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