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Items: 1 to 50 of 102

1.

Discovery of a new Pro-Pro endopeptidase, PPEP-2, provides mechanistic insights into the differences in substrate specificity within the PPEP family.

Klychnikov OI, Shamorkina TM, Weeks SD, van Leeuwen HC, Corver J, Drijfhout JW, van Veelen PA, Sluchanko NN, Strelkov SV, Hensbergen PJ.

J Biol Chem. 2018 Jul 13;293(28):11154-11165. doi: 10.1074/jbc.RA118.003244. Epub 2018 May 23.

PMID:
29794027
2.

Minimal Information About an Immuno-Peptidomics Experiment (MIAIPE).

Lill JR, van Veelen PA, Tenzer S, Admon A, Caron E, Elias JE, Heck AJR, Marcilla M, Marino F, Müller M, Peters B, Purcell A, Sette A, Sturm T, Ternette N, Vizcaíno JA, Bassani-Sternberg M.

Proteomics. 2018 Jun;18(12):e1800110. doi: 10.1002/pmic.201800110.

3.

A flexible MHC class I multimer loading system for large-scale detection of antigen-specific T cells.

Luimstra JJ, Garstka MA, Roex MCJ, Redeker A, Janssen GMC, van Veelen PA, Arens R, Falkenburg JHF, Neefjes J, Ovaa H.

J Exp Med. 2018 May 7;215(5):1493-1504. doi: 10.1084/jem.20180156. Epub 2018 Apr 17.

4.

Molecular Pathways for Immune Recognition of Preproinsulin Signal Peptide in Type 1 Diabetes.

Kronenberg-Versteeg D, Eichmann M, Russell MA, de Ru A, Hehn B, Yusuf N, van Veelen PA, Richardson SJ, Morgan NG, Lemberg MK, Peakman M.

Diabetes. 2018 Apr;67(4):687-696. doi: 10.2337/db17-0021. Epub 2018 Jan 17.

PMID:
29343547
5.

Specific T Cell Responses against Minor Histocompatibility Antigens Cannot Generally Be Explained by Absence of Their Allelic Counterparts on the Cell Surface.

Bijen HM, Hassan C, Kester MGD, Janssen GMC, Hombrink P, de Ru AH, Drijfhout JW, Meiring HD, de Jong AP, Falkenburg JHF, Jimenez CR, Heemskerk MHM, van Veelen PA.

Proteomics. 2018 Jun;18(12):e1700250. doi: 10.1002/pmic.201700250. Epub 2018 Feb 23.

PMID:
29251415
6.

Pitfalls in the detection of citrullination and carbamylation.

Verheul MK, van Veelen PA, van Delft MAM, de Ru A, Janssen GMC, Rispens T, Toes REM, Trouw LA.

Autoimmun Rev. 2018 Feb;17(2):136-141. doi: 10.1016/j.autrev.2017.11.017. Epub 2017 Dec 2. Review.

7.

A Specialist Macaque MHC Class I Molecule with HLA-B*27-like Peptide-Binding Characteristics.

de Groot NG, Heijmans CMC, de Ru AH, Janssen GMC, Drijfhout JW, Otting N, Vangenot C, Doxiadis GGM, Koning F, van Veelen PA, Bontrop RE.

J Immunol. 2017 Nov 15;199(10):3679-3690. doi: 10.4049/jimmunol.1700502. Epub 2017 Oct 11.

PMID:
29021373
8.

The SysteMHC Atlas project.

Shao W, Pedrioli PGA, Wolski W, Scurtescu C, Schmid E, Vizcaíno JA, Courcelles M, Schuster H, Kowalewski D, Marino F, Arlehamn CSL, Vaughan K, Peters B, Sette A, Ottenhoff THM, Meijgaarden KE, Nieuwenhuizen N, Kaufmann SHE, Schlapbach R, Castle JC, Nesvizhskii AI, Nielsen M, Deutsch EW, Campbell DS, Moritz RL, Zubarev RA, Ytterberg AJ, Purcell AW, Marcilla M, Paradela A, Wang Q, Costello CE, Ternette N, van Veelen PA, van Els CACM, Heck AJR, de Souza GA, Sollid LM, Admon A, Stevanovic S, Rammensee HG, Thibault P, Perreault C, Bassani-Sternberg M, Aebersold R, Caron E.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1237-D1247. doi: 10.1093/nar/gkx664.

9.

Abrogation of Immunogenic Properties of Gliadin Peptides through Transamidation by Microbial Transglutaminase Is Acyl-Acceptor Dependent.

Zhou L, Kooy-Winkelaar YMC, Cordfunke RA, Dragan I, Thompson A, Drijfhout JW, van Veelen PA, Chen H, Koning F.

J Agric Food Chem. 2017 Aug 30;65(34):7542-7552. doi: 10.1021/acs.jafc.7b02557. Epub 2017 Aug 17.

10.

Breach of autoreactive B cell tolerance by post-translationally modified proteins.

Dekkers JS, Verheul MK, Stoop JN, Liu B, Ioan-Facsinay A, van Veelen PA, de Ru AH, Janssen GMC, Hegen M, Rapecki S, Huizinga TWJ, Trouw LA, Toes REM.

Ann Rheum Dis. 2017 Aug;76(8):1449-1457. doi: 10.1136/annrheumdis-2016-210772. Epub 2017 Apr 25.

PMID:
28442530
11.

Identification of carbamylated alpha 1 anti-trypsin (A1AT) as an antigenic target of anti-CarP antibodies in patients with rheumatoid arthritis.

Verheul MK, Yee A, Seaman A, Janssen GM, van Veelen PA, Drijfhout JW, Toes REM, Mahler M, Trouw LA.

J Autoimmun. 2017 Jun;80:77-84. doi: 10.1016/j.jaut.2017.02.008. Epub 2017 Mar 11.

PMID:
28291659
12.

Autoimmunity against a defective ribosomal insulin gene product in type 1 diabetes.

Kracht MJ, van Lummel M, Nikolic T, Joosten AM, Laban S, van der Slik AR, van Veelen PA, Carlotti F, de Koning EJ, Hoeben RC, Zaldumbide A, Roep BO.

Nat Med. 2017 Apr;23(4):501-507. doi: 10.1038/nm.4289. Epub 2017 Feb 27.

PMID:
28263308
13.

TCR-based therapy for multiple myeloma and other B-cell malignancies targeting intracellular transcription factor BOB1.

Jahn L, Hombrink P, Hagedoorn RS, Kester MG, van der Steen DM, Rodriguez T, Pentcheva-Hoang T, de Ru AH, Schoonakker MP, Meeuwsen MH, Griffioen M, van Veelen PA, Falkenburg JH, Heemskerk MH.

Blood. 2017 Mar 9;129(10):1284-1295. doi: 10.1182/blood-2016-09-737536. Epub 2017 Jan 4.

14.

CD4 T-cell cytokines synergize to induce proliferation of malignant and nonmalignant innate intraepithelial lymphocytes.

Kooy-Winkelaar YM, Bouwer D, Janssen GM, Thompson A, Brugman MH, Schmitz F, de Ru AH, van Gils T, Bouma G, van Rood JJ, van Veelen PA, Mearin ML, Mulder CJ, Koning F, van Bergen J.

Proc Natl Acad Sci U S A. 2017 Feb 7;114(6):E980-E989. doi: 10.1073/pnas.1620036114. Epub 2017 Jan 3.

15.

Generation of CD20-specific TCRs for TCR gene therapy of CD20low B-cell malignancies insusceptible to CD20-targeting antibodies.

Jahn L, van der Steen DM, Hagedoorn RS, Hombrink P, Kester MG, Schoonakker MP, de Ridder D, van Veelen PA, Falkenburg JH, Heemskerk MH.

Oncotarget. 2016 Nov 22;7(47):77021-77037. doi: 10.18632/oncotarget.12778.

16.

Parallel reaction monitoring of clinical Mycobacterium tuberculosis lineages reveals pre-existent markers of rifampicin tolerance in the emerging Beijing lineage.

de Keijzer J, Mulder A, de Ru AH, van Soolingen D, van Veelen PA.

J Proteomics. 2017 Jan 6;150:9-17. doi: 10.1016/j.jprot.2016.08.022. Epub 2016 Aug 26.

PMID:
27576137
17.

A CD22-reactive TCR from the T-cell allorepertoire for the treatment of acute lymphoblastic leukemia by TCR gene transfer.

Jahn L, Hagedoorn RS, van der Steen DM, Hombrink P, Kester MG, Schoonakker MP, de Ridder D, van Veelen PA, Falkenburg JH, Heemskerk MH.

Oncotarget. 2016 Nov 1;7(44):71536-71547. doi: 10.18632/oncotarget.12247.

18.

Tumor Eradication by Cisplatin Is Sustained by CD80/86-Mediated Costimulation of CD8+ T Cells.

Beyranvand Nejad E, van der Sluis TC, van Duikeren S, Yagita H, Janssen GM, van Veelen PA, Melief CJ, van der Burg SH, Arens R.

Cancer Res. 2016 Oct 15;76(20):6017-6029. Epub 2016 Aug 28.

19.

Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors.

Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, Isserlin R, van Veelen PA, Broekhuis MJ, Janssen GM, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HW, Bader GD, Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G.

Cell Stem Cell. 2016 Sep 1;19(3):383-96. doi: 10.1016/j.stem.2016.06.008. Epub 2016 Jul 14.

20.

Multimodal Mass Spectrometry Imaging of N-Glycans and Proteins from the Same Tissue Section.

Heijs B, Holst S, Briaire-de Bruijn IH, van Pelt GW, de Ru AH, van Veelen PA, Drake RR, Mehta AS, Mesker WE, Tollenaar RA, Bovée JV, Wuhrer M, McDonnell LA.

Anal Chem. 2016 Aug 2;88(15):7745-53. doi: 10.1021/acs.analchem.6b01739. Epub 2016 Jul 14.

PMID:
27373711
21.

An ER-Associated Pathway Defines Endosomal Architecture for Controlled Cargo Transport.

Jongsma ML, Berlin I, Wijdeven RH, Janssen L, Janssen GM, Garstka MA, Janssen H, Mensink M, van Veelen PA, Spaapen RM, Neefjes J.

Cell. 2016 Jun 30;166(1):152-66. doi: 10.1016/j.cell.2016.05.078.

22.

Thioridazine Alters the Cell-Envelope Permeability of Mycobacterium tuberculosis.

de Keijzer J, Mulder A, de Haas PE, de Ru AH, Heerkens EM, Amaral L, van Soolingen D, van Veelen PA.

J Proteome Res. 2016 Jun 3;15(6):1776-86. doi: 10.1021/acs.jproteome.5b01037. Epub 2016 May 9.

PMID:
27068340
23.

Dendritic Cells Guide Islet Autoimmunity through a Restricted and Uniquely Processed Peptidome Presented by High-Risk HLA-DR.

van Lummel M, van Veelen PA, de Ru AH, Janssen GM, Pool J, Laban S, Joosten AM, Nikolic T, Drijfhout JW, Mearin ML, Aanstoot HJ, Peakman M, Roep BO.

J Immunol. 2016 Apr 15;196(8):3253-63. doi: 10.4049/jimmunol.1501282. Epub 2016 Mar 4.

24.

Mechanisms of Phenotypic Rifampicin Tolerance in Mycobacterium tuberculosis Beijing Genotype Strain B0/W148 Revealed by Proteomics.

de Keijzer J, Mulder A, de Beer J, de Ru AH, van Veelen PA, van Soolingen D.

J Proteome Res. 2016 Apr 1;15(4):1194-204. doi: 10.1021/acs.jproteome.5b01073. Epub 2016 Mar 24.

PMID:
26930559
25.

Differentiating samples and experimental protocols by direct comparison of tandem mass spectra.

van der Plas-Duivesteijn SJ, Wulff T, Klychnikov O, Ohana D, Dalebout H, van Veelen PA, de Keijzer J, Nessen MA, van der Burgt YE, Deelder AM, Palmblad M.

Rapid Commun Mass Spectrom. 2016 Mar 30;30(6):731-8. doi: 10.1002/rcm.7494.

PMID:
26864526
26.

Human islets and dendritic cells generate post-translationally modified islet autoantigens.

McLaughlin RJ, de Haan A, Zaldumbide A, de Koning EJ, de Ru AH, van Veelen PA, van Lummel M, Roep BO.

Clin Exp Immunol. 2016 Aug;185(2):133-40. doi: 10.1111/cei.12775. Epub 2016 May 17.

27.

Discovery of a Selective Islet Peptidome Presented by the Highest-Risk HLA-DQ8trans Molecule.

van Lummel M, van Veelen PA, de Ru AH, Pool J, Nikolic T, Laban S, Joosten A, Drijfhout JW, Gómez-Touriño I, Arif S, Aanstoot HJ, Peakman M, Roep BO.

Diabetes. 2016 Mar;65(3):732-41. doi: 10.2337/db15-1031. Epub 2015 Dec 30.

28.

Discovery of an essential nucleotidylating activity associated with a newly delineated conserved domain in the RNA polymerase-containing protein of all nidoviruses.

Lehmann KC, Gulyaeva A, Zevenhoven-Dobbe JC, Janssen GM, Ruben M, Overkleeft HS, van Veelen PA, Samborskiy DV, Kravchenko AA, Leontovich AM, Sidorov IA, Snijder EJ, Posthuma CC, Gorbalenya AE.

Nucleic Acids Res. 2015 Sep 30;43(17):8416-34. doi: 10.1093/nar/gkv838. Epub 2015 Aug 24.

29.

Proteasomal Degradation of Proinsulin Requires Derlin-2, HRD1 and p97.

Hoelen H, Zaldumbide A, van Leeuwen WF, Torfs EC, Engelse MA, Hassan C, Lebbink RJ, de Koning EJ, Resssing ME, de Ru AH, van Veelen PA, Hoeben RC, Roep BO, Wiertz EJ.

PLoS One. 2015 Jun 24;10(6):e0128206. doi: 10.1371/journal.pone.0128206. eCollection 2015.

30.

ICL-induced miR139-3p and miR199a-3p have opposite roles in hematopoietic cell expansion and leukemic transformation.

Alemdehy MF, Haanstra JR, de Looper HW, van Strien PM, Verhagen-Oldenampsen J, Caljouw Y, Sanders MA, Hoogenboezem R, de Ru AH, Janssen GM, Smetsers SE, Bierings MB, van Veelen PA, von Lindern M, Touw IP, Erkeland SJ.

Blood. 2015 Jun 18;125(25):3937-48. doi: 10.1182/blood-2014-11-612507. Epub 2015 Mar 16.

31.

Temporal SILAC-based quantitative proteomics identifies host factors involved in chikungunya virus replication.

Treffers EE, Tas A, Scholte FE, Van MN, Heemskerk MT, de Ru AH, Snijder EJ, van Hemert MJ, van Veelen PA.

Proteomics. 2015 Jul;15(13):2267-80. doi: 10.1002/pmic.201400581. Epub 2015 Apr 22.

PMID:
25764339
32.

The first step of peptide selection in antigen presentation by MHC class I molecules.

Garstka MA, Fish A, Celie PH, Joosten RP, Janssen GM, Berlin I, Hoppes R, Stadnik M, Janssen L, Ovaa H, van Veelen PA, Perrakis A, Neefjes J.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):1505-10. doi: 10.1073/pnas.1416543112. Epub 2015 Jan 20.

33.

Identification of Biological Relevant Minor Histocompatibility Antigens within the B-lymphocyte-Derived HLA-Ligandome Using a Reverse Immunology Approach.

Hombrink P, Hassan C, Kester MG, Jahn L, Pont MJ, de Ru AH, van Bergen CA, Griffioen M, Falkenburg JH, van Veelen PA, Heemskerk MH.

Clin Cancer Res. 2015 May 1;21(9):2177-86. doi: 10.1158/1078-0432.CCR-14-2188. Epub 2015 Jan 14.

34.

Extensive glycosylation of ACPA-IgG variable domains modulates binding to citrullinated antigens in rheumatoid arthritis.

Rombouts Y, Willemze A, van Beers JJ, Shi J, Kerkman PF, van Toorn L, Janssen GM, Zaldumbide A, Hoeben RC, Pruijn GJ, Deelder AM, Wolbink G, Rispens T, van Veelen PA, Huizinga TW, Wuhrer M, Trouw LA, Scherer HU, Toes RE.

Ann Rheum Dis. 2016 Mar;75(3):578-85. doi: 10.1136/annrheumdis-2014-206598. Epub 2015 Jan 13.

PMID:
25587188
35.

Comprehensive analysis of the mouse brain proteome sampled in mass spectrometry imaging.

Heijs B, Carreira RJ, Tolner EA, de Ru AH, van den Maagdenberg AM, van Veelen PA, McDonnell LA.

Anal Chem. 2015 Feb 3;87(3):1867-75. doi: 10.1021/ac503952q. Epub 2015 Jan 13.

PMID:
25535922
36.

Naturally processed non-canonical HLA-A*02:01 presented peptides.

Hassan C, Chabrol E, Jahn L, Kester MG, de Ru AH, Drijfhout JW, Rossjohn J, Falkenburg JH, Heemskerk MH, Gras S, van Veelen PA.

J Biol Chem. 2015 Jan 30;290(5):2593-603. doi: 10.1074/jbc.M114.607028. Epub 2014 Dec 12.

37.

Therapeutic targeting of the BCR-associated protein CD79b in a TCR-based approach is hampered by aberrant expression of CD79b.

Jahn L, Hombrink P, Hassan C, Kester MG, van der Steen DM, Hagedoorn RS, Falkenburg JH, van Veelen PA, Heemskerk MH.

Blood. 2015 Feb 5;125(6):949-58. doi: 10.1182/blood-2014-07-587840. Epub 2014 Nov 20.

38.

Identification and characterisation of peptide binding motifs of six autoimmune disease-associated human leukocyte antigen-class I molecules including HLA-B*39:06.

Eichmann M, de Ru A, van Veelen PA, Peakman M, Kronenberg-Versteeg D.

Tissue Antigens. 2014 Oct;84(4):378-88. doi: 10.1111/tan.12413. Epub 2014 Aug 25.

PMID:
25154780
39.

Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes.

Hassan C, Kester MG, Oudgenoeg G, de Ru AH, Janssen GM, Drijfhout JW, Spaapen RM, Jiménez CR, Heemskerk MH, Falkenburg JH, van Veelen PA.

J Proteomics. 2014 Sep 23;109:240-4. doi: 10.1016/j.jprot.2014.07.009. Epub 2014 Jul 19.

PMID:
25050860
40.

Disclosure of selective advantages in the "modern" sublineage of the Mycobacterium tuberculosis Beijing genotype family by quantitative proteomics.

de Keijzer J, de Haas PE, de Ru AH, van Veelen PA, van Soolingen D.

Mol Cell Proteomics. 2014 Oct;13(10):2632-45. doi: 10.1074/mcp.M114.038380. Epub 2014 Jul 14.

41.

Transactivation of programmed ribosomal frameshifting by a viral protein.

Li Y, Treffers EE, Napthine S, Tas A, Zhu L, Sun Z, Bell S, Mark BL, van Veelen PA, van Hemert MJ, Firth AE, Brierley I, Snijder EJ, Fang Y.

Proc Natl Acad Sci U S A. 2014 May 27;111(21):E2172-81. doi: 10.1073/pnas.1321930111. Epub 2014 May 13.

42.

The human peptidylarginine deiminases type 2 and type 4 have distinct substrate specificities.

Assohou-Luty C, Raijmakers R, Benckhuijsen WE, Stammen-Vogelzangs J, de Ru A, van Veelen PA, Franken KL, Drijfhout JW, Pruijn GJ.

Biochim Biophys Acta. 2014 Apr;1844(4):829-36. doi: 10.1016/j.bbapap.2014.02.019. Epub 2014 Mar 2.

PMID:
24594197
43.

Carbamylation and antibodies against carbamylated proteins in autoimmunity and other pathologies.

Shi J, van Veelen PA, Mahler M, Janssen GM, Drijfhout JW, Huizinga TW, Toes RE, Trouw LA.

Autoimmun Rev. 2014 Mar;13(3):225-30. doi: 10.1016/j.autrev.2013.10.008. Epub 2013 Oct 28. Review.

PMID:
24176675
44.

Posttranslational modification of HLA-DQ binding islet autoantigens in type 1 diabetes.

van Lummel M, Duinkerken G, van Veelen PA, de Ru A, Cordfunke R, Zaldumbide A, Gomez-Touriño I, Arif S, Peakman M, Drijfhout JW, Roep BO.

Diabetes. 2014 Jan;63(1):237-47. doi: 10.2337/db12-1214. Epub 2013 Oct 2.

45.

Unique peptide-binding motif for Mamu-B*037:01: an MHC class I allele common to Indian and Chinese rhesus macaques.

de Groot NG, Heijmans CM, de Ru AH, Hassan C, Otting N, Doxiadis GG, Koning F, van Veelen PA, Bontrop RE.

Immunogenetics. 2013 Dec;65(12):897-900. doi: 10.1007/s00251-013-0734-5. Epub 2013 Sep 17.

PMID:
24042460
46.

Dendritic cells process synthetic long peptides better than whole protein, improving antigen presentation and T-cell activation.

Rosalia RA, Quakkelaar ED, Redeker A, Khan S, Camps M, Drijfhout JW, Silva AL, Jiskoot W, van Hall T, van Veelen PA, Janssen G, Franken K, Cruz LJ, Tromp A, Oostendorp J, van der Burg SH, Ossendorp F, Melief CJ.

Eur J Immunol. 2013 Oct;43(10):2554-65. doi: 10.1002/eji.201343324. Epub 2013 Aug 5.

47.

Polyubiquitination and proteasomal turnover controls the anti-apoptotic activity of Bcl-B.

van de Kooij B, Rooswinkel RW, Kok F, Herrebout M, de Vries E, Paauwe M, Janssen GM, van Veelen PA, Borst J.

Oncogene. 2013 Nov 28;32(48):5439-48. doi: 10.1038/onc.2013.99. Epub 2013 Apr 8.

48.

The human leukocyte antigen-presented ligandome of B lymphocytes.

Hassan C, Kester MG, de Ru AH, Hombrink P, Drijfhout JW, Nijveen H, Leunissen JA, Heemskerk MH, Falkenburg JH, van Veelen PA.

Mol Cell Proteomics. 2013 Jul;12(7):1829-43. doi: 10.1074/mcp.M112.024810. Epub 2013 Mar 12.

49.

Discovery of T cell epitopes implementing HLA-peptidomics into a reverse immunology approach.

Hombrink P, Hassan C, Kester MG, de Ru AH, van Bergen CA, Nijveen H, Drijfhout JW, Falkenburg JH, Heemskerk MH, van Veelen PA.

J Immunol. 2013 Apr 15;190(8):3869-77. doi: 10.4049/jimmunol.1202351. Epub 2013 Mar 8.

50.

Efficient -2 frameshifting by mammalian ribosomes to synthesize an additional arterivirus protein.

Fang Y, Treffers EE, Li Y, Tas A, Sun Z, van der Meer Y, de Ru AH, van Veelen PA, Atkins JF, Snijder EJ, Firth AE.

Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):E2920-8. doi: 10.1073/pnas.1211145109. Epub 2012 Oct 4.

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