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Publications of the IST/ISYS Sysbio Group

Journal Articles

[1]
Katja Bettenbrock, Sophia Fischer, Andreas Kremling, Knut Jahreis, Thomas Sauter, and Ernst-Dieter Gilles. A Quantitative Approach to Catabolite Repression in Escherichia coli. J Biol Chem, 281(5):2578–84, Feb 2006.
[2]
Holger Conzelmann, Julio Saez-Rodriguez, Thomas Sauter, Boris Kholodenko, and Ernst Gilles. A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. BMC Bioinformatics, 7(1):34, Jan 2006.
[3]
T. Eißing, F. Allgöwer, and E. Bullinger. Robustness properties of apoptosis models with respect to parameter variations and stochastic influences. IEE Proc. Syst. Biol., 152(4):221–228, 2005.
[4]
Haiping Hao, Daniel E Zak, Thomas Sauter, James Schwaber, and Babatunde A Ogunnaike. Modeling the VPAC2 activated cAMP/PKA signaling pathway: From receptor to circadian clock gene induction. Biophys J, Dec 2005.
[5]
H. Conzelmann, J. Saez-Rodriguez, T. Sauter, E. Bullinger, F. Allgöwer, and E. D. Gilles. Reduction of mathematical models of signal transduction networks: Simulation-based approach applied to EGF receptor signaling. IEE Systems Biology, 1(1):159 – 169, 2004.
[6]
T. Eissing, H. Conzelmann, E.D. Gilles, F. Allgöwer, E. Bullinger, and P. Scheurich. Bistability analyses of a caspase activation model for receptor-induced apoptosis. J. Biol. Chem., 279(35):36892–36897, 2004.
[7]
A. Kremling, S. Fischer, K. Gadkar, F.J. Doyle, T. Sauter, E. Bullinger, F. Allgöwer, and ED. Gilles. A benchmark for methods in reverse engineering and model discrimination: Problem formulation and solutions. Genome Res., 14(9):1773–1785, 2004.
[8]
A. Kremling, S. Fischer, T. Sauter, E. Bettenbrock, and E.D. Gilles. Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism. BioSystems, 73:57–71, 2004.
[9]
T. Sauter and E. Bullinger. Detailed mathematical modeling of metabolic and regulatory networks. BIOforum Europe, 2004(2):62–64, 2004.
[10]
T. Sauter and E.D. Gilles. Modeling and experimental validation of the signal transduction via the Escherichia coli sucrose phosphotransferase system. J. Biotechnol., 110:181–199, 2004.
[11]
Joachim W Schmid, Klaus Mauch, Matthias Reuss, Ernst D Gilles, and Andreas Kremling. Metabolic design based on a coupled gene expression-metabolic network model of tryptophan production in Escherichia coli. Metab Eng, 6(4):364–77, Oct 2004.
[12]
Jörg Stelling, Ernst Dieter Gilles, and Francis J Doyle. Robustness properties of circadian clock architectures. Proc Natl Acad Sci U S A, 101(36):13210–5, Sep 2004.
[13]
M. Ederer, T. Sauter, E. Bullinger, E.D. Gilles, and F. Allgöwer. An approach for dividing models of biological reaction networks into functional units. Simulation: Trans. Society for Modeling and Simulation International, 79(12):703–716, 2003.
[14]
B. Schoeberl, C. Eichler-Jonsson, E. D. Gilles, and G. Müller. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat. Biotechnol., 20(4):370–375, 2002.

Conference Proceedings

[1]
C. Cimatoribus, T. Eißing, N. Elvassore, F. Allgöwer, and E. Bullinger. Model discrimination tools in apoptosis. In 1st Foundations of Systems Biology in Engineering, pages 197–200, Santa Barbara, CA, 2005.
[2]
T. Eißing, C. Cimatoribus, F. Allgöwer, P. Scheurich, and E. Bullinger. System properties of the core reactions of apoptosis. In 1st FEBS Advanced Lecture Course Systems Biology, page 164, Gosau, Austria, 2005.
[3]
T. Sauter, J. Saez-Rodriguez, H. Conzelmann, T. Eissing, E. D. Gilles, and P. Scheurich. Cellect, project c4: Mathematical modeling of cellular regulation networks of apoptosis and cell proliferation. In 2nd BMBF Colloquium 'Proteomics', Potsdam, Germany, 2005. May 30 - Jun 1.
[4]
T. Sauter, M. Schliemann, T. Eissing, E. Bullinger, E. D. Gilles, F. Allgöwer, and P. Scheurich. Mathematical modeling of tnf induced apoptotic and anti-apoptotic crosstalk in mammalian cells. In 6th International Conference on Systems Biology, Boston, MA, 2005.
[5]
T. Eißing, H. Conzelmann, E. D. Gilles, F. Allgöwer, E. Bullinger, and P. Scheurich. Mathematical modeling and system analysis of caspase activation. In International Workshop on Theoretical Biophysics, page 11, Hiddensee Island, Germany, 2004.
[6]
T. Eißing, H. Conzelmann, E. D. Gilles, F. Allgöwer, E. Bullinger, and P. Scheurich. Mathematical modeling applied to caspase activation reveals a requirement for additional control. In 5th International Conference on Systems Biology, page 207, Heidelberg, Germany, 2004.
[7]
T. Eißing, H. Conzelmann, G. Zimmermann, M. Branschädel, C. Cimatoribus, T. Sauter, E. D. Gilles, F. Allgöwer, E. Bullinger, and P. Scheurich. Mathematical modeling applied to caspase activation downstream of death receptors: A missing guardian for caspase 8. In 2nd International Symposium of the SFB 495, Hohenheim, Germany, 2004.
[8]
E. Bullinger, T. Sauter, F. Allgöwer, and E.D. Gilles. On deriving a hybrid model for carbohydrate uptake in Escherichia Coli. In 15th IFAC World Congress, Barcelona, Spain, 2002. Paper Number 1231.
[9]
B. Schoeberl, T. Eißing, M. Fotin, E. D. Gilles, and P. Scheurich. A mathematical model of tnf receptor interaction. In 1st International Symposium of the SFB 495, Stuttgart, Germany, 2002.
[10]
A. Kremling, T. Sauter, E. Bullinger, M. Ederer, F. Allgöwer, and E.D. Gilles. Perspectives in biosystems engineering. In 2nd Int. Conf. Systems Biology, Pasadena, CA, USA, pages 282–290, 2001.
[11]
E. Bullinger, C.W. Frei, T.J. Sieber, A.H. Glattfelder, F. Allgöwer, and A.M. Zbinden. Adaptive λ-tracking in anesthesia. In E. Carson and E. Salzsieder, editors, Proc. of the 4th IFAC Symposium Modelling and Control in Biomedical Systems, pages 181–186, Greifswald, 2000.

Other

[1]
K. Bettenbrock, T. Sauter, A. Kremling, S. Fischer, and E.D. Gilles. Biochemical analysis of the crp-modulon of e. coli with regard to model reduction. 2nd International E. Coli Alliance Conference on Systems Biology, Banff, June 18-22, 2004.
[2]
H. Hao, D. Zak, T. Sauter, J. Schwaber, and B. Ogunnaike. VIP signal transduction pathway modeling in SCN 2.2 cells. AIChE Annual Meeting, Nov 7-12, Austin, TX, 2004.
[3]
T. Sauter, R. Vadigepalli, H. Hao, D. Zak, B. Ogunnaike, and J. Schwaber. Computational modeling of Angiotensin II and VIP signaling via G-protein coupled receptors in neurons. Biotechnology 2004, Santiago, Chile, 2004.
[4]
R. Vadigepalli, T. Sauter, H. Hao, and J. Schwaber. Mathematical modeling of neuronal response to neuropeptides: Angiotensin II signaling via G-protein coupled receptor. AIChE Annual Meeting, Austin, TX, 2004.
[5]
H. Conzelmann, T. Sauter, E. Bullinger, F. Allgöwer, and E.D. Gilles. Modellreduktion und Analyse des metabolen Netzwerks der Zuckeraufnahme in Escherichia coli. Dechema Jahrestagung, München, 2003.
[6]
H. Hao, T. Sauter, D. Zak, J. Schwaber, and B. Ogunnaike. VIP signal transduction pathway modeling in SCN 2.2 cells. Greater Philadelphia Bioinformatics Alliance retreat, Haverford, PA, 2003.
[7]
T. Sauter, R. Vadigepalli, H. Hao, and J. Schwaber. Modeling of Angiotensin II responses via AT1 in neurons. Greater Philadelphia Bioinformatics Alliance retreat, Haverford, PA, 2003.
[8]
E. Bullinger, T. Sauter, B. Schoeberl, F. Allgöwer, and E.D. Gilles. Model reduction in biological systems applied to a MAP kinase model. AIChE Annual Meeting, Indianapolis, IN, 2002.
[9]
A. Haubelt, E. Bullinger, T. Sauter, F. Allgöwer, and E.D. Gilles. Systems biology - a glossary from two perspectives. 3rd Int. Conf. Systems Biology, Stockholm, Sweden, December 2002.
[10]
A. Kremling, S. Fischer, F.J. Doyle, K. Gadkar, T. Sauter, E. Bullinger, F. Allgöwer, and E.D. Gilles. A benchmark for methods in reverse engineering and model discrimination: Problem formulation and solutions. 3rd Int. Conf. Systems Biology, Stockholm, Sweden, December 2002.
[11]
T. Sauter, E. Bullinger, F. Allgöwer, and E.D. Gilles. Analysis of the control structure of the PTS and glycolysis pathway in Escherichia coli. SIAM Meeting, Washington D.C., 2002.
[12]
T. Sauter and E.D. Gilles. Measurements and modeling of the dynamic sucrose response of Escherichia coli. 1st International MTBio Workshop on Function and Regulation of Cellular Systems, Dresden, 2001.
[13]
T. Sauter and E.D. Gilles. Signaltransduction in Escherichia coli via the phosphotransferase system - modeling and experimental validation. 10th European Congress on Biotechnology, Madrid, 2001.
[14]
T. Sauter, E. Bullinger, F. Allgöwer, and E.D. Gilles. Hypothesis testing in Escherichia coli using mathematical modeling. Workshop: Complexity in Biosystems: Innovative Approaches at the Interface of Experimental and Computational Modeling, DIMACS, Rutgers University, Picataway, NJ, April 2001.
[15]
T. Sauter and E.D. Gilles. Calculating steady state characteristics of the bacterial phosphotransferase system for describing its in vivo functionality. Biotechnology 2000, Berlin, 2000.
[16]
T. Sauter and E.D. Gilles. Simulation studies on the bacterial phosphotransferase system and experimental validation. 4th Int. Congress on Biochemical Engineering, Stuttgart, 2000.

Student Projects

Master theses and student projects supervised by members of the Systems Biology group.
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