List of Publications by Steffen Waldherr

Copyright Note: The PDF files may be downloaded for personal use only. Any other use requires prior permission of the author and the copyright holder(s). Due to copyright constraints, only unreviewed (preprint) versions or no PDFs are publicly available in some cases. Final versions are usually available upon email request, or via the link to the publisher's online version.

Journal articles

1. M. Daub, S. Waldherr, F. Allgöwer, P. Scheurich, and G. Schneider.
   Death wins against life in a spatially extended model of the caspase-3/8 feedback loop.
   Biosystems, 108:45–51, 2012. (PDF, 471.6 kBytes)
2. Steffen Waldherr and Bernard Haasdonk.
   Efficient parametric analysis of the chemical master equation through model order reduction..
   BMC Syst. Biol., 6:81, 2012. (PDF, 1655.7 kBytes)
3. S. Waldherr, S. Streif, and F. Allgöwer.
   Design of biomolecular network modifications to achieve adaptation.
   IET Systems Biology, 6:223–231, December 2012. (PDF, 313.4 kBytes)
4. 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.
5. 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)
6. 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)
7. M. Lang, T. Marquez-Lago, J. Stelling, and S. Waldherr.
   Autonomous synchronization of chemically coupled synthetic oscillators.
   Bull. Math. Biol., 73:2678–2706, 2011.
8. 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)
9. S. Waldherr and F. Allgöwer.
   Robust stability and instability of biochemical networks with parametric uncertainty.
   Automatica, 47:1139–1146, 2011. (PDF, 587.6 kBytes)
10. 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)
11. 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)
12. 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)
13. 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)
14. 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)
15. 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)
16. 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)
17. 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)
18. 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)
19. 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)
20. 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. S. Waldherr and F. Allgöwer.
   Network-level dynamics of diffusively coupled cells.
   In Proc. 51st IEEE Conference on Decision and Control (CDC), pages 5517–5522, Maui, Hawaii, USA, December 10–13 2012. (PDF, 385.8 kBytes)
2. S. Waldherr, F. Allgöwer, E. W. Jacobsen, and S. Streif.
   Robustness and adaptation of biological networks under kinetic perturbations.
   In F. Allgöwer, V. Blondel, and U. Helmke, editors, Control Theory: Mathematical Perspectives on Complex Networked Systems, pages 663–664. Mathematisches Forschungsinstitut Oberwolfach, 2012. Report No. 12/2012.
3. S. Waldherr, J. Hasenauer, and Frank Allgöwer.
   Set based uncertainty analysis and parameter estimation of biological networks with the bioSDP toolbox.
   In Proc. of the of the 9th International Workshop on Computational Systems Biology (WCSB), Ulm, Germany, 2012. (PDF, 218.5 kBytes)
4. 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)
5. 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.
6. 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)
7. 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)
8. 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)
9. 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)
10. 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)
11. S. Waldherr, F. Allgöwer, and N. Radde.
    Generic bifurcations in the dynamics of biochemical networks.
    In Proc. of the IEEE Int. Conf. Contr. Appl. (CCA), Yokohama, Japan, pages 135–141, 2010. (PDF, 363.1 kBytes)
12. 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.
13. 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)
14. 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)
15. 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)
16. 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.
17. S. Waldherr.
    Uncertainty and robustness analysis of biochemical reaction networks.
    In F. Allgöwer, U. Helmke, and E. Sontag, editors, Control Theory: On the Way to New Application Fields, pages 663–664. Mathematisches Forschungsinstitut Oberwolfach, 2009. Report No. 11/2009.
18. 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)
19. 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)
20. 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)
21. 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)
22. 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.
23. 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)
24. 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)
25. 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 recent research presentations

12.04.2013

Mathematical analysis of biological switches.
Workshop of the Graduate School "Computational Systems Biology",
Humboldt-Universität Berlin, Chorin, Deutschland.
Link

12.12.2012

Network-level dynamics of diffusively coupled cells.
51St IEEE Conference on Decision and Control, Maui, USA.
(PDF)

11.10.2012

A robustness mechanism via sensitivity regulation in the TRPV1 ion channel.
Workshop "Statistical and dynamical models in biology and medicine", Stuttgart, Germany.
Link

18.06.2012

Complexity in biological networks. From molecular interactions to heterogeneous cell populations.
Otto-von-Guericke-Universität Magdeburg, Germany.

29.02.2012

Adaptation and robustness of biological networks under kinetic perturbations.
Workshop "Control Theory: Mathematical Perspectives on Complex Networked Systems",
Mathematisches Forschungsinstitut Oberwolfach, Germany. Plenary talk.

21.10.2011

Dynamical robustness from biomolecular networks to interacting cell populations.
Humboldt-Universität Berlin, Germany.

27.09.2011

Linear robustness analysis of nonlinear biomolecular networks with kinetic perturbations.
IEEE Conference on Control Applications, Denver, USA.
(PDF)

28.08.2011

Modeling biochemical signal transduction in heterogeneous cell populations.
Tutorial on the International Conference on Systems Biology, Heidelberg, Germany.
(PDF)

19.05.2011

Robustness analysis of biomolecular networks via polynomial programming.
SIAM Conference on Optimization, Darmstadt, Germany.

12.04.2011

Uncertainty and robustness analysis of dynamics in biomolecular networks.
BISON Seminar, ETH Zürich, Switzerland.