Publication list for the IST systems biology group

For the most up-to-date information on IST publications in systems biology, go to the IST publication database. The lists below are compiled from the database on a more or less regular basis.

Journal publications and book chapter

• T. Eissing, M. Chaves, and F. Allgöwer.
  Live and let die–a systems biology view on cell death.
  Computers and Chemical Engineering, 33:583–589, 2009.
• M. Lang, S. Waldherr, and F. Allgöwer.
  Amplitude distribution of stochastic oscillations in biochemical networks due to intrinsic noise.
  PMC Biophysics, 2:10, 2009.
• S. Waldherr and F. Allgöwer.
  Searching bifurcations in high-dimensional parameter space via a feedback loop breaking approach.
  International Journal of Systems Science, 40(7):769–782, 2009.
• M. Chaves, T. Eissing, and F. Allgöwer.
  Bistable biological systems: A characterization through local compact input-to-state stability.
  IEEE Trans. Automat. Control, 53:87–100, 2008.
• Solvey Maldonado, Rolf Findeisen, and Frank Allgöwer.
  Describing force-induced bone groth and adaptation by a mathematical model.
  J. Musculoskel. Neuronal Interact., 8(1):15–17, March 2008.
• Solvey Maldonado, Rolf Findeisen, and Frank Allgöwer.
  Understanding the process of force-induced bone growth and adaptation through a mathematical model.
  Bone, 42:S61, March 2008.
• S. Waldherr, T. Eissing, and F. Allgöwer.
  Rückkopplungen im Leben und Sterben einer Zelle: Ansätze zur systemtheoretischen Analyse.
  at – Automatisierungstechnik, 56:233–240, 2008.
• T. Eißing, S. Waldherr, F. Allgöwer, P. Scheurich, and E. Bullinger.
  Response to bistability in apoptosis: Roles of Bax, Bcl-2, and mitochondrial permeability transition pores.
  Biophysical Journal, 92:3332–34, 2007.
• T. Eißing, S. Waldherr, F. Allgöwer, P. Scheurich, and E. Bullinger.
  Steady state and (bi-) stability evaluation of simple protease signalling networks.
  BioSystems, 90(3):591–601, December 2007.
• M. Chaves, E. D. Sontag, and R. Albert.
  Methods of robustness analysis for boolean models of gene control networks.
  IEE Systems Biology, 153(4):154–167, July 2006.
• T. Eißing, F. Allgöwer, and E. Bullinger.
  Robustness properties of apoptosis models with respect to parameter variations and stochastic influences.
  IEE Systems Biology, 152(4):221–228, 2005.
• 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.
• 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, August 2004.
• A. Kremling, S. Fischer, F.J. Doyle III, 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.
  Genome Research, 14(9):1773–1785, 2004.
• T. Sauter and E. Bullinger.
  Detailed mathematical modeling of metabolic and regulatory networks.
  BIOforum Europe, 2004(2):62–64, 2004.
• 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.

Conference proceedings

• C. Breindl and F. Allgöwer.
  Verification of multistability in gene regulation networks: A combinatorial approach.
  In Proc. 48th IEEE Conf. Decision and Control (CDC), pages 5637–5642, 2009.
• C. Breindl, S. Waldherr, A Hausser, and F. Allgöwer.
  Modeling cofilin mediated regulation of cell migration as a biochemical two-input switch.
  In Proc. of the 3rd Foundations of Systems Biology in Engineering (FOSBE), pages 60–63, 2009.
• J. Hasenauer, P. Rumschinski, S. Waldherr, S. Borchers, F. Allgöwer, and R. Findeisen.
  Guaranteed steady-state bounds for uncertain chemical processes.
  In Proceedings of the International Symposium on Advanced Control of Chemical Processes, pages 674–679, July 2009.
• S. Maldonado, F. Allgöwer, and R. Findeisen.
  Global sensitivity analysis of force-induced bone growth and adaptation using semidefinite programming.
  In Proc. of the 3rd Foundations of Systems Biology in Engineering (FOSBE), pages 141–144, 2009.
• M. A. Müller, S. Waldherr, and F. Allgöwer.
  The transcritical bifurcation in absolutely stable feedback systems.
  In Proc. 10th Europ. Contr. Conf. (ECC), pages 2146–2151, 2009.
• S. Waldherr, F. Allgöwer, and E. W. Jacobsen.
  Kinetic perturbations as robustness analysis tool for biochemical reaction networks.
  In Proc. 48th IEEE Conf. Decision and Control (CDC), pages 4572–4577, 2009.
• S. Waldherr, J. Hasenauer, and F. Allgöwer.
  Estimation of biochemical network parameter distributions in cell populations.
  In Proc. of the 15th IFAC Symp. Syst. Ident. (SYSID), pages 1265–1270, 2009.
• S. Waldherr, T. Eissing, and F. Allgöwer.
  Analysis of feedback mechanisms in cell-biological systems.
  In Proc.of the 17th IFAC World Congress, Seoul, Korea, pages 15861–15866, 2008.
• S. Waldherr, R. Findeisen, and F. Allgöwer.
  Global sensitivity analysis of biochemical reaction networks via semidefinite programming.
  In Proc.of the 17th IFAC World Congress, Seoul, Korea, pages 9701–9706, 2008.
• Solvey Maldonado, Rolf Findeisen, and Frank Allgöwer.
  Phenomenological mathematical modeling and analysis of force-induced bone growth and adaptation.
  In Proc. of 2nd. Foundations of Systems Biology in Engineering, pages 147–152, September 2007.
• S. Waldherr and F. Allgöwer.
  A feedback approach to bifurcation analysis in biochemical networks with many parameters.
  In Proc. of the 2nd Foundations of Systems Biology in Engineering (FOSBE), pages 479–484, 2007.
• S. Waldherr, T. Eissing, M. Chaves, and F. Allgöwer.
  Bistability preserving model reduction in apoptosis.
  In Proc. of the 10th IFAC Comp. Appl. Biotechn., pages 327–332, Cancun, Mexico, 2007.
• S. Borchers, S. Maldonado, R. Findeisen, and F. Allgöwer.
  Modeling the bone remodeling cycle due to mechanical force.
  In Agostino G. Bruzzone, Antoni Guasch, Miquel Angel Piera, and Jerzy Rozenblit, editors, International Mediterranean Modelling Conference 2006. 2nd European Modeling and Simulation Symposium (EMSS2006), Barcelona, Spain, pages 385–394, Barcelona, Spain, 2006. ISBN: 84-690-0726-2.
• E. Bullinger, R. Findeisen, D. Kalamatianos, and P. Wellstead.
  System and control theory allows to further understanding of biological signal transduction. 2006. Proceedings of Workshop CNRS-NSF Biology and control theory: current challenges, Toulouse, France.
• M. Chaves.
  Stability of rate-controlled zero-deficiency networks.
  In Proc. 45th IEEE Conf. Decision and Control (CDC), pages 5766–5771, Dec. 2006.
• M. Chaves, T. Eißing, and F. Allgöwer.
  Identifying mechanisms for bistability in an apoptosis network.
  In Réseaux d'Interactions: Analyse, Modélisation et Simulation (RIAMS'06), 2006.
• M. Chaves, E.D. Sontag, and R. Albert.
  Structure and timescale analysis in genetic regulatory networks.
  In Proc. 45th IEEE Conf. Decision and Control (CDC), pages 2358–2363, Dec. 2006.
• T. Eißing, S. Waldherr, E. Bullinger, C. Gondro, O. Sawodny, F. Allgöwer, P. Scheurich, and T. Sauter.
  Sensitivity analysis of programmed cell death and implications for crosstalk phenomena during Tumor Necrosis Factor stimulation.
  In IEEE Conference on Control Applications (CCA), Munich, Germany, pages 1746–52, Munich, Germany, 2006.
• M. Farina, R. Findeisen, E. Bullinger, S. Bittanti, F. Allgöwer, and P. Wellstead.
  Results towards identifiability properties of biochemical reaction networks.
  In Proc. 45th IEEE Conf. Decision and Control (CDC), pages 2104–2109, San Diego, CA, 2006.
• S Maldonado, S. Borchers, R. Findeisen, and F. Allgöwer.
  Mathematical modeling and analysis of force induced bone growth.
  In Proc. 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC06), pages 3154–3157, New York, NY, 2006.
• S. Maldonado, S. Borchers, R. Findeisen, and F. Allgöwer.
  Modeling bone adaptation and remodeling initiated by mechanical stimuli.
  In Agostino G. Bruzzone, Antoni Guasch, Miquel Angel Piera, and Jerzy Rozenblit, editors, International Mediterranean Modelling Conference 2006 2nd European Modeling and Simulation Symposium (EMSS2006), Barcelona, Spain, pages 403–409, 2006. ISBN: 84-690-0726-2.
• S. Streif, R. Findeisen, and E. Bullinger.
  Relating cross grammians and sensitivity ananlysis in systems biology.
  In Proc. 17th Int. Symp. Mathematical Theory of Networks and Systems (MTNS), pages 437–442, Kyoto, 2006.
• E. Bullinger.
  System analysis of a programmed cell death model.
  In Proc. 44th IEEE Conf. Decision and Control (CDC), European Control Conf. (ECC), pages 7994–7999, 2005.
• 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, USA, August 7-­10 2005.
• I.R. Ofiteru, V. Lavric, F. Allgöwer, and E. Bullinger.
  Sensitivity analysis of Escherichia coli's Tricarboxilic Acid Cycle under anaerobic conditions.
  In Proc. Foundations of Systems Biology (FOSBE), pages 337–340, 2005.
• A. Kremling, T. Sauter, E. Bullinger, M. Ederer, F. Allgöwer, and E.D. Gilles.
  Biosystems engineering: Applying methods from systems theory to biological systems.
  In The Second International Conference on Systems Biology, Pasadena, CA, USA, pages 282–290, 2001.

Other publications

• S. Waldherr and F. Allgöwer.
  A feedback approach to bifurcation analysis in biochemical networks with many parameters.
  Workshop ``Engineering Principles in Biological Systems'', Cambridge, UK, 10 2009.
• S. Waldherr, J. Hasenauer, M. Schliemann, P. Scheurich, and F. Allgöwer.
  Modelling and parameter estimation for heterogeneous cell populations.
  German Symposium on Systems Biology, Heidelberg, May 2009.
• S. Waldherr, J. Hasenauer, M. Schliemann, P. Scheurich, and F. Allgöwer.
  Modelling and parameter estimation for heterogeneous cell populations.
  Talk, September 2009. Workshop Data 2 Dynamics, Freising, Germany.
• Steffen Waldherr, Malgorzata Doszczak, Monica Schliemann, Jens Schreiner, Peter Scheurich, and Frank Allgöwer.
  The tnf receptor signalling network: Modular modelling and cell-type specific analysis.
  International Conference on Systems Biology, Stanford, USA, September 2009.
• Solvey Maldonado, Rolf Findeisen, and Frank Allgöwer.
  Towards optimal treatment design: Model predicts the synergistic effects of pge2 and mechanical loading during bone remodeling.
  International Workshop for Musculoskeletal and Neuronal Interactions, May 2008.
• Solvey Maldonado, Rolf Findeisen, and Frank Allgöwer.
  Understanding the process of force-induced bone growth and adaptation by a mathematical model.
  8th World Congress on Computational Mechanics, June-July 2008.
• S. Waldherr, M. Doszczak, M. Schliemann, J. Schreiner, P. Scheurich, and F. Allgöwer.
  The TNF receptor signalling network: Modular modelling and cell-type specific analysis.
  In 2nd Conference on Systems Biology of the Mammalian Cell, Dresden, 2008.
• S. Waldherr, J. Hasenauer, and F. Allgöwer.
  Global sensitivity analysis of uncertain biochemical reaction networks.
  In 2nd International Workshop on Systems Biology, 2008.
• S. Waldherr, T. Eissing, and F. Allgöwer.
  Analysing biological feedback with tools from control theory.
  In FEBS Advanced Lecture Couse on Systems Biology, 2007. Poster.
• S. Borchers, S. Maldonado, R. Findeisen, and F. Allgöwer.
  Modeling the bone remodeling cycle due to mechanical force.
  J. Bone. V 39(5) S15–S16, November 2006. International Conference on Progress in Bone Mineral Research 2006.
• T. Eißing, F. Allgöwer, P. Scheurich, and E. Bullinger.
  Bistability in cell signalling and applications to apoptosis - principles and robustness aspects.
  In Proceedings of the Hamilton Institute International Workshop on Systems Biology, page 39, NUI Maynooth, Ireland, July 2006.
• T. Eißing, T. Sauter, M. Schliemann, E. Bullinger, F. Allgöwer, O. Sawodny, and P. Scheurich.
  Mathematical modeling of TNF induced apoptotic and anti-apoptotic crosstalk in mammalian cells.
  In Conference on Systems Biology of Mammalian Cells (SBMC), page 66, 2006.
• T. Eißing, S. Waldherr, F. Allgöwer, and E. Bullinger.
  Modelling and Analysis of Death and Survival Signalling: Achievements and Trends.
  In Workshop CNRS-NSF - Biology and control theory: current challenges, Toulouse, France, April, 24-25 2006.
• S. Maldonado, S. Borchers, R. Findeisen, and F. Allgöwer.
  Modeling and analysis of force induced bone growth.
  International Workshop on Systems Biology, NUI Maynooth, Ireland, July 2006.
• S. Waldherr and F. Allgöwer.
  Hopf bifurcations and feedback gain in signaling pathways.
  In Conference on Systems Biology of Mammalian Cells, Heidelberg, 2006. Poster.
• S. Waldherr, T. Eißing, M. Chaves, and F. Allgöwer.
  Preservation of bistability in the reduction of an apoptosis model.
  In Genomes To Systems Conference, Manchester, 2006. Poster.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.