;405:199-203. doi: 10.1016/j.jim.2014.01.013. Epub 2014 Feb 7.

PMID:
24512815
24.

Complementarity of Binding Motifs is a General Property of HLA-A and HLA-B Molecules and Does Not Seem to Effect HLA Haplotype Composition.

Rao X, De Boer RJ, van Baarle D, Maiers M, Kesmir C.

Front Immunol. 2013 Nov 14;4:374. doi: 10.3389/fimmu.2013.00374. eCollection 2013. Review.

25.

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.

PLoS Comput Biol. 2013 Oct;9(10):e1003266. doi: 10.1371/journal.pcbi.1003266. Epub 2013 Oct 24.

26.

HIV-1 evolution in patients undergoing immunotherapy with Tat, Rev, and Nef expressing dendritic cells followed by treatment interruption.

de Goede AL, van Deutekom HW, Vrancken B, Schutten M, Allard SD, van Baalen CA, Osterhaus AD, Thielemans K, Aerts JL, Keşmir C, Lemey P, Gruters RA.

AIDS. 2013 Nov 13;27(17):2679-89. doi: 10.1097/01.aids.0000433813.67662.92.

PMID:
24149085
27.

Virus encoded MHC-like decoys diversify the inhibitory KIR repertoire.

Carrillo-Bustamante P, Keşmir C, de Boer RJ.

PLoS Comput Biol. 2013;9(10):e1003264. doi: 10.1371/journal.pcbi.1003264. Epub 2013 Oct 10.

28.

Tumor exome analysis reveals neoantigen-specific T-cell reactivity in an ipilimumab-responsive melanoma.

van Rooij N, van Buuren MM, Philips D, Velds A, Toebes M, Heemskerk B, van Dijk LJ, Behjati S, Hilkmann H, El Atmioui D, Nieuwland M, Stratton MR, Kerkhoven RM, Kesmir C, Haanen JB, Kvistborg P, Schumacher TN.

J Clin Oncol. 2013 Nov 10;31(32):e439-42. doi: 10.1200/JCO.2012.47.7521. Epub 2013 Sep 16. No abstract available.

29.

CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigenic complex.

Koning D, Costa AI, Hoof I, Miles JJ, Nanlohy NM, Ladell K, Matthews KK, Venturi V, Schellens IM, Borghans JA, Kesmir C, Price DA, van Baarle D.

J Immunol. 2013 Feb 1;190(3):931-9. doi: 10.4049/jimmunol.1202466. Epub 2012 Dec 24.

30.

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.

Hum Immunol. 2013 Mar;74(3):290-6. doi: 10.1016/j.humimm.2012.12.004. Epub 2012 Dec 8.

PMID:
23232063
31.

Systemic inflammation in childhood obesity: circulating inflammatory mediators and activated CD14++ monocytes.

Schipper HS, Nuboer R, Prop S, van den Ham HJ, de Boer FK, Kesmir Ç, Mombers IMH, van Bekkum KA, Woudstra J, Kieft JH, Hoefer IE, de Jager W, Prakken B, van Summeren M, Kalkhoven E.

Diabetologia. 2012 Oct;55(10):2800-2810. doi: 10.1007/s00125-012-2641-y. Epub 2012 Jul 18.

PMID:
22806355
32.

Estimating the fitness cost of escape from HLA presentation in HIV-1 protease and reverse transcriptase.

Mostowy R, Kouyos RD, Hoof I, Hinkley T, Haddad M, Whitcomb JM, Petropoulos CJ, Keşmir C, Bonhoeffer S.

PLoS Comput Biol. 2012;8(5):e1002525. doi: 10.1371/journal.pcbi.1002525. Epub 2012 May 24.

33.

Proteome sampling by the HLA class I antigen processing pathway.

Hoof I, van Baarle D, Hildebrand WH, Keşmir C.

PLoS Comput Biol. 2012;8(5):e1002517. doi: 10.1371/journal.pcbi.1002517. Epub 2012 May 17.

34.

Degenerate T-cell recognition of peptides on MHC molecules creates large holes in the T-cell repertoire.

Calis JJ, de Boer RJ, Keşmir C.

PLoS Comput Biol. 2012;8(3):e1002412. doi: 10.1371/journal.pcbi.1002412. Epub 2012 Mar 1.

35.

A comparative analysis of viral peptides presented by contemporary human and chimpanzee MHC class I molecules.

van Deutekom HW, Hoof I, Bontrop RE, Keşmir C.

J Immunol. 2011 Dec 1;187(11):5995-6001. doi: 10.4049/jimmunol.1102236. Epub 2011 Oct 31.

36.

HLA class I allele promiscuity revisited.

Rao X, Hoof I, Costa AI, van Baarle D, Keşmir C.

Immunogenetics. 2011 Nov;63(11):691-701. doi: 10.1007/s00251-011-0552-6. Epub 2011 Jun 22.

37.

Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic.

Schellens IM, Navis M, van Deutekom HW, Boeser-Nunnink B, Berkhout B, Kootstra N, Miedema F, Keşmir C, Schuitemaker H, van Baarle D, Borghans JA.

AIDS. 2011 Sep 10;25(14):1691-700. doi: 10.1097/QAD.0b013e32834981b3.

PMID:
21681058
38.

Quantifying how MHC polymorphism prevents pathogens from adapting to the antigen presentation pathway.

Schmid BV, Kęsmir C, de Boer RJ.

Epidemics. 2010 Sep;2(3):99-108. doi: 10.1016/j.epidem.2010.05.003. Epub 2010 Jun 9.

PMID:
21352780
39.

MHC class I molecules exploit the low G+C content of pathogen genomes for enhanced presentation.

Calis JJ, Sanchez-Perez GF, Keşmir C.

Eur J Immunol. 2010 Oct;40(10):2699-709. doi: 10.1002/eji.201040339.

40.

HLA-B molecules target more conserved regions of the HIV-1 proteome.

Fontaine Costa AI, Rao X, Lechenadec E, van Baarle D, Keşmir C.

AIDS. 2010 Jan 16;24(2):211-5. doi: 10.1097/QAD.0b013e328334442e.

PMID:
19904197
41.

The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes.

Schmid BV, Keşmir C, de Boer RJ.

BMC Evol Biol. 2009 Aug 4;9:184. doi: 10.1186/1471-2148-9-184.

42.
43.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

Schmid BV, Keşmir C, de Boer RJ.

PLoS One. 2008;3(10):e3525. doi: 10.1371/journal.pone.0003525. Epub 2008 Oct 24. Erratum in: PLoS ONE. 2009;4(1). doi: 10.1371/annotation/98c3dca8-871e-475e-aaed-c10af4dcf35c. Schmid, Boris [corrected to Schmid, Boris V].

44.

Humans with chimpanzee-like major histocompatibility complex-specificities control HIV-1 infection.

Hoof I, Keşmir C, Lund O, Nielsen M.

AIDS. 2008 Jul 11;22(11):1299-303. doi: 10.1097/QAD.0b013e328302f39f.

PMID:
18580609
45.

Amino acid similarity accounts for T cell cross-reactivity and for "holes" in the T cell repertoire.

Frankild S, de Boer RJ, Lund O, Nielsen M, Kesmir C.

PLoS One. 2008 Mar 19;3(3):e1831. doi: 10.1371/journal.pone.0001831.

46.

An unanticipated lack of consensus cytotoxic T lymphocyte epitopes in HIV-1 databases: the contribution of prediction programs.

Schellens IM, Keşmir C, Miedema F, van Baarle D, Borghans JA.

AIDS. 2008 Jan 2;22(1):33-7.

PMID:
18090389
47.

Modeling the adaptive immune system: predictions and simulations.

Lundegaard C, Lund O, Kesmir C, Brunak S, Nielsen M.

Bioinformatics. 2007 Dec 15;23(24):3265-75. Epub 2007 Nov 28.

PMID:
18045832
48.

Increased sequence diversity coverage improves detection of HIV-specific T cell responses.

Frahm N, Kaufmann DE, Yusim K, Muldoon M, Kesmir C, Linde CH, Fischer W, Allen TM, Li B, McMahon BH, Faircloth KL, Hewitt HS, Mackey EW, Miura T, Khatri A, Wolinsky S, McMichael A, Funkhouser RK, Walker BD, Brander C, Korber BT.

J Immunol. 2007 Nov 15;179(10):6638-50.

49.

HLA alleles associated with slow progression to AIDS truly prefer to present HIV-1 p24.

Borghans JA, Mølgaard A, de Boer RJ, Keşmir C.

PLoS One. 2007 Sep 19;2(9):e920.

50.

Modelling the human immune system by combining bioinformatics and systems biology approaches.

Rapin N, Kesmir C, Frankild S, Nielsen M, Lundegaard C, Brunak S, Lund O.

J Biol Phys. 2006 Oct;32(3-4):335-53. doi: 10.1007/s10867-006-9019-7. Epub 2006 Oct 27.

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