Publications until 2020

Thoene S, Mandal T, Vegi NM, Quintanilla-Martinez L, Rösler R, Wiese S, Metzeler KH, Herold T, Haferlach T, Döhner K, Döhner H, Schwarzmüller L, Klingmüller U, Buske C, Rawat VPS, Feuring-Buske M. The ParaHox gene Cdx4 induces acute erythroid leukemia in mice. Blood Adv. 2019 Nov 26;3(22):3729-3739.

Lucarelli P, Schilling M, Kreutz C, Vlasov A, Boehm ME, Iwamoto N, Steiert B, Lattermann S, Wäsch M, Stepath M, Matter MS, Heikenwälder M, Hoffmann K, Deharde D, Damm G, Seehofer D, Muciek M, Gretz N, Lehmann WD, Timmer J, Klingmüller U. Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression. Cell Syst. 2018; 6(1):75-89.e11.

Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O. Whither systems medicine? Exp Mol Med. 2018; 50(3):e453.

Oppelt A, Kaschek D, Huppelschoten S, Sison-Young R, Zhang F, Buck-Wiese M, Herrmann F, Malkusch S, Krüger CL, Meub M, Merkt B, Zimmermann L, Schofield A, Jones RP, Malik H, Schilling M, Heilemann M, van de Water B, Goldring CE, Park BK, Timmer J, Klingmüller U. Model-based identification of TNFα-induced IKKβ-mediated and IκBα-mediated regulation of NFκB signal transduction as a tool to quantify the impact of drug-induced liver injury compounds. NPJ Syst Biol Appl. 2018; 4:23.

Dvornikov D, Schneider MA, Ohse S, Szczygieł M, Titkova I, Rosenblatt M, Muley T, Warth A, Herth FJ, Dienemann H, Thomas M, Timmer J, Schilling M, Busch H, Boerries M, Meister M, Klingmüller U. Expression ratio of the TGFβ-inducible gene MYO10 is prognostic for overall survival of squamous cell lung cancer patients and predicts chemotherapy response. Sci Rep. 2018; 8(1):9517.

Melnik S, Dvornikov D, Müller-Decker K, Depner S, Stannek P, Meister M, Warth A, Thomas M, Muley T, Risch A, Plass C, Klingmüller U, Niehrs C, Glinka A. Cancer cell specific inhibition of Wnt/β-catenin signaling by forced intracellular acidification. Cell Discov. 2018; 4:37.

Sobotta S, Raue A, Huang X, Vanlier J, Jünger A, Bohl S, Albrecht U, Hahnel MJ, Wolf S, Mueller NS, D'Alessandro LA, Mueller-Bohl S, Boehm ME, Lucarelli P, Bonefas S, Damm G, Seehofer D, Lehmann WD, Rose-John S, van der Hoeven F, GretzN, Theis FJ, Ehlting C, Bode JG, Timmer J, Schilling M, Klingmüller U. Model Based Targeting of IL-6-Induced Inflammatory Responses in Cultured Primary Hepatocytes to Improve Application of the JAK Inhibitor Ruxolitinib. Front Physiol. 2017;8:775.

Kallenberger SM, Unger AL, Legewie S, Lymperopoulos K, Klingmüller U, Eils R, Herten DP. Correlated receptor transport processes buffer single-cell heterogeneity. PLoS Comput Biol. 2017;13(9):e1005779.

Adlung L, Kar S, Wagner MC, She B, Chakraborty S, Bao J, Lattermann S, Boerries M, Busch H, Timmer J, Schilling M, Höfer T, Klingmüller U: Protein abundance of AKT and ERK pathway components governs cell-type-specific regulation of proliferation. Molecular Systems Biology 13 (1), 904, 2017.

Albrecht M, Stichel D, Müller BF, Merkle R, Sticht C, Gretz N, Klingmüller U+, Breuhahn K, Matthäus F: TTCA:An R package for the identification of differentially expressed genes in time course microarray data. BMC Bioinformatics 18 (1), 33, 2017.

Schneider MA, Christopoulos P, Muley T, Warth A, Klingmueller U, Thomas M, Herth FJ, Dienemann H, Mueller NS, Theis F, Meister M: AURKA, DLGAP5, TPX2, KIF11 and CKAP5: Five specific mitosis-associated genes correlate with poor prognosis for non-small cell lung cancer patients. International Journal of Oncology 50 (2), 365-372, 2017.

Breitkopf-Heinlein, K., Meyer, C., Koenig, C., Gaitantzi, H., Addante, A., Thomas, M., Wiercinska, E., Cai, C., Li, Q., Wan, F., Hellerbrand, C., Valous, N.A., Hahnel, M., Ehlting, C., Bode, J.G., Mueller-Bohl, S., Klingmüller, U., Altenoder, J., Ilkavets, I., Goumans, M.J, Hawinkels, L.J., Lee, S.J., Wieland, M., Mogler, C., Ebert, M.P., Herrera, B., Augustin, H., Sanchez, A., Dooley, S., Ten Dijke, P. BMP-9 interferes with liver regeneration and promotes liver fibrosis. Gut (2017), 66(5): 939-954.

Kulawik, A., Engesser, R., Ehlting, C., Raue, A., Albrecht, U., Hahn, B., Lehmann, W.D., Gaestel, M., Klingmüller, U., Haussinger, D., Timmer, J., Bode, J.G. IL-1 beta-induced and p38(MAPK)-dependent activation of the mitogen-activated protein kinase-activated protein kinase 2 (MK2) in hepatocytes: Signal transduction with robust and concentration-independent signal amplification. Journal of Biological Chemistry (2017), 292(15), 6291-6301.

Lucarelli P, Schilling M, Kreutz C, Vlasov A, Boehm ME, Iwamoto N, Steiert B, Lattermann S, Wäsch M, Stepath M, Matter MS, Heikenwälder M, Hoffmann K, Deharde D, Damm G, Seehofer D, Muciek M, Gretz N, Lehmann WD, Timmer J, Klingmüller U. Resolving the Combinatorial Complexity of Smad Protein Complex Formation and Its Link to Gene Expression. Cell Syst. 2018; 6(1):75-89.e11.

Iwamoto, N., D’Alessandro, L.A., Depner, S., Hahn, B., Kramer, B.A., Lucarelli, P., Vlasov, A., Stepath, M., Böhm, M.E., Deharde, D., Damm, G., Seehofer, D., Lehmann, W.D., Klingmüller, U., Schilling, M. Context-specific flow through the MEK/ERK module produces cell- and ligand-specific patterns of ERK single and double phosphorylation. Science Signaling, 9(413), ra13, 2016.

Marwitz, S., Depner, S., Dvornikov, D., Merkle, R., Szczygiel, M., Müller-Decker, K., Lucarelli, P., Wäsch, M., Mairbäurl, H., Rabe, K.F., Kugler, C., Vollmer, E., Reck, M., Scheufele, S., Kröger, M., Ammerpohl, O., Siebert, R., Goldmann, T., Klingmüller, U. Downregulation of the TGF-ß pseudoreceptor BAMBI in non-small cell lung cancer enhances TGF-ß signaling and invasion. Cancer Res, May 17, 2016.

Merkle R, Steiert B, Salopiata F, Depner S, Raue A, Iwamoto N, Schelker M, Hass H, Waesch M, Boehm ME, Muecke O, Lipka DB, Plass C, Lehmann WD, Kreutz C, Timmer J, Schilling M, Klingmueller U: Identification of Cell Type-Specific Differences in Erythropoietin Receptor Signaling in Primary Erythroid and Lung Cancer Cells. PloS Computational Biology 12 (8), e1005049, 2016.

Stichel D, Middleton AM, Müller BF, Depner S, Klingmüller U, Breuhahn K, Matthäus F: An individual-based model for collective cancer cell migration explains speed dynamics and phenotype variability in response to growth factors. NPJ Systems Biology and Applications 2016.

Ucar O, Li K, Dvornikov D, Kreutz C, Timmer J, Matt S, Brenner L, Smedley C, Travis MA, Hofmann TG, Klingmueller U, Kyewski B: A Thymic Epithelial Stem Cell Pool Persists throughout Ontogeny and Is Modulated by TGF-beta. Cell Reports 17 (2), 448-457, 2016.

Kuchenov D, Laketa V, Stein F, Salopiata F, Klingmueller U, Schultz C: High-Content Imaging Platform for Profiling Intracellular Signaling Network Activity in Living Cells. Cell Chemical Biology 23 (12), 1550-1559, 2016.

Doleschel, D., Rix, A., Arns, S., Palmowski, K., Gremse, F., Merkle, R., Salopiata, F., Klingmueller, U., Jarsch, M., Kiessling, F., Lederle, W. Erythropoietin improves the accumulation and therapeutic effects of carboplatin by enhancing tumor vascularization and perfusion. Theranostics 5(8),905-918, 2015.

D'Alessandro LA, Samaga R, Maiwald T, Rho SH, Bonefas S, Raue A, Iwamoto N, Kienast A, Waldow K, Meyer R, Schilling M, Timmer J, Klamt S, Klingmüller U. Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. PLoS Computational Biology. 2015 Apr 23;11(4):e1004192.

Konstantinidis, D. G., Giger, K. M., Risinger, M, Pushkaran, S., Zhou, P., Dexheimer, P., Yerneni, S., Andreassen, P., Klingmüller, U., Palis, J., Zheng, Y., Kalfa, T. A. Cytokinesis failure in RhoA-deficient mouse erythroblasts involves actomysin and midbody dysregulation and triggers p53 activation. Blood 126(12), 1473-1482, 2015.

Mueller S, Huard J, Waldow K, Huang X, D'Alessandro LA, Bohl S, Börner K, Grimm D, Klamt S, Klingmüller U, Schilling M. T160-phosphorylated CDK2 defines threshold for HGF-dependent proliferation in primary hepatocytes. Molecular Systems Biology. 2015 Mar 14;11:795.

Raue, A., Steiert, B., Schelker, M, Kreutz, C., Maiwald, T., Hass, H., Vanlier, J., Tönsing, C., Adlung, L., Engesser, R., Mader, W., Heinemann, T., Hasenauer, J., Schilling, M., Höfer, T., Klipp, E., Theis, F., Klingmüller, U., Schöberl, B., Timmer, J. Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics 31(21), 3558-3560, 2015.

Adlung L: Global collaboration. Science 346 (6205), 49-49, 2014.

Boehm ME, Adlung L, Schilling M, Roth S, Klingmüller U, Lehmann WD: Identification of Isoform-Specific Dynamics in Phosphorylation-Dependent STAT5 Dimerization by Quantitative Mass Spectrometry and Mathematical Modeling. Journal of Proteome Research 13 (12), 5685-5694, 2014.

Boehm ME, Hahn B, Lehmann WD: One-source peptide/phosphopeptide ratio standards for accurate and site-specific determination of the degree of phosphorylation. Methods in Molecular Biology 1156, 367-378, 2014.

Conrad E, Resch TK, Gogesch P, Kalinke U, Bechmann I, Bogdan C, Waibler Z: Protection against RNA-induced liver damage by myeloid cells requires type I interferon and IL-1 receptor antagonist in mice. Hepatology 59 (4), 1555-1563, 2014.

D'Alessandro LA, Hoehme S, Henney A, Drasdo D, Klingmüller U: Unraveling liver complexity from molecular to organ level: Challenges and perspectives. Progress in Biophysics and Molecular Biology, Nov 26, 2014.

Drasdo D, Bode J, Dahmen U, Dirsch O, Dooley S, Gebhardt R, Ghallab A, Godoy P, Haussinger D, Hammad S, Holzhutter HG, Klingmüller U, Kuepfer L, Timmer J, Zerial M, Hengstler J: The virtual liver: state of the art and future perspectives. Archives of Toxicology 88 (12), 2071-2075, 2014.

Feng S, Laketa V, Stein F, Rutkowska A, MacNamara A, Depner S, Klingmüller U, Saez-Rodriguez J, Schultz C: A rapidly reversible chemical dimerizer system to study lipid signalling in living cells. Angewandte Chemie - International Edition 53 (26), 6720-6723, 2014.

Mleczko-Sanecka K, Roche F, da Silva AR, Call D,  D'Alessio F, Ragab A, Lapinski PE, Ummanni R, Korf U, Oakes C, Damm G, D'Alessandro LA, Klingmüller U, King PD, Boutros M, Hentze MW, Muckenthaler MU: Unbiased RNAi screen for hepcidin regulators links hepcidin suppression to proliferative Ras/RAF and nutrient-dependent mTOR signaling. Blood 123 (10), 1574-1585, 2014.

Usenko, T., Chan, G., Torlakovic, E., Klingmüller, U., Neel, B. G. Leukemogenic Ptpn11 allele causes defective erythropoiesis in mice. PLoS One 9(10), e109682. 2014.

Esteghamat F, Gillemans N, Bilic I, van den Akker E, Cantu I, van Gent T, Klingmüller U, van Lom K, von Lindern M, Grosveld F, Bryn van Dijk T, Busslinger M, and Philipsen S: Erythropoiesis and globin switching in compound Klf1::Bcl11a mutant mice. Blood 121 (13), 2553-2562, 2013.

D'Alessandro LA, Meyer R, Klingmüller U. Hepatocellular carcinoma: a systems biology perspective. Front Physiol 4, 28, 2013.

Gutschalk CM, Yanamandra AK, Linde N, Meides A, Depner S, and Mueller MM: GM-CSF enhances tumor invasion by elevated MMP-2, -9, and -26 expression. Cancer Med 2 (2), 117-129, 2013.

Hahn B, D'Alessandro LA, Depner S, Waldow K, Böhm ME, Bachmann J, Schilling M, Klingmüller U, and Lehmann WD: Cellular ERK phospho-form profiles with conserved preference for a switch-like pattern. J Proteome Res 12 (2), 637-646, 2013.

Hug S, Raue A, Hasenauer J, Bachmann J, Klingmüller U, Timmer J, Theis FJ. High-dimensional Bayesian parameter estimation: Case study for a model of JAK2/STAT5 signaling. Math Biosci. 246 (2), 293-304, 2013.

Kuhns S, Schmidt KN, Reymann J, Gilbert DF, Neuner A, Hub B, Carvalho R, Wiedemann P, Zentgraf H, Erfle H, Klingmüller U, Boutros M, and Pereira G: The microtubule affinity regulating kinase MARK4 promotes axoneme extension during early ciliogenesis. J Cell Biol 200 (4), 505-522, 2013.

Raue A, Schilling M, Bachmann J, Matteson A, Schelker M, Kaschek D, Hug S, Kreutz C, Harms BD, Theis FJ, Klingmüller U, Timmer J: Lessons learned from quantitative dynamical modeling in systems biology. PLoS One 8 (9), e74335, 2013.

Shi L, Jong L, Wittig U, Lucarelli P, Stepath M, Mueller S, D'Alessandro LA, Klingmüller U, and Müller W: Excemplify: a flexible template based solution, parsing and managing data in spreadsheets for experimentalists. J Integr Bioinform 10 (2), 220, 2013.

Bachmann J, Raue A, Schilling M, Becker V, Timmer J, Klingmüller U: Predictive mathematical models of cancer signalling pathways. Journal of Internal Medicine 271 (2), 155-165, 2012.

Becker V, Timmer J, Klingmüller U: Receptor dynamics in signaling. Advances in Experimental Medicine and Biology 736, 313-323, 2012.

Benesova K, Vujic Spasic M, Schaefer SM, Stolte J, Baehr-Ivacevic T, Waldow K, Zhou Z, Klingmüller U, Benes V, Mall MA, Muckenthaler MU: Hfe deficiency impairs pulmonary neutrophil recruitment in response to inflammation. PLoS ONE 7 (6), e39363, 2012.

Bochtler,T., Kirsch,M., Maier,B., Bachmann,J., Klingmüller,U., Anderhub,S., Ho,A.D., Kraemer,A.: Centrosomal targeting of tyrosine kinase activity does not enhance oncogenicity in chronic myeloproliferative disorders. Leukemia 26 (4), 728-735, 2012.

Claus, J., Friedmann, E., Klingmueller, U., Rannacher, R., Szekeres, T.: Spatial aspects in the SMAD signaling pathway. Journal of Mathematical Biology , 2012.

Depner S, Lederle W, Gutschalk C, Linde N, Zajonz A, and Mueller MM: Cell type specific interleukin-6 induced responses in tumor keratinocytes and stromal fibroblasts are essential for invasive growth. Int J Cancer 2012.

Doleschel D, Mundigl O, Wessner A, Gremse F, Bachmann J, Rodriguez A, Klingmüller U, Jarsch M, Kiessling F, Lederle W: Targeted Near-Infrared Imaging of the Erythropoietin Receptor in Human Lung Cancer Xenografts. Journal of Nuclear Medicine 53 (2), 304-311, 2012.

Huard J, Mueller S, Gilles ED, Klingmüller U, Klamt: An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS Journal 279 (18), 3290-3313, 2012.

Linde N, Lederle W, Depner S, van Rooijen N, Gutschalk CM, Mueller MM: Vascular endothelial growth factor-induced skin carcinogenesis depends on recruitment and alternative activation of macrophages. Journal of Pathology 227 (1), 17-28, 2012. [Version-Id: 31404; Published-Id: 31383; Kst: A101, B200]

Maiwald T, Blumberg J, Raue A, Hengl S, Schilling M, Sy SK, Becker V, Klingmueller U, Timmer J: In silico labeling reveals the time-dependent label half-life and transit-time in dynamical systems. BMC Systems Biology 6, 13, 2012.

Meyer,R., D'Alessandro,LA., Kar,S., Kramer,B., She,B., Kaschek,D., Hahn,B., Wrangborg,D., Karlsson,J., Kvarnstroem,M., Jirstrand,M., Lehmann,WD., Timmer,J., Höfer,T., Klingmüller,U.: Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration. Frontiers in Physiology 3, 451, 2012.

Pinna F, Sahle S, Beuke K, Bissinger M, Tuncay S, D'Alessandro LA, Gauges R, Raue A, Timmer J, Klingmüller U, Schirmacher P, Kummer U, and Breuhahn K: A Systems Biology Study on NFkappaB Signaling in Primary Mouse Hepatocytes. Front Physiol 3 466, 2012.

Schilling M, Klingmüller U: Mathematical modeling of hematological malignancies. Frontiers in Bioscience / Elite 1 (4), 1648-1653, 2012.

Schneider A, Klingmueller U, Schilling M: Short-term information processing, long-term responses: Insights by mathematical modeling of signal transduction: Early activation dynamics of key signaling mediators can be predictive for cell fate decisions. BioEssays 34 (7), 542-550, 2012.

Wegner, K, Bachmann, A, Schad, J-U, Lucarelli, P, Sahle, S, Nickel, P, Meyer, C, Klingmuüller, U, Dooley, S, Kummer, U: Dynamics and feedback loops in the transforming growth factor beta signaling pathway. Biophysical Chemistry 162, 22-34, 2012.

Wiechert L, Nemeth J, Pusterla T, Bauer C, De Ponti A, Manthey S, Marhenke S, Vogel A, Klingmüller U, Hess J, and Angel P: Hepatocyte-specific S100a8 and S100a9 transgene expression in mice causes Cxcl1 induction and systemic neutrophil enrichment. Cell Commun Signal 10 (1), 40, 2012.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.