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1

The evolution of natural killer cell receptors

Carrillo-Bustamante, Paola, Keşmir, Can, de Boer, Rob J.

Journal:

Year:

2016

Language:

english

File:

PDF, 541 KB

english, 2016

2

From image processing to classification: II. Classification of electrophoretic patterns using self-organizing feature maps and feed-forward neural networks

Can Keşmir, Dr. Ib Søndergaard, Kirsten Jensen

Journal:

ELECTROPHORESIS

Year:

1995

Language:

english

File:

PDF, 654 KB

english, 1995

3

From image processing to classification: IV. Classification of electrophoretic patterns by neural networks and statistical methods enable quality assessment of wheat varieties for breadmaking

Kristen Jensen, Can Kesmir, Dr. Ib Søndergaard

Journal:

ELECTROPHORESIS

Year:

1996

Language:

english

File:

PDF, 562 KB

english, 1996

4

Exploratory Study of Predicted Indirectly ReCognizable HLA Epitopes in Mismatched Hematopoietic Cell Transplantations

Geneugelijk, Kirsten, Thus, Kirsten A., van Deutekom, Hanneke W. M., Calis, Jorg J. A., Borst, Eric, Keşmir, Can, Oudshoorn, Machteld, van der Holt, Bronno, Meijer, Ellen, Zeerleder, Sacha, de Groot,

Journal:

Frontiers in Immunology

Year:

2019

Language:

english

File:

PDF, 723 KB

english, 2019

5

Identification of wheat varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry and an artificial neural network

Helle Aagaard Bloch, Can Keşmir, Marianne Petersen, Susanne Jacobsen, Ib Søndergaard

Journal:

Rapid Communications in Mass Spectrometry

Year:

1999

Language:

english

File:

PDF, 55 KB

english, 1999

6

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

Jorg J. A. Calis, Gabino F. Sanchez-Perez, Can Keşmir

Journal:

European Journal of Immunology

Year:

2010

Language:

english

File:

PDF, 438 KB

english, 2010

7

A spatial model of germinal center reactions: cellular adhesion based sorting of B cells results in efficient affinity maturation

Can Keşmir, Rob J De Boer

Journal:

Journal of Theoretical Biology

Year:

2003

Language:

english

File:

PDF, 476 KB

english, 2003

8

Clonal Exhaustion as a Result of Immune Deviation

Can Keşmir, Rob J De Boer

Journal:

Bulletin of Mathematical Biology

Year:

2003

Language:

english

File:

PDF, 178 KB

english, 2003

9

The role of antigen presenting cells in high and low zone tolerance: A model study

C. Kesmir, R. de Boer

Journal:

Immunology Letters

Year:

1997

Language:

english

File:

PDF, 186 KB

english, 1997

10

Sensitive quantitative predictions of peptide-MHC binding by a ‘Query by Committee’ artificial neural network approach

S. Buus, S.L. Lauemøller, P. Worning, C. Kesmir, T. Frimurer, S. Corbet, A. Fomsgaard, J. Hilden, A. Holm, S. Brunak

Journal:

Tissue Antigens

Year:

2003

Language:

english

File:

PDF, 141 KB

english, 2003

11

How does Cytopathicity Affect the Production of Neutralizing Antibody?

Keşmir, De Boer

Journal:

Scandinavian Journal of Immunology

Year:

1998

Language:

english

File:

PDF, 60 KB

english, 1998

12

Identification of barley and rye varieties using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry with neural networks

Helle Aagaard Bloch, Marianne Petersen, Maria Maddalena Sperotto, Can Keşmir, Louise Radzikowski, Susanne Jacobsen, Ib Søndergaard

Journal:

Rapid Communications in Mass Spectrometry

Year:

2001

Language:

english

File:

PDF, 166 KB

english, 2001

13

Variety identification of wheat using mass spectrometry with neural networks and the influence of mass spectra processing prior to neural network analysis

Helle Aagaard Sørensen, Maria Maddalena Sperotto, Marianne Petersen, Can Keşmir, Louise Radzikowski, Susanne Jacobsen, Ib Søndergaard

Journal:

Rapid Communications in Mass Spectrometry

Year:

2002

Language:

english

File:

PDF, 125 KB

english, 2002

14

Heterozygote advantage fails to explain the high degree of polymorphism of the MHC

Rob J. Boer, José A. M. Borghans, Michiel Boven, Can Keşmir, Franz J. Weissing

Journal:

Year:

2004

Language:

english

File:

PDF, 237 KB

english, 2004

15

Bioinformatic analysis of functional differences between the immunoproteasome and the constitutive proteasome

Can Kesmir, Vera Noort, RobJ. Boer, Paulien Hogeweg

Journal:

Year:

2003

Language:

english

File:

PDF, 488 KB

english, 2003

16

Discriminating self from nonself with short peptides from large proteomes

Nigel J. Burroughs, Rob J. de Boer, Can Keşmir

Journal:

Year:

2004

Language:

english

File:

PDF, 176 KB

english, 2004

17

Definition of supertypes for HLA molecules using clustering of specificity matrices

Ole Lund, Morten Nielsen, Can Kesmir, AndersGorm Petersen, Claus Lundegaard, Peder Worning, Christina Sylvester-Hvid, Kasper Lamberth, Gustav Røder, Sune Justesen, Søren Buus, Søren Brunak

Journal:

Year:

2004

Language:

english

File:

PDF, 910 KB

english, 2004

18

The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage

Morten Nielsen, Claus Lundegaard, Ole Lund, Can Keşmir

Journal:

Year:

2005

Language:

english

File:

PDF, 237 KB

english, 2005

19

HLA class I allele promiscuity revisited

Xiangyu Rao, Ilka Hoof, Ana Isabel C. A. Fontaine Costa, Debbie van Baarle, Can Keşmir

Journal:

Year:

2011

Language:

english

File:

PDF, 641 KB

english, 2011

20

Modelling the Human Immune System by Combining Bioinformatics and Systems Biology Approaches

Nicolas Rapin, Can Kesmir, Sune Frankild, Morten Nielsen, Claus Lundegaard, Søren Brunak, Ole Lund

Journal:

Journal of Biological Physics

Year:

2006

Language:

english

File:

PDF, 441 KB

english, 2006

21

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

Boris V Schmid, Can Keşmir, Rob J de Boer

Journal:

BMC Evolutionary Biology

Year:

2009

Language:

english

File:

PDF, 2.02 MB

english, 2009

22

Prediction of Human Protein Function from Post-translational Modifications and Localization Features

L.J. Jensen, R. Gupta, N. Blom, D. Devos, J. Tamames, C. Kesmir, H. Nielsen, H.H. Stærfeldt, K. Rapacki, C. Workman, C.A.F. Andersen, S. Knudsen, A. Krogh, A. Valencia, S. Brunak

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 431 KB

english, 2002

23

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

B.V. Schmid, C. Kęsmir, R.J. de Boer

Journal:

Year:

2010

Language:

english

File:

PDF, 1.16 MB

english, 2010

24

A Mathematical Model of Protein Degradation by the Proteasome

Luciani, Fabio, Keşmir, Can, Mishto, Michele, Or-Guil, Michal, de Boer, Rob J.

Journal:

Biophysical Journal

Year:

2005

Language:

english

File:

PDF, 193 KB

english, 2005

25

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

Schipper, H. S., Nuboer, R., Prop, S., Ham, H. J., Boer, F. K., Kesmir, Ã., Mombers, I. M. H., Bekkum, K. A., Woudstra, J., Kieft, J. H., Hoefer, I. E., Jager, W., Prakken, B., Summeren, M., Kalkhove

Journal:

Year:

2012

Language:

english

File:

PDF, 436 KB

english, 2012

26

CD8+ TCR Repertoire Formation Is Guided Primarily by the Peptide Component of the Antigenic Complex

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.

Journal:

The Journal of Immunology

Year:

2013

Language:

english

File:

PDF, 1.42 MB

english, 2013

27

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

Koning, Dan, Costa, Ana I., Hasrat, Raiza, Grady, Bart P.X., Spijkers, Sanne, Nanlohy, Nening, Keşmir, Can, van Baarle, Debbie

Journal:

Journal of Immunological Methods

Year:

2014

Language:

english

File:

PDF, 297 KB

english, 2014

28

A Universal Approach to Identify Permissible HLA-Mismatches in HSCT: Predicted Indirectly Recognizable HLA Epitopes

Thus, Kirsten A., Furst, Daniel, van Deutekom, Hanneke, Calis, Jorg, Borst, Eric, Kesmir, Can, Kuball, Jurgen, Mytilineos, Joannis, Spierings, Eric

Journal:

Biology of Blood and Marrow Transplantation

Year:

2014

Language:

english

File:

PDF, 249 KB

english, 2014

29

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, Henny G., Calis, Jorg J.A., Keşmir, Can, van Zuilen, Arjan D., Spierings, Eric

Journal:

Human Immunology

Year:

2013

Language:

english

File:

PDF, 601 KB

english, 2013

30

50-OR

Thus, Kirsten A., Kesmir, Can, Borst, Eric, de Weger, Roel A., Boelens, Jaap Jan, Spierings, Eric

Journal:

Human Immunology

Year:

2013

Language:

english

File:

PDF, 33 KB

english, 2013

31

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

Yusim, K., Kesmir, C., Gaschen, B., Addo, M. M., Altfeld, M., Brunak, S., Chigaev, A., Detours, V., Korber, B. T.

Journal:

Journal of Virology

Year:

2002

Language:

english

File:

PDF, 1.82 MB

english, 2002

32

Classification of Potato Varieties Using Isoelectrophoretic Focusing Patterns, Neural Nets, and Statistical Methods

Jensen, Kirsten, Tygesen, Thomas K., Keşmir, Can, Skovgaard, Ib M., Søndergaard, Ib

Journal:

Journal of Agricultural and Food Chemistry

Year:

1997

Language:

english

File:

PDF, 102 KB

english, 1997

33

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

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,

Journal:

Journal of Experimental Medicine

Year:

2014

Language:

english

File:

PDF, 6.80 MB

english, 2014

34

Complex T-Cell Receptor Repertoire Dynamics Underlie the CD8 + T-Cell Response to HIV-1

Costa, Ana I., Koning, Dan, Ladell, Kristin, McLaren, James E., Grady, Bart P. X., Schellens, Ingrid M. M., van Ham, Petra, Nijhuis, Monique, Borghans, José A. M., Keşmir, Can, Price, David A., van Ba

Journal:

Journal of Virology

Year:

2015

Language:

english

File:

PDF, 1.63 MB

english, 2015

35

Biomarkers in Cancer Immunotherapy

Schumacher, Ton N., Kesmir, Can, van Buuren, Marit M.

Journal:

Year:

2015

Language:

english

File:

PDF, 632 KB

english, 2015

36

A Comparative Analysis of Viral Peptides Presented by Contemporary Human and Chimpanzee MHC Class I Molecules

van Deutekom, H. W. M., Hoof, I., Bontrop, R. E., Kesmir, C.

Journal:

The Journal of Immunology

Year:

2011

Language:

english

File:

PDF, 1.01 MB

english, 2011

37

A Comparative Study of HLA Binding Affinity and Ligand Diversity: Implications for Generating Immunodominant CD8+ T Cell Responses

Rao, X., Fontaine Costa, A. I. C. A., van Baarle, D., Kesmir, C.

Journal:

The Journal of Immunology

Year:

2009

Language:

english

File:

PDF, 1.28 MB

english, 2009

38

Increased Sequence Diversity Coverage Improves Detection of HIV-Specific T Cell Responses

Frahm, N., Kaufmann, D. E., Yusim, K., Muldoon, M., Kesmir, C., Linde, C. H., Fischer, W., Allen, T. M., Li, B., McMahon, B. H., Faircloth, K. L., Hewitt, H. S., Mackey, E. W., Miura, T., Khatri, A.,

Journal:

The Journal of Immunology

Year:

2007

Language:

english

File:

PDF, 1.23 MB

english, 2007

39

Role of peptide processing predictions in T cell epitope identification: contribution of different prediction programs

Calis, Jorg J. A., Reinink, Peter, Keller, Christin, Kloetzel, Peter M., Keşmir, Can

Journal:

Year:

2015

Language:

english

File:

PDF, 1.90 MB

english, 2015

40

Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

Calis, Jorg J. A., de Boer, Rob J., Keşmir, Can, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 497 KB

english, 2012

41

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, Xiangyu, De Boer, Rob J., van Baarle, Debbie, Maiers, Martin, Kesmir, Can

Journal:

Frontiers in Immunology

Year:

2013

Language:

english

File:

PDF, 454 KB

english, 2013

42

Proteome Sampling by the HLA Class I Antigen Processing Pathway

Hoof, Ilka, van Baarle, Debbie, Hildebrand, William H., Keşmir, Can, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 375 KB

english, 2012

43

Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase

Mostowy, Rafal, Kouyos, Roger D., Hoof, Ilka, Hinkley, Trevor, Haddad, Mojgan, Whitcomb, Jeannette M., Petropoulos, Christos J., Keşmir, Can, Bonhoeffer, Sebastian, Peters, Bjoern

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 666 KB

english, 2012

44

Modeling the adaptive immune system: predictions and simulations

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

Journal:

Year:

2007

Language:

english

File:

PDF, 177 KB

english, 2007

45

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

Carrillo-Bustamante, Paola, Keşmir, Can, de Boer, Rob J.

Journal:

Frontiers in Immunology

Year:

2014

Language:

english

File:

PDF, 1.37 MB

english, 2014

46

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

Carrillo-Bustamante, Paola, Keşmir, Can, de Boer, Rob J.

Journal:

Molecular Biology and Evolution

Year:

2015

Language:

english

File:

PDF, 504 KB

english, 2015

47

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

van Deutekom, Hanneke W. M., Keşmir, Can

Journal:

Year:

2015

Language:

english

File:

PDF, 694 KB

english, 2015

48

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

Schellens, Ingrid M.M., Navis, Marjon, van Deutekom, Hanneke W.M., Boeser-Nunnink, Brigitte, Berkhout, Ben, Kootstra, Neeltje, Miedema, Frank, Keşmir, Can, Schuitemaker, Hanneke, van Baarle, Debbie, B

Journal:

Year:

2011

Language:

english

File:

PDF, 398 KB

english, 2011

49

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

Geneugelijk, K., Hönger, G., van Deutekom, H. W. M., Thus, K. A., Keşmir, C., Hösli, I., Schaub, S., Spierings, E.

Journal:

American Journal of Transplantation

Year:

2015

Language:

english

File:

PDF, 260 KB

english, 2015

50

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

Schellens, Ingrid MM, Keşmir, Can, Miedema, Frank, van Baarle, Debbie, Borghans, José AM

Journal:

Year:

2008

Language:

english

File:

PDF, 130 KB

english, 2008