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Krijgsveld TeamPublications

Rapid temporal dynamics of transcription, protein synthesis and secretion during macrophage activation.
Eichelbaum, K. & Krijgsveld, J.
Mol Cell Proteomics. 2014 Jan 6. Europe PMC

CHD4 Is a RanGTP-Dependent MAP that Stabilizes Microtubules and Regulates Bipolar Spindle Formation.
Yokoyama, H., Nakos, K., Santarella-Mellwig, R., Rybina, S., Krijgsveld, J., Koffa, M.D. & Mattaj, I.W.
Curr Biol. 2013 Nov 20. pii: S0960-9822(13)01252-9. doi:10.1016/j.cub.2013.09.062. Europe PMC

Proteomic analysis of cell fate decision.
Hansson, J. & Krijgsveld, J.
Curr Opin Genet Dev. 2013 Oct;23(5):540-7. doi: 10.1016/j.gde.2013.06.004. Epub2013 Aug 10. Europe PMC

The RNA-binding protein repertoire of embryonic stem cells.
Kwon, S.C., Yi, H., Eichelbaum, K., Fohr, S., Fischer, B., You, K.T., Castello, A., Krijgsveld, J., Hentze, M.W. & Kim, V.N.
Nat Struct Mol Biol. 2013 Sep;20(9):1122-30. doi: 10.1038/nsmb.2638. Epub 2013Aug 4. Europe PMC

Properties of isotope patterns and their utility for peptide identification in large-scale proteomic experiments.
Okawa, S., Fischer, B. & Krijgsveld, J.
Rapid Commun Mass Spectrom. 2013 May 15;27(9):1067-75. doi: 10.1002/rcm.6551. Europe PMC

Comprehensive histone phosphorylation analysis and identification of pf14-3-3 protein as a histone h3 phosphorylation reader in malaria parasites.
Dastidar, E.G., Dzeyk, K., Krijgsveld, J., Malmquist, N.A., Doerig, C., Scherf, A. & Lopez-Rubio, J.J.
PLoS One. 2013;8(1):e53179. doi: 10.1371/journal.pone.0053179. Epub 2013 Jan 7. Europe PMC

System-wide identification of RNA-binding proteins by interactome capture.
Castello, A., Horos, R., Strein, C., Fischer, B., Eichelbaum, K., Steinmetz, L.M., Krijgsveld, J. & Hentze, M.W.
Nat Protoc. 2013 Feb 14;8(3):491-500. doi: 10.1038/nprot.2013.020. Epub 2013 Feb14. Europe PMC

Origin of monocytes and macrophages in a committed progenitor.
Hettinger, J., Richards, D.M., Hansson, J., Barra, M.M., Joschko, A.C., Krijgsveld, J. & Feuerer, M.
Nat Immunol. 2013 Aug;14(8):821-30. doi: 10.1038/ni.2638. Epub 2013 Jun 30. Europe PMC

Developments in quantitative mass spectrometry for the analysis of proteome dynamics.
Hughes, C. & Krijgsveld, J.
Trends Biotechnol. 2012 Dec;30(12):668-76. doi: 10.1016/j.tibtech.2012.09.007.Epub 2012 Oct 27. Europe PMC

Selective enrichment of newly synthesized proteins for quantitative secretome analysis.
Eichelbaum, K., Winter, M., Diaz, M.B., Herzig, S. & Krijgsveld, J.
Nat Biotechnol. 2012 Oct;30(10):984-90. doi: 10.1038/nbt.2356. Epub 2012 Sep 23. Europe PMC

Proteomic cornerstones of hematopoietic stem cell differentiation: distinct signatures of multipotent progenitors and myeloid committed cells.
Klimmeck, D., Hansson, J., Raffel, S., Vakhrushev, S.Y., Trumpp, A. & Krijgsveld, J.
Mol Cell Proteomics. 2012 Aug;11(8):286-302. doi: 10.1074/mcp.M111.016790. Epub2012 Mar 27. Europe PMC

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins.
Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B.M., Strein, C., Davey, N.E., Humphreys, D.T., Preiss, T., Steinmetz, L.M., Krijgsveld, J. & Hentze, M.W.
Cell. 2012 Jun 8;149(6):1393-406. Epub 2012 May 31. Europe PMC

Proteomic analysis of stem cell differentiation and early development.
van Hoof, D., Krijgsveld, J. & Mummery, C.
Cold Spring Harb Perspect Biol. 2012 Mar 1;4(3). pii: a008177. doi:10.1101/cshperspect.a008177. Europe PMC

Highly Coordinated Proteome Dynamics during Reprogramming of Somatic Cells to Pluripotency.
Hansson J., Rafiee M.R., Reiland S., Polo J.M., Gehring J., Okawa S., Huber W., Hochedlinger K., Krijgsveld J.
Cell Rep. 2012 Dec 27;2(6):1579-92. doi: 10.1016/j.celrep.2012.10.014. Europe PMC

MSQuant: a platform for stable isotope-based quantitative proteomics.
Gouw, J.W. & Krijgsveld, J.
Methods Mol Biol. 2012;893:511-22. doi: 10.1007/978-1-61779-885-6_31. Europe PMC

Native thrombocidin-1 and unfolded thrombocidin-1 exert antimicrobial activity via distinct structural elements.
Kwakman, P.H., Krijgsveld, J., de Boer, L., Nguyen, L.T., Boszhard, L., Vreede, J., Dekker, H.L., Speijer, D., Drijfhout, J.W., te Velde, A.A., Crielaard, W., Vogel, H.J., Vandenbroucke-Grauls, C.M. & Zaat, S.A.
J Biol Chem. 2011 Dec 16;286(50):43506-14. Epub 2011 Oct 24. Europe PMC

Progressive methylation of ageing histones by Dot1 functions as a timer.
De Vos, D., Frederiks, F., Terweij, M., van Welsem, T., Verzijlbergen, K.F., Iachina, E., de Graaf, E.L., Altelaar, A.F., Oudgenoeg, G., Heck, A.J., Krijgsveld, J., Bakker, B.M. & van Leeuwen, F.
EMBO Rep. 2011 Sep 1;12(9):956-62. doi: 10.1038/embor.2011.131. Europe PMC

Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.
Huang, H.Y., Houwing, S., Kaaij, L.J., Meppelink, A., Redl, S., Gauci, S., Vos, H., Draper, B.W., Moens, C.B., Burgering, B.M., Ladurner, P., Krijgsveld, J., Berezikov, E. & Ketting, R.F.
EMBO J. 2011 Jul 8;30(16):3298-308. doi: 10.1038/emboj.2011.228. Europe PMC

The ecoresponsive genome of Daphnia pulex.
Colbourne, J.K., Pfrender, M.E., Gilbert, D., Thomas, W.K., Tucker, A., Oakley, T.H., Tokishita, S., Aerts, A., Arnold, G.J., Basu, M.K., Bauer, D.J., Caceres, C.E., Carmel, L., Casola, C., Choi, J.H., Detter, J.C., Dong, Q., Dusheyko, S., Eads, B.D., Frohlich, T., Geiler-Samerotte, K.A., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E.V., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J.R., Muller, J., Pangilinan, J., Patwardhan, R.P., Pitluck, S., Pritham, E.J., Rechtsteiner, A., Rho, M., Rogozin, I.B., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y.I., Yamagata, H., Yamada, T., Ye, Y., Shaw, J.R., Andrews, J., Crease, T.J., Tang, H., Lucas, S.M., Robertson, H.M., Bork, P., Koonin, E.V., Zdobnov, E.M., Grigoriev, I.V., Lynch, M. & Boore, J.L.
Science. 2011 Feb 4;331(6017):555-61. doi: 10.1126/science.1197761. Europe PMC

Defining pluripotent stem cells through quantitative proteomic analysis.
Reiland, S., Salekdeh, G.H. & Krijgsveld, J.
Expert Rev Proteomics. 2011 Feb;8(1):29-42. doi: 10.1586/epr.10.100. Europe PMC

Metabolic labeling of model organisms using heavy nitrogen (15N).
Gouw J.W., Tops B.B. & Krijgsveld J.
Methods Mol Biol. 2011;753:29-42. doi: 10.1007/978-1-61779-148-2_2. Europe PMC

Identification of cell surface proteins for antibody-based selection of human embryonic stem cell-derived cardiomyocytes.
Van Hoof, D., Dormeyer, W., Braam, S.R., Passier, R., Monshouwer-Kloots, J., Ward-van Oostwaard, D., Heck, A.J., Krijgsveld, J. & Mummery, C.L.
J Proteome Res. 2010 Mar 5;9(3):1610-8. Europe PMC

A P4-ATPase protein interaction network reveals a link between aminophospholipid transport and phosphoinositide metabolism.
Puts, C.F., Lenoir, G., Krijgsveld, J., Williamson, P. & Holthuis, J.C.
J Proteome Res. 2010 Feb 5;9(2):833-42. Europe PMC

Worms from venus and mars: proteomics profiling of sexual differences in Caenorhabditis elegans using in vivo 15N isotope labeling.
Tops, B.B., Gauci, S., Heck, A.J. & Krijgsveld, J.
J Proteome Res. 2010 Jan;9(1):341-51. Europe PMC

Quantitative proteomics by metabolic labeling of model organisms.
Gouw, J.W., Krijgsveld, J. & Heck, A.J.
Mol Cell Proteomics. 2010 Jan;9(1):11-24. Epub 2009 Nov 19. Europe PMC

On-the-fly targeted selection of labeled peptides in liquid chromatography/mass spectrometry based quantitative proteomics.
Barbu, I.M., Smith, D.F., van Breukelen, B., van der Burgt, Y.E., Duursma, M.C., Heck, A.J., Heeren, R.M. & Krijgsveld, J.
Rapid Commun Mass Spectrom. 2010 Jan;24(2):239-41. Europe PMC

Novel Hsp90 partners discovered using complementary proteomic approaches.
Tsaytler, P.A., Krijgsveld, J., Goerdayal, S.S., Rudiger, S. & Egmond, M.R.
Cell Stress Chaperones. 2009 Nov;14(6):629-38. doi: 10.1007/s12192-009-0115-z.Epub 2009 Apr 26. Europe PMC

Cooperative binding of two acetylation marks on a histone tail by a single bromodomain.
Moriniere, J., Rousseaux, S., Steuerwald, U., Soler-Lopez, M., Curtet, S., Vitte, A.L., Govin, J., Gaucher, J., Sadoul, K., Hart, D.J., Krijgsveld, J., Khochbin, S., Muller, C.W. & Petosa, C.
Nature. 2009 Oct 1;461(7264):664-8. Europe PMC

Phosphorylation dynamics during early differentiation of human embryonic stem cells.
Van Hoof, D., Munoz, J., Braam, S.R., Pinkse, M.W., Linding, R., Heck, A.J., Mummery, C.L. & Krijgsveld, J.
Cell Stem Cell. 2009 Aug 7;5(2):214-26. Europe PMC

In vivo stable isotope labeling of fruit flies reveals post-transcriptional regulation in the maternal-to-zygotic transition.
Gouw, J.W., Pinkse, M.W., Vos, H.R., Moshkin, Y., Verrijzer, C.P., Heck, A.J. & Krijgsveld, J.
Mol Cell Proteomics. 2009 Jul;8(7):1566-78. doi: 10.1074/mcp.M900114-MCP200. Epub2009 Mar 24. Europe PMC

Orthogonal separation techniques for the characterization of the yeast nuclear proteome.
Gauci, S., Veenhoff, L.M., Heck, A.J. & Krijgsveld, J.
J Proteome Res. 2009 Jul;8(7):3451-63. Europe PMC

An AC-5 cathepsin B-like protease purified from Haemonchus contortus excretory secretory products shows protective antigen potential for lambs.
De Vries, E., Bakker, N., Krijgsveld, J., Knox, D.P., Heck, A.J. & Yatsuda, A.P.
Vet Res. 2009 Jul-Aug;40(4):41. Epub 2009 Apr 30. Europe PMC

Exosomal secretion of cytoplasmic prostate cancer xenograft-derived proteins.
Jansen, F.H., Krijgsveld, J., van Rijswijk, A., van den Bemd, G.J., van den Berg, M.S., van Weerden, W.M., Willemsen, R., Dekker, L.J., Luider, T.M. & Jenster, G.
Mol Cell Proteomics. 2009 Jun;8(6):1192-205. doi: 10.1074/mcp.M800443-MCP200.Epub 2009 Feb 9. Europe PMC

Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.
Gauci, S., Helbig, A.O., Slijper, M., Krijgsveld, J., Heck, A.J. & Mohammed, S.
Anal Chem. 2009 Jun 1;81(11):4493-501. Europe PMC

Human Proteome Organisation's 7th World Congress, 2008.
Krijgsveld, J.
Expert Rev Proteomics. 2008 Dec;5(6):775-7. Europe PMC

A versatile peptide pI calculator for phosphorylated and N-terminal acetylated peptides experimentally tested using peptide isoelectric focusing.
Gauci, S., van Breukelen, B., Lemeer, S.M., Krijgsveld, J. & Heck, A.J.
Proteomics. 2008 Dec;8(23-24):4898-906. Europe PMC

Feeder-free monolayer cultures of human embryonic stem cells express an epithelial plasma membrane protein profile.
Van Hoof, D., Braam, S.R., Dormeyer, W., Ward-van Oostwaard, D., Heck, A.J., Krijgsveld, J. & Mummery, C.L.
Stem Cells. 2008 Nov;26(11):2777-81. Epub 2008 Aug 14. Europe PMC

Optimizing identification and quantitation of 15N-labeled proteins in comparative proteomics.
Gouw, J.W., Tops, B.B., Mortensen, P., Heck, A.J. & Krijgsveld, J.
Anal Chem. 2008 Oct 15;80(20):7796-803. Epub 2008 Sep 23. Europe PMC

A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells.
Dormeyer, W., van Hoof, D., Mummery, C.L., Krijgsveld, J. & Heck, A.J.
Proteomics. 2008 Oct;8(19):4036-53. Europe PMC

Proteomics and human embryonic stem cells.
Van Hoof, D., Heck, A.J., Krijgsveld, J. & Mummery, C.L.
Stem Cell Res. 2008 Sep;1(3):169-82. Epub 2008 May 29. Europe PMC

Immediate protein targets of photodynamic treatment in carcinoma cells.
Tsaytler, P.A., C O'Flaherty, M., Sakharov, D.V., Krijgsveld, J. & Egmond, M.R.
J Proteome Res. 2008 Sep;7(9):3868-78. Epub 2008 Jul 25. Europe PMC

Plasma membrane proteomics of human embryonic stem cells and human embryonal carcinoma cells.
Dormeyer, W., van Hoof, D., Braam, S.R., Heck, A.J., Mummery, C.L. & Krijgsveld, J.
J Proteome Res. 2008 Jul;7(7):2936-51. Epub 2008 May 20. Europe PMC

Nonprocessive methylation by Dot1 leads to functional redundancy of histone H3K79 methylation states.
Frederiks, F., Tzouros, M., Oudgenoeg, G., van Welsem, T., Fornerod, M., Krijgsveld, J. & van Leeuwen, F.
Nat Struct Mol Biol. 2008 Jun;15(6):550-7. Epub 2008 May 30. Europe PMC

The time is right: proteome biology of stem cells.
Whetton, A.D., Williamson, A.J., Krijgsveld, J., Lee, B.H., Lemischka, I., Oh, S., Pera, M., Mummery, C. & Heck, A.J.
Cell Stem Cell. 2008 Mar 6;2(3):215-7. Europe PMC

Proteome biology of stem cells: a new joint HUPO and ISSCR initiative.
Krijgsveld, J., Whetton, A.D., Lee, B., Lemischka, I., Oh, S., Pera, M., Mummery, C. & Heck, A.J.
Mol Cell Proteomics. 2008 Jan;7(1):204-5. Europe PMC

Targeted analysis of protein termini.
Dormeyer, W., Mohammed, S., Breukelen, B., Krijgsveld, J. & Heck, A.J.
J Proteome Res. 2007 Dec;6(12):4634-45. Epub 2007 Oct 10. Europe PMC

Proteome biology of stem cells.
Heck, A.J., Mummery, C., Whetton, A., Oh, S., Lee, B., Pera, M., Lemischka, I. & Krijgsveld, J.
Stem Cell Res. 2007 Oct;1(1):7-8. Epub 2007 Aug 24. Europe PMC

An experimental correction for arginine-to-proline conversion artifacts in SILAC-based quantitative proteomics.
Van Hoof, D., Pinkse, M.W., Oostwaard, D.W., Mummery, C.L., Heck, A.J. & Krijgsveld, J.
Nat Methods. 2007 Sep;4(9):677-8. Europe PMC

A high-quality catalog of the Drosophila melanogaster proteome.
Brunner, E., Ahrens, C.H., Mohanty, S., Baetschmann, H., Loevenich, S., Potthast, F., Deutsch, E.W., Panse, C., de Lichtenberg, U., Rinner, O., Lee, H., Pedrioli, P.G., Malmstrom, J., Koehler, K., Schrimpf, S., Krijgsveld, J., Kregenow, F., Heck, A.J., Hafen, E., Schlapbach, R. & Aebersold, R.
Nat Biotechnol. 2007 May;25(5):576-83. Epub 2007 Apr 22. Europe PMC

Novel binding partners of Ldb1 are required for haematopoietic development.
Meier, N., Krpic, S., Rodriguez, P., Strouboulis, J., Monti, M., Krijgsveld, J., Gering, M., Patient, R., Hostert, A. & Grosveld, F.
Development. 2006 Dec;133(24):4913-23. Epub 2006 Nov 15. Europe PMC

Mass spectrometric identification of human prostate cancer-derived proteins in serum of xenograft-bearing mice.
van den Bemd, G.J., Krijgsveld, J., Luider, T.M., van Rijswijk, A.L., Demmers, J.A. & Jenster, G.
Mol Cell Proteomics. 2006 Oct;5(10):1830-9. Epub 2006 May 19. Europe PMC

Embryonic stem cell proteomics.
Van Hoof, D., Mummery, C.L., Heck, A.J. & Krijgsveld, J.
Expert Rev Proteomics. 2006 Aug;3(4):427-37. Europe PMC

A quest for human and mouse embryonic stem cell-specific proteins.
Van Hoof, D., Passier, R., Ward-Van Oostwaard, D., Pinkse, M.W., Heck, A.J., Mummery, C.L. & Krijgsveld, J.
Mol Cell Proteomics. 2006 Jul;5(7):1261-73. Epub 2006 Apr 6. Europe PMC

In-gel isoelectric focusing of peptides as a tool for improved protein identification.
Krijgsveld, J., Gauci, S., Dormeyer, W. & Heck, A.J.
J Proteome Res. 2006 Jul;5(7):1721-30. Europe PMC

Identification of secreted cysteine proteases from the parasitic nematode Haemonchus contortus detected by biotinylated inhibitors.
Yatsuda, A.P., Bakker, N., Krijgsveld, J., Knox, D.P., Heck, A.J. & de Vries, E.
Infect Immun. 2006 Mar;74(3):1989-93. Europe PMC

GATA-1 forms distinct activating and repressive complexes in erythroid cells.
Rodriguez, P., Bonte, E., Krijgsveld, J., Kolodziej, K.E., Guyot, B., Heck, A.J., Vyas, P., de Boer, E., Grosveld, F. & Strouboulis, J.
EMBO J. 2005 Jul 6;24(13):2354-66. Epub 2005 May 26. Europe PMC

Mass spectrometric analysis of the Schistosoma mansoni tegumental sub-proteome.
van Balkom, B.W., van Gestel, R.A., Brouwers, J.F., Krijgsveld, J., Tielens, A.G., Heck, A.J. & van Hellemond, J.J.
J Proteome Res. 2005 May-Jun;4(3):958-66. Europe PMC

GMP synthetase stimulates histone H2B deubiquitylation by the epigenetic silencer USP7.
van der Knaap, J.A., Kumar, B.R., Moshkin, Y.M., Langenberg, K., Krijgsveld, J., Heck, A.J., Karch, F. & Verrijzer, C.P.
Mol Cell. 2005 Mar 4;17(5):695-707. Europe PMC

Munc13-4 is an effector of rab27a and controls secretion of lysosomes in hematopoietic cells.
Neeft, M., Wieffer, M., de Jong, A.S., Negroiu, G., Metz, C.H., van Loon, A., Griffith, J., Krijgsveld, J., Wulffraat, N., Koch, H., Heck, A.J., Brose, N., Kleijmeer, M. & van der Sluijs, P.
Mol Biol Cell. 2005 Feb;16(2):731-41. Epub 2004 Nov 17. Europe PMC

Mass spectrometry-based quantitative proteomics.
Heck, A.J. & Krijgsveld, J.
Expert Rev Proteomics. 2004 Oct;1(3):317-26. Europe PMC

Quantitative cancer proteomics: stable isotope labeling with amino acids in cell culture (SILAC) as a tool for prostate cancer research.
Everley, P.A., Krijgsveld, J., Zetter, B.R. & Gygi, S.P.
Mol Cell Proteomics. 2004 Jul;3(7):729-35. Epub 2004 Apr 21. Europe PMC

Differential targeting of two distinct SWI/SNF-related Drosophila chromatin-remodeling complexes.
Mohrmann, L., Langenberg, K., Krijgsveld, J., Kal, A.J., Heck, A.J. & Verrijzer, C.P.
Mol Cell Biol. 2004 Apr;24(8):3077-88. Europe PMC

Lung proteome alterations in a mouse model for nonallergic asthma.
Houtman, R., Krijgsveld, J., Kool, M., Romijn, E.P., Redegeld, F.A., Nijkamp, F.P., Heck, A.J. & Humphery-Smith, I.
Proteomics. 2003 Oct;3(10):2008-18. Europe PMC

Metabolic labeling of C. elegans and D. melanogaster for quantitative proteomics.
Krijgsveld, J., Ketting, R.F., Mahmoudi, T., Johansen, J., Artal-Sanz, M., Verrijzer, C.P., Plasterk, R.H. & Heck, A.J.
Nat Biotechnol. 2003 Aug;21(8):927-31. Epub 2003 Jul 13. Europe PMC

Recent liquid chromatographic-(tandem) mass spectrometric applications in proteomics.
Romijn, E.P., Krijgsveld, J. & Heck, A.J.
J Chromatogr A. 2003 Jun 6;1000(1-2):589-608. Europe PMC

Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice.
de Boer, E., Rodriguez, P., Bonte, E., Krijgsveld, J., Katsantoni, E., Heck, A., Grosveld, F. & Strouboulis, J.
Proc Natl Acad Sci U S A. 2003 Jun 24;100(13):7480-5. Epub 2003 Jun 11. Europe PMC

Comprehensive analysis of the secreted proteins of the parasite Haemonchus contortus reveals extensive sequence variation and differential immune recognition.
Yatsuda, A.P., Krijgsveld, J., Cornelissen, A.W., Heck, A.J. & de Vries, E.
J Biol Chem. 2003 May 9;278(19):16941-51. Epub 2003 Feb 7. Europe PMC