Key Publications

Rafiee MR, Girardot C, Sigismondo G, Krijgsved J. Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins. Mol Cell. (2016);64(3):624-635.  (Featured article); Preview' by Tu S, LeRoy G, Reinberg D. Chromatin Starts to Come Clean. Mol Cell (2016);64(3):439-441; 'News and views' by Bensaddek D, Lamond AI. Unlocking the chromatin code by deciphering protein–DNA interactions. Mol Syst Biol (2016);12:887;  'Research Highlight' by S. Larochelle. A pluripotent approach. Nature Methods (2016);13:975

Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsved J, Hentze MW. Comprehensive Identification of RNA-Binding Domains in Human Cells. Mol Cell (2016), 63(4): 696–710

Virant-Klun I, Leicht S, Hughes C, Krijgsved J. Identification of maturation-specific proteins by
single-cell proteomics of human oocytes. Mol Cell Proteomics. (2016), 15(8):2616-27

Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast AM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsved J, Essers MA. Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors. Cell Stem Cell. (2015), 17(4):422-34

Hughes C, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsved J. Ultrasensitive proteome analysis using paramagnetic bead technology. Molecular Systems Biology (2014); 10: 757 'News and Views' by Kanshin and Thibault, Molecular Systems Biology (2014); 10: 758

Cabezas-Wallscheid N, Klimmeck D, Hansson J, Lipka DB, Reyes A, Wang Q, Weichenhan D, Lier A, von Paleske L, Renders S, Wünsche P, Zeisberger P, Brocks D, Gu L, Herrmann C, Haas S, Essers MA, Brors B, Eils R, Huber W*, Milsom MD*, Plass C*, Krijgsved J*, Trumpp A*. Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis. *Joint last author. Cell Stem Cell (2014), 15(4):507-22

Eichelbaum K, Winter M, Diaz MB, Herzig S, Krijgsved J (2012). Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nature Biotechnology 30(10):984-90

Hansson J, Rafiee MR, Reiland S, Polo JM, Gehring J, Okawa S, Huber W, Hochedlinger K, Krijgsved J (2012). Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Reports 2(6):1579-92

Castello A, Fischer B, Schuschke K, Horos R, Beckmann B, Strein C, Humphreys DT, Preiss T, Steinmetz L, Krijgsved J* and Hentze MW* (2012). Insights into RNA biology from a mammalian cell mRNA interactome. Cell 149(6):1393-406. *Joint last author

D. Van Hoof, J. Muñoz, S.R. Braam, M.W.H. Pinkse, R. Linding, A.J.R. Heck, C.L. Mummery, and Krijgsved J. Phosphorylation dynamics during early differentiation of human embryonic stem cells (2009). Cell Stem Cell 5(2): 214-226

All publications (2012 - present)

2016

Kramer G, Krijgsved J. Turning Over Paradigms in Protein Decay. Dev Cell (2016);39(3):284-285

Okawa S, Gagrica S, Blin C, Ender C, Pollard SM, Krijgsved J. Proteome and Secretome Characterisation of Glioblastoma-derived Neural Stem Cells. Stem Cells. (2016) doi: 10.1002/stem.2542. [Epub ahead of print]

Rafiee MR, Girardot C, Sigismondo G, Krijgsved J. Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins. Mol Cell. (2016);64(3):624-635

Liao Y, Castello A, Fischer B, Leicht S, Föehr S, Frese CK, Ragan C, Kurscheid S, Pagler E, Yang H, Krijgsved J, Hentze MW, Preiss T. The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease. Cell Reports (2016);16(5):1456-69

Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsved J, Hentze MW. Comprehensive Identification of RNA-Binding Domains in Human Cells. Mol Cell (2016), 63(4): 696–710

Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsved J, Hentze MW, Castello A, Ephrussi A. Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila. Nat Commun. (2016), 7:12128

Virant-Klun I, Leicht S, Hughes C, Krijgsved J. Identification of maturation-specific proteins by single-cell proteomics of human oocytes. Mol Cell Proteomics. (2016), 15(8):2616-27

Liepelt A, Naarmann-de Vries IS, Simons N, Eichelbaum K, Foehr S, Archer SK, Castello A, Usadel B, Krijgsved J, Preiss T, Marx G, Hentze MW, Ostareck DH, Ostareck-Lederer A. Identification of RNA-binding proteins in macrophages by interactome capture. Mol Cell Proteomics (2016), 15(8):2699-714

Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE. Proteomic analysis reveals branch-specific regulation of the unfolded protein response by nonsense-mediated mRNA decay. Mol. Cell. Proteomics (2016), 15(5):1584-97

Vargel Ö, Zhang Y, Kosim K, Ganter K, Foehr S, Mardenborough Y, Shvartsman M, Enright AJ, Krijgsveld J, Lancrin C. Activation of the TGFβ pathway impairs endothelial to haematopoietic transition. Sci. Rep. (2016), 6:21518

Haberkant P, Stein F, Höglinger D, Gerl MJ, Brügger B, Van Veldhoven PP, Krijgsveld J, Gavin AC, Schultz C. Bifunctional Sphingosine for Cell-Based Analysis of Protein-Sphingolipid Interactions. ACS Chem Biol. (2016) 11(1):222-30

Dunne M, Leicht S, Krichel B, Mertens HD, Thompson A, Krijgsveld J, Svergun DI, Gómez-Torres N, Garde S, Uetrecht C, Narbad A, Mayer MJ, Meijers R. Crystal Structure of the CTP1L Endolysin Reveals How Its Activity Is Regulated by a Secondary Translation Product. J Biol Chem. (2016), 291(10):4882-93

 

2015

Schäfer M, Oeing CU, Rohm M, Baysal-Temel E, Lehmann LH, Bauer R, Volz HC, Boutros M, Sohn D, Sticht C, Gretz N, Eichelbaum K, Werner T, Hirt MN, Eschenhagen T, Müller-Decker K, Strobel O, Hackert T, Krijgsveld J, Katus HA, Berriel Diaz M, Backs J, Herzig S. Ataxin-10 is part of a cachexokine cocktail triggering cardiac metabolic dysfunction in cancer cachexia. Mol Metab. (2015), 5:67-78.

Beckmann BM, Horos R, Fischer B, Castello A, Eichelbaum K, Alleaume AM, Schwarzl T, Curk T, Foehr S, Huber W, Krijgsveld J, Hentze MW. The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs. Nat Commun. (2015), 6:10127.

Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW. Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture. Methods Mol Biol. 2016;1358:131-9

Barra MM, Richards DM, Hansson J, Hofer AC, Delacher M, Hettinger J, Krijgsveld J, Feuerer M. Transcription Factor 7 Limits Regulatory T Cell Generation in the Thymus. J Immunol. (2015), 195(7):3058-70

Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast AM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsveld J, Essers MA. Inflammation-Induced Emergency Megakaryopoiesis Driven by Hematopoietic Stem Cell-like Megakaryocyte Progenitors. Cell Stem Cell. (2015), 17(4):422-34

2014

Bhuvanagiri M, Lewis J, Putzker K, Becker JP, Leicht S, Krijgsveld J, Batra R, Turnwald B, Jovanovic B, Hauer C, Sieber J, Hentze MW, Kulozik AE. 5-azacytidine inhibits nonsense-mediated decay in a MYC-dependent fashion. EMBO Mol Med. (2014) 6(12):1593-609

Klimmeck D, Cabezas-Wallscheid N, Reyes A, Von Paleske L, Renders S, Hansson J, Krijgsveld J, Huber W, Trumpp A. Transcriptome-wide Profiling and Posttranscriptional Analysis of Hematopoietic Stem/Progenitor Cell Differentiation toward Myeloid Commitment. Stem Cell Reports (2014), 3(5):858–875

Kronja I, Whitfield ZJ, Yuan B, Dzeyk K, Kirkpatrick J, Krijgsveld J, Orr-Weaver TL. Quantitative proteomics reveals the dynamics of protein changes during Drosophila oocyte maturation and the oocyte-to-embryo transition.  PNAS (2014); 111(45):16023-8

Hughes C, Foehr S, Garfield DA, Furlong EE, Steinmetz LM, Krijgsveld J, Ultrasensitive proteome analysis using paramagnetic bead technology.Molecular Systems Biology (2014); 10: 757 Highlighted in 'News and Views' by Kanshin and Thibault, Molecular Systems Biology  (2014); 10: 758

Cabezas-Wallscheid N, Klimmeck D, Hansson J, Lipka DB, Reyes A, Wang Q, Weichenhan D, Lier A, von Paleske L, Renders S, Wünsche P, Zeisberger P, Brocks D, Gu L, Herrmann C, Haas S, Essers MA, Brors B, Eils R, Huber W*, Milsom MD*, Plass C*, Krijgsveld J*, Trumpp A*. Identification of Regulatory Networks in HSCs and Their Immediate Progeny via Integrated Proteome, Transcriptome, and DNA Methylome Analysis. *Joint last author Cell Stem Cell (2014), 15(4):507-22

Eichelbaum K and Krijgsveld J. Combining Pulsed SILAC Labeling and Click-Chemistry for Quantitative Secretome Analysis. Methods Mol Biol. (2014), 1174:101-14.

Kronja I, Yuan B, Eichhorn SW, Dzeyk K, Krijgsveld J, Bartel DP, Orr-Weaver TL. Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition. Cell Reports (2014), 7(5):1495-508

Eichelbaum K and Krijgsveld J Rapid temporal dynamics of transcription, protein synthesis and secretion during macrophage activation. Mol Cell Proteomics (2014), 13(3):792-810

Virant-Klun I. and Krijgsveld J (2014). Proteomes of animal oocytes: what can we learn for human oocytes in the in vitro fertilization programme? BioMed Research International, (2014), 2014:856907. doi: 10.1155/2014/856907

Gonzalez D, Hamidi N, Del Sol R, Benschop JJ, Nancy T, Li C, Francis L, Tzouros M, Krijgsveld J, Holstege FCP, and Conlan RS. Suppression of Mediator is regulated by Cdk8-dependent Grr1 turnover of the Med3 coactivator. PNAS, (2014), 111(7):2500-5

Polonio-Vallon T, Kirkpatrick J, Krijgsveld J, and Hofmann TG. Src kinase modulates the apoptotic p53 pathway by altering HIPK2 localization. Cell Cycle (2014), 13(1):115-25

 

2013

Yokoyama H, Nakos K, Santarella-Mellwig R, Rybina S, Krijgsveld J, Koffa MD, and Mattaj IW (2013). CHD4 Is a RanGTP-Dependent MAP that Stabilizes Microtubules and Regulates Bipolar Spindle Formation. Curr Biol. 23(24):2443-51

Hettinger J, Richards D, Hansson J, Barra MM, Krijgsveld J, and Feuerer M (2013). Identification of a monocyte/macrophage-restricted progenitor in the bone marrow. Nature Immunology 14(8):821-30.

Kwon SC, Yi H, Eichelbaum K, Föhr S, Fischer B, You KT, Castello A, Krijgsveld J, Hentze MW, and Kim VN (2013).The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol. 20(9):1122-30

Hansson, J. and Krijgsveld, J (2013). Proteomic analysis of cell fate decision. Curr Opin Genet Dev. 23(5):540-7

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

Castello A, Horos R, Strein C, Fischer B, Eichelbaum K, Steinmetz LM, Krijgsveld J, Hentze MW (2013). System-wide identification of RNA-binding proteins by interactome capture. Nature Protocols 8(3):491-500

Dastidar EG, Dzeyk K, Krijgsveld J, Malmquist NA, Doerig C, Scherf A, Lopez-Rubio JJ. (2013). Comprehensive histone phosphorylation analysis and identification of Pf14-3-3 protein as a histone H3 phosphorylation reader in malaria parasites. PLoS One 8(1):e53179

2012

Eichelbaum K, Winter M, Diaz MB, Herzig S, Krijgsveld J (2012). Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nature Biotechnology 30(10):984-90

Hansson J, Rafiee MR, Reiland S, Polo JM, Gehring J, Okawa S, Huber W, Hochedlinger K, Krijgsveld J (2012). Highly coordinated proteome dynamics during reprogramming of somatic cells to pluripotency. Cell Reports 2(6):1579-92

Castello A, Fischer B, Schuschke K, Horos R, Beckmann B, Strein C, Humphreys DT, Preiss T, Steinmetz L, Krijgsveld J* and Hentze MW* (2012). Insights into RNA biology from a mammalian cell mRNA interactome. Cell 149(6):1393-406. *Joint last author

Hughes C, Krijgsveld J (2012). Developments in quantitative mass spectrometry for the analysis of proteome dynamics. Trends Biotechnol. 30(12):668-76.

Klimmeck D.**, Hansson J.**,  Raffel S., Vakhrushev S., Trumpp A.* and Krijgsveld J.* (2012). Proteomic cornerstones of multipotent hematopoietic stem and progenitor cells.  Mol Cell Proteomics 11(8):286-302. ** Joint first author, *Joint last author

Gouw JW, Krijgsveld J (2012). MSQuant: a platform for stable isotope-based quantitative proteomics. Methods Mol Biol. 2012;893:511-22.

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

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