List of Publications by Steffen Waldherr

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Journal articles

1. C. Breindl, S. Waldherr, D. M. Wittmann, F. J. Theis, and F. Allgöwer.
   Steady-state robustness of qualitative gene regulation networks.
   Int. J. Robust. Nonlinear Control, 21(15):1742–1758, October 2011.
2. J. Hasenauer, S. Waldherr, M. Doszczak, N. Radde, P. Scheurich, and F. Allgöwer.
   Identification of models of heterogeneous cell populations from population snapshot data.
   BMC Bioinformatics, 12:125, 2011. (PDF, 2508.3 kBytes)
3. J. Hasenauer, S. Waldherr, M. Doszczak, P. Scheurich, N. Radde, and F. Allgöwer.
   Analysis of heterogeneous cell populations: A density-based modeling and identification framework.
   J. Process Control, 21(10):1417–1425, 2011. (PDF, 534.5 kBytes)
4. M. Lang, T. Marquez-Lago, J. Stelling, and S. Waldherr.
   Autonomous synchronization of chemically coupled synthetic oscillators.
   Bulletin of Mathematical Biology, 73:2678–2706, 2011.
5. Ralf Steuer, Steffen Waldherr, Victor Sourjik, and Markus Kollmann.
   Robust signal processing in living cells.
   PLoS Comput. Biol., 7(11):e1002218, November 2011. (PDF, 1065.5 kBytes)
6. S. Waldherr and F. Allgöwer.
   Robust stability and instability of biochemical networks with parametric uncertainty.
   Automatica, 47:1139–1146, 2011. (PDF, 587.6 kBytes)
7. S. Waldherr, D. Dylus, and F. Allgöwer.
   Bifurcation search via feedback loop breaking in biochemical signaling pathways with time delay.
   Asian Journal of Control, 13(5):691–700, September 2011. (PDF, 280.5 kBytes)
8. J. Hasenauer, P. Rumschinski, S. Waldherr, S. Borchers, F. Allgöwer, and R. Findeisen.
   Guaranteed steady state bounds for uncertain (bio-)chemical processes using infeasibility certificates.
   J. Process Control, 20(9):1076–1083, 2010. (PDF, 311.5 kBytes)
9. J. Hasenauer, S. Waldherr, K. Wagner, and F. Allgöwer.
   Parameter identification, experimental design and model falsification for biological network models using semidefinite programming.
   IET Syst. Biol., 4(2):119–130, 2010. (PDF, 497.5 kBytes)
10. D. Schittler, J. Hasenauer, F. Allgöwer, and S. Waldherr.
    Cell differentiation modeled via a coupled two-switch regulatory network.
    Chaos, 20(4):045121, 2010. (PDF, 439.7 kBytes)
11. S. Waldherr, J. Wu, and F. Allgöwer.
    Bridging time scales in cellular decision making with a stochastic bistable switch.
    BMC Syst. Biol., 4:108, 2010. (PDF, 1444.6 kBytes)
12. M. Lang, S. Waldherr, and F. Allgöwer.
    Amplitude distribution of stochastic oscillations in biochemical networks due to intrinsic noise.
    PMC Biophysics, 2:10, 2009. (PDF, 841.0 kBytes)
13. S. Waldherr and F. Allgöwer.
    Searching bifurcations in high-dimensional parameter space via a feedback loop breaking approach.
    Int. J. Syst. Sci., 40:769–782, 2009. (PDF, 286.0 kBytes)
14. S. Waldherr and M. Zeitz.
    Conditions for the existence of a flat input.
    Int. J. Control, 81(3):439–443, 2008. (PDF, 146.7 kBytes)
15. S. Waldherr, T. Eissing, and F. Allgöwer.
    Rückkopplungen im Leben und Sterben einer Zelle: Ansätze zur systemtheoretischen Analyse.
    at – Automatisierungstechnik, 56(5):233–240, 2008. (PDF, 459.3 kBytes)
16. 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.
    Biophys. J., 92(9):3332–34, May 2007. (PDF, 69.6 kBytes)
17. T. Eissing, S. Waldherr, F. Allgöwer, P. Scheurich, and E. Bullinger.
    Steady state and (bi-)stability evaluation of simple protease signalling networks.
    BioSystems, 90:591–601, 2007. (PDF, 676.2 kBytes)

Book chapters and conference papers (peer-reviewed)

1. C. Breindl, D. Schittler, S. Waldherr, and F. Allgöwer.
   Structural requirements and discrimination of cell differentiation networks.
   In Preprints of the 18th IFAC World Congress, pages 11767–11772, 2011. Milano (Italy), August 28 - September 2. (PDF, 285.9 kBytes)
2. R. Krause, D. Schittler, M. Reiter, S. Waldherr, F. Allgöwer, D. Karastoyanova, F. Leymann, B. Markert, and W. Ehlers.
   Bone remodelling: A combined biomechanical and systems-biological challenge.
   In G. Brenn, G.A. Holzapfel, M. Schanz, and O. Steinbach, editors, Proceedings in Applied Mathematics and Mechanics, volume 11, pages 99–100, December 2011.
3. C. Breindl, S. Waldherr, and F. Allgöwer.
   A robustness measure for the stationary behavior of qualitative gene regulation networks.
   In Proc. of the 11th IFAC Symp. Comp. Appl. Biotechn., pages 36–41, Leuven, Belgium, 2010. (PDF, 349.5 kBytes)
4. J. Hasenauer, C. Breindl, S. Waldherr, and F. Allgöwer.
   Approximative classification of regions in parameter spaces of nonlinear ODEs yielding different qualitative behavior.
   In Proc. of the 49th IEEE Conf. on Dec. and Control, Atlanta, USA, pages 4114–4119, 2010. (PDF, 471.4 kBytes)
5. J. Hasenauer, S. Waldherr, M. Doszczak, P. Scheurich, and F. Allgöwer.
   Density-based modeling and identification of biochemical networks in cell populations.
   In Proc. of the 9th IFAC Symp. Dynam. Contr. Proc. Syst., pages 306–311, Leuven, Belgium, 2010. (PDF, 212.7 kBytes)
6. J. Hasenauer, S. Waldherr, N. Radde, M. Doszczak, P. Scheurich, and F. Allgöwer.
   A maximum likelihood estimator for parameter distributions in heterogeneous cell populations.
   In Procedia Computer Science, volume 1, pages 1649–1657, 2010. (PDF, 336.4 kBytes)
7. S. Waldherr and M. Zeitz.
   Flat inputs in the MIMO case.
   In Proc. of the IFAC Nonlinear Control Systems Design, NOLCOS10, Milano, Italy, pages 695–700, 2010. (PDF, 158.2 kBytes)
8. S. Waldherr, F. Allgöwer, and N. Radde.
   Generic bifurcations in the dynamics of biochemical networks.
   In Proc. of the IEEE International Conference on Control Applications (CCA), Yokohama, Japan, pages 135–141, 2010. (PDF, 363.1 kBytes)
9. S. Waldherr, J. Hasenauer, M. Doszczak, P. Scheurich, and F. Allgöwer.
   Global uncertainty analysis for a model of TNF-induced NF-κB signalling.
   In Jean Lévine and Philippe Müllhaupt, editors, Advances in the Theory of Control, Signals and Systems with Physical Modeling, volume 407 of LNCIS, pages 365–377. Springer Verlag, Berlin Heidelberg, 2010.
10. 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 Found. Syst. Biol. Engin. (FOSBE), Denver, USA, 2009. (PDF, 145.1 kBytes)
11. J. Hasenauer, P. Rumschinski, S. Waldherr, S. Borchers, F. Allgöwer, and R. Findeisen.
    Guaranteed steady-state bounds for uncertain chemical processes.
    In Proc. Intern. Symp. Adv. Contr. Chem. Proc. (ADCHEM), pages 674–679, Istanbul, Turkey, 2009. (PDF, 315.4 kBytes)
12. M. A. Müller, S. Waldherr, and F. Allgöwer.
    The transcritical bifurcation in absolutely stable feedback systems.
    In Proc. of the 10th Europ. Contr. Conf. (ECC), pages 2146–2151, Budapest, Hungary, 2009. (PDF, 280.3 kBytes)
13. S. Streif, S. Waldherr, F. Allgöwer, and R. Findeisen.
    Steady state sensitivity analysis of biochemical reaction networks: A brief review and new methods.
    In A. Jayaraman and J. Hahn, editors, Systems Analysis of Biological Networks, Methods in Bioengineering, pages 129–148. Artech House, Boston, USA, 2009.
14. S. Waldherr, F. Allgöwer, and E. W. Jacobsen.
    Kinetic perturbations as robustness analysis tool for biochemical reaction networks.
    In Proc. of the 48th IEEE Conf. on Dec. and Control, Shanghai, China, pages 4572–4577, 2009. (PDF, 360.9 kBytes)
15. 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, Saint-Malo, France, 2009. (PDF, 259.6 kBytes)
16. 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 15861–66, 2008. (PDF, 562.3 kBytes)
17. 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 9701–06, 2008. (PDF, 306.0 kBytes)
18. T. Eissing, S. Waldherr, and F. Allgöwer.
    Modelling and analysis of cell death signalling.
    In I. Queinnec, S. Tarbouriech, G. Garcia, and S.-I. Niculescu, editors, Biology and Control Theory: Current Challenges, volume 357 of LNCIS, pages 161–180. Springer, Berlin, 2007.
19. S. Waldherr and F. Allgöwer.
    A feedback approach to bifurcation analysis in biochemical networks with many parameters.
    In Proc. of the 2nd Found. Syst. Biol. Engin. (FOSBE), pages 479–484, Stuttgart, Germany, 2007. (PDF, 346.7 kBytes)
20. S. Waldherr, T. Eissing, M. Chaves, and F. Allgöwer.
    Bistability preserving model reduction in apoptosis.
    In Proc. of the 10th IFAC Comp. Appl. in Biotechn., Cancun, Mexico, pages 327–332, 2007. (PDF, 351.0 kBytes)
21. 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 Proc. IEEE Conf. Contr. Appl. (CCA), pages 1746–52, 2006. (PDF, 524.6 kBytes)

Selected poster presentations

1. S. Waldherr, J. Hasenauer, M. Schliemann, P. Scheurich, and F. Allgöwer.
   Modelling and parameter estimation for heterogeneous cell populations.
   Poster, 12–15 May 2009. German Symposium on Systems Biology, Heidelberg.
2. 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.
   Poster, 22–24 May 2008. 2nd Conference on Systems Biology of Mammalian Cells, Dresden.
3. S. Waldherr, J. Hasenauer, and F. Allgöwer.
   Global sensitivity analysis of uncertain biochemical reaction networks.
   Poster, 17–20 August 2008. 2nd International Workshop on Systems Biology, Maynooth, Ireland.
4. S. Waldherr, T. Eissing, and F. Allgöwer.
   Analysing biological feedback with tools from control theory.
   Poster, 10–16 March 2007. 2nd FEBS Advanced Lecture Course on Systems Biology.
5. S. Waldherr and F. Allgöwer.
   Hopf bifurcations and feedback gain in signaling pathways.
   Poster, 12–14 July 2006. Conference on Systems Biology of Mammalian Cells, Heidelberg.