Publications
2011
Welsch T, Zschäbitz S, Becker V, Giese T, Bergmann F, Hinz U, Keleg S, Heller A, Sipos B, Klingmüller U, Büchler MW, Werner J, Giese NA.
Prognostic significance of erythropoietin in pancreatic adenocarcinoma.
PLoS One. 2011;6(8):e23151. Epub 2011 Aug 1.
Bachmann J, Raue A, Schilling M, Böhm ME, Kreutz C, Kaschek D, Busch H, Gretz N, Lehmann WD, Timmer J, Klingmüller U.
Division of labor by dual feedback regulators controls JAK2/STAT5 signaling over broad ligand range.
Mol Syst Biol. 2011 Jul 19;7:516. doi: 10.1038/msb.2011.50.
Transcription factors KLF1 and KLF2 positively regulate embryonic and fetal beta-globin genes through direct promoter binding.
Alhashem YN, Vinjamur DS, Basu M, Klingmüller U, Gaensler KM, Lloyd JA.
J Biol Chem. 2011 Jul 15;286(28):24819-27. Epub 2011 May 24.
The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice.
Castoldi M, Vujic Spasic M, Altamura S, Elmén J, Lindow M, Kiss J, Stolte J, Sparla R, D'Alessandro LA, Klingmüller U, Fleming RE, Longerich T, Gröne HJ, Benes V, Kauppinen S, Hentze MW, Muckenthaler MU.
J Clin Invest. 2011 Apr 1;121(4):1386-96.
One-source peptide/phosphopeptide standards for accurate phosphorylation degree determination.
Hahn B, Böhm M, Raia V, Zinn N, Möller P, Klingmüller U, Lehmann WD.
Proteomics. 2011 Feb;11(3):490-4. doi: 10.1002/pmic.201000569. Epub 2011 Jan 13.
Raia V, Schilling M, Böhm M, Hahn B, Kowarsch A, Raue A, Sticht C, Bohl S, Saile M, Möller P, Gretz N, Timmer J, Theis F, Lehmann WD, Lichter P, Klingmüller U.
Dynamic Mathematical Modeling of IL13-Induced Signaling in Hodgkin and Primary Mediastinal B-Cell Lymphoma Allows Prediction of Therapeutic Targets
Cancer Res, 71(3):693-704.
Abstract
Reprint (pdf)
Supplementary data (zip)
*Supplementary information
*SBML model file – MedB-1 model
*Data analyzed in the paper - MedB-1
*SBML model file – L1236 model
*Data analyzed in the paper – L1236
2010
Raue A, Becker V, Klingmüller U, Timmer J.
Identifiability and observability analysis for experimental design in nonlinear dynamical models.
Chaos. 2010 Dec;20(4):045105.
Theis FJ, Bohl S, Klingmüller U.
Theoretical analysis of time-to-peak responses in biological reaction networks.
Bull Math Biol in press. Published online 25 May 2010.
Becker V, Schilling M, Bachmann J, Baumann U, Raue A, Maiwald T, Timmer J, Klingmüller U.
Covering a broad dynamic range: Information processing at the Erythropoietin receptor.
Science. 2010 Jun 11;328(5984):1404-8. Epub 2010 May 20.
Abstract
Reprint
Supplementary information
SBML model files – core model
Data analyzed in the paper - Epo
SBML model files – auxiliary model
Data analyzed in the paper – SAv
Drogat B, Kalucka J, Gutiérrez L, Hammad H, Goossens S, Farhang Ghahremani M, Bartunkova S, Haigh K, Deswarte K, Nyabi O, Naessens M, Ferrara N, Klingmüller U, Lambrecht BN, Nagy A, Philipsen S, and Haigh JJ.
Vegf regulates embryonic erythroid development through Gata1 modulation. Blood, 116(12):2141-2151.
Pfeifer AC, Kaschek D, Bachmann J, Klingmüller U, and Timmer J.
Model-based extension of high-throughput to high-content data.
BMC Syst Biol, 4:106.
Stöhr K, Siegberg D, Ehrhard T, Lymperopoulos K, Öz S, Schulmeister S, Pfeifer AC, Bachmann J, Klingmüller U, Sourjik V, and Herten DP. (2010).
Quenched substrates for live-cell labeling of SNAP-tagged fusion proteins with improved fluorescent background.
Anal Chem, 82(19):8186-8193.
Maiwald T, Schneider A, Busch H, Sahle S, Gretz N, Weiss TS, Kummer U, and Klingmüller U.
Combining theoretical analysis and experimental data generation reveals IRF9 as a crucial factor for accelerating interferon α-induced early antiviral signalling.
FEBS J, 277(22):4741-4754.
Hahn B, Böhm M, Raia V, Zinn N, Möller P, Klingmüller U, and Lehmann WD.
One-Source Peptide/Phosphopeptide Standards for Accurate Phosphorylation Degree Determination.
Proteomics, in press.
Kowarsch A, Blöchl F, Bohl S, Saile M, Gretz N, Klingmüller U, and Theis F.
Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation.
BMC Bioinformatics, in press.
2009
Schilling M, Maiwald T, Hengl S, Winter D, Kreutz C, Kolch W, Lehmann WD, Timmer J, Klingmüller U.
Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions.
Mol Syst Biol. 2009;5:334.
Reprint
Supplementary information
SBML model file
Data analyzed in the paper
Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingmüller U, Timmer J.
Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood.
Bioinformatics. 2009 Aug 1;25(15):1923-9.
Pan C, Kumar C, Bohl S, Klingmüller U, Mann M.
Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type specific functions.
Mol Cell Proteomics. 2009 Mar;8(3):443-50. Epub 2008 Oct 23.
Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J, Cufer T, Ferrell J, Galas D, Gallahan D, Gatenby R, Goldbeter A, Hace N, Henney A, Hood L, Iyengar R, Jackson V, Kallioniemi O, Klingmüller U, Kolar P, Kolch W, Kyriakopoulou C, Laplace F, Lehrach H, Marcus F, Matrisian L, Nolan G, Pelkmans L, Potti A, Sander C, Seljak M, Singer D, Sorger P, Stunnenberg H, Superti-Furga G, Uhlen M, Vidal M, Weinstein J, Wigle D, Williams M, Wolkenhauer O, Zhivotovsky B, Zinovyev A, Zupan B.
Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008).
Mol Oncol. 2009 Feb;3(1):9-17.
2008
Becker V, Sengupta D, Ketteler R, Ullmann GM, Smith JC, Klingmüller U.
Packing density of the erythropoietin receptor transmembrane domain correlates with amplification of biological responses.
Biochemistry. 2008 Nov 11;47(45):11771-82. Epub 2008 Oct 15.
Korf U, Derdak S, Tresch A, Henjes F, Schumacher S, Schmidt C, Hahn B, Lehmann WD, Poustka A, Beissbarth T, Klingmüller U.
Quantitative protein microarrays for time-resolved measurements of protein phosphorylation.
Proteomics. 2008 Nov;8(21):4603-12.
Lemke U, Krones-Herzig A, Berriel Diaz M, Narvekar P, Ziegler A, Vegiopoulos A, Cato AC, Bohl S, Klingmüller U, Screaton RA, Müller-Decker K, Kersten S,Herzig S.
The glucocorticoid receptor controls hepatic dyslipidemia through Hes1.
Cell Metab. 2008 Sep;8(3):212-23.
Schilling M, Pfeifer AC, Bohl S, Klingmüller U.
Standardizing experimental protocols.
Curr Opin Biotechnol. 2008 Aug;19(4):354-9. Epub 2008 Jul 19. Review.
Grebien F, Kerenyi MA, Kovacic B, Kolbe T, Becker V, Dolznig H, Pfeffer K, Klingmüller U, Müller M, Beug H, Müllner EW, Moriggl R.
Stat5 activation enables erythropoiesis in the absence of EpoR and Jak2.
Blood. 2008 May 1;111(9):4511-22. Epub 2008 Jan 31.
Vera J, Bachmann J, Pfeifer AC, Becker V, Hormiga JA, Darias NV, Timmer J, Klingmüller U, Wolkenhauer O.
A systems biology approach to analyse amplification in the JAK2-STAT5 signalling pathway.
BMC Syst Biol. 2008 Apr 25;2:38.
Pfeifer AC, Timmer J, Klingmüller U.
Systems biology of JAK/STAT signalling.
Essays Biochem. 2008;45:109-20. Review.
2007
Maiwald T, Kreutz C, Pfeifer AC, Bohl S, Klingmüller U, Timmer J.
Dynamic pathway modeling: feasibility analysis and optimal experimental design.
Ann N Y Acad Sci. 2007 Dec;1115:212-20.
Maetens M, Doumont G, Clercq SD, Francoz S, Froment P, Bellefroid E, Klingmüller U, Lozano G, Marine JC.
Distinct roles of Mdm2 and Mdm4 in red cell production.
Blood. 2007 Mar 15;109(6):2630-3.
2006
Klingmüller U., Bauer A., Bohl S, P.J. Nickel, K. Breitkopf, S. Dooley, S. Zellmer, C. Kern, I. Merfort, T. Sparna, J. Donauer, G. Walz, M. Geyer, C. Kreutz, M. Hermes, F. Götschel, A. Hecht, D. Walter, L. Egger, K. Neubert, C. Borner, M. Brulport, W. Schormann, C. Sauer, F. Baumann, R. Preiss, S. MacNelly, P. Godoy, E. Wiercinska, L. Ciuclan, J. Edelmann, K. Zeilinger, M. Heinrich, U.M. Zanger, R. Gebhardt, T. Maiwald, R. Heinrich, J. Timmer, F. von Weizsäcker, and J.G. Hengstler
Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways.
IEE Proc. Syst-Biol. 2006; Syst-Biol. 2006; 153(6):433-447.
Dumitriu B, Patrick MR, Petschek JP, Cherukuri S, Klingmüller U, Fox PL, Lefebvre V.
Sox6 cell-autonomously stimulates erythroid cell survival, proliferation, and terminal maturation and is thereby an important enhancer of definitive erythropoiesis during mouse development.
Blood. 2006 Aug 15;108(4):1198-207.
Stuhlmann-Laeisz C, Lang S, Chalaris A, Krzysztof P, Enge S, Eichler J, Klingmüller U, Samuel M, Ernst M, Rose-John S, Scheller J.
Forced dimerization of gp130 leads to constitutive STAT3 activation, cytokine-independent growth, and blockade of differentiation of embryonic stem cells.
Mol Biol Cell. 2006 Jul;17(7):2986-95.
2005
Schilling M, Maiwald T, Bohl S, Kollmann M, Kreutz C, Timmer J, Klingmüller U.
Quantitative data generation for systems biology - the impact of randomisation, calibrators and normalisers.
IEE Proc. Syst-Biol. 2005; 152(4):193-200.
Schilling M, Maiwald T, Bohl S, Kollmann M, Kreutz C, Timmer J, Klingmüller U.
Computational processing and error reduction strategies for standardized quantitative data in biological networks.
FEBS J. 2005 Dec;272(24):6400-11.
2004
Zimmermann S, Glaser S, Ketteler R, Waller CF, Klingmüller U, Martens UM.
Effects of telomerase modulation in human hematopoietic progenitor cells.
Stem Cells. 2004;22(5):741-9.
Heinrich AC, Pelanda R, Klingmüller U.
A mouse model for visualization and conditional mutations in the erythroid lineage.
Blood. 2004 Aug 1;104(3):659-66.
Ruan W, Becker V, Klingmüller U, Langosch D.
The interface between self-assembling erythropoietin receptor transmembrane segments corresponds to a membrane-spanning leucine zipper.
J Biol Chem. 2004 Jan 30;279(5):3273-9.
Cohen J, Oren-Young L, Klingmüller U, Neumann D.
Protein tyrosine phosphatase 1B participates in the down-regulation of erythropoietin receptor signalling.
Biochem J. 2004 Jan 15;377(Pt 2):517-24.
2003
D. Faller, U. Klingmüller, J. Timmer.
Simulation methods for optimal experimental design in systems biology.
In press in Simulation: Trans. Soc. Modeling Computer Simulation.
T. G. Müller, I. Swameye, O. Sandra, U. Klingmüller, and J. Timmer.
Tests for cycling in a signalling pathway.
in press in Journal of the Royal Statistical Society: Series C (Applied Statistics).
J. Timmer, T. G. Müller, I. Swameye, O. Sandra, and U. Klingmüller.
Modeling the non-linear dynamics of cellular signal transduction.
in press in International Journal of Bifurcation and Chaos.
I. Swameye, T. G. Müller, J. Timmer, O. Sandra, and U. Klingmüller.
Identification of nucleocytoplasmic cycling as a remote sensor in cellular signalling by data-based dynamic modeling.
Proc. Natl. Acad. Sci. USA, 100, 1028-33.
2002
R. Ketteler, C. Moghraby, J. G. Hsiao, O. Sandra, H. F. Lodish and U. Klingmüller (2002).
The cytokine-inducible SH2 domain containing protein CIS negatively regulates signaling by promoting apoptosis in erythroid progenitor cells.
J. Biol. Chem., 278, 2654-60.
R. Ketteler, A. Heinrich, J. K. Offe, V. Becker, J. Cohen, D. Neumann, and U. Klingmüller.
A Functional GFP-Tagged Erythropoietin Receptor Despite Separation of JAK2 Binding Sites and Tyrosine Residues.
J. Biol. Chem., 277, 26547-26552.
R. Ketteler, S. Glaser, O. Sandra, U. M. Martens, and U. Klingmüller.
Enhanced transgene expression in primitive hematopoietic progenitor cells and embryonic stem cells efficiently transduced by optimized retroviral hybrid vectors .
Gene Therapy, 9, 477-487.
2001
K. F. Kubatzky, W. Ruan, R. Gurezka, J. Cohen, R. Ketteler, S. S. Watowich, D. Neumann, D. Langosch, and U. Klingmüller.
Self assembly of the transmembrane domain promotes signal transduction through the erythropoietin receptor.
Current Biology, 11, 110-115.
1997
U. Klingmüller, H. Wu, J. G. Hsiao, A. Toker, B. C. Duckworth, L. C. Cantley, and H. F. Lodish.
Identification of a novel pathway important for proliferation and differentiation of primary erythroid progenitors.
Proc. Natl. Acad. Sci. USA, 94, 3016-3021.
1996
U. Klingmüller, S. Bergelson, J. G. Hsiao, and H. F. Lodish.
Multiple tyrosine residues in the cytosolic domain of the erythropoietin receptor promote activation of STAT5.
Proc. Natl. Acad. Sci. USA, 93, 8324-8328.
1995
U. Klingmüller, U. Lorenz, L. C. Cantley, B. G. Neel, and H. F. Lodish.
Specific Recruitment of SH-PTP1 to the Erythropoietin Receptor Causes Inactivation of JAK2 and Termination of Proliferative Signals.
Cell 80. 729-738.
