Steffen Waldherr

Dr.-Ing.
Research Associate

Address:  Institute for Systems Theory and Automatic Control Universität Stuttgart Pfaffenwaldring 9 70550 Stuttgart Contact:  Office room 3.236 Phone: +49 711 685 67657 Mail: waldherr@ist.uni-stuttgart.de (Public PGP key)

Research interests

• analysis of complex dynamics in biological systems;
• robustness and uncertainty analysis of biomolecular networks;
• stochastic effects in biochemical signal transduction and gene regulation;
• model reduction for biochemical reaction networks;
• TNF signalling pathways;
• signalling networks in bone cell differentiation;
• parameter estimation in heterogeneous cell populations;
• dynamics of communicating cell populations.

Selected recent publications

• S. Waldherr and F. Allgöwer.
  Robust stability and instability of biochemical networks with parametric uncertainty.
  Automatica, 47:1139–1146, 2011.
• D. Schittler, J. Hasenauer, F. Allgöwer, and S. Waldherr.
  Cell differentiation modeled via a coupled two-switch regulatory network.
  Chaos, 20(4):045121, 2010.
• S. Waldherr, J. Wu, and F. Allgöwer.
  Bridging time scales in cellular decision making with a stochastic bistable switch.
  BMC Systems Biology, 4:108, 2010.
• J. Hasenauer, S. Waldherr, K. Wagner, and F. Allgöwer.
  Parameter identification, experimental design and model falsification for biological network models using semidefinite programming.
  IET Systems Biology, 4(2):119–130, 2010.
• 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.

Please see also the complete publication list with PDF files for download.

Software

• bioSDP: a Matlab toolbox for uncertainty analysis of biomolecular networks
• pybrn: a Python package for simulation and analysis of biomolecular networks

Teaching

• Mehrskalensimulation von Zellpopulationen (SS 2012)
• Wissenschaftliches Arbeiten für Naturwissenschaftler und Ingenieure (WS 2011/12)
• Practical course Systembiologie: Vom Experiment zur Simulation (SS 2011, SS 2012)
• SimTech Seminar Identification of Predictive Simulation Models (SS 2010)
• Substitute lecturer for Regelungstechnik I (WS 2009/10)
• SimTech Seminar Stochastic Simulation in Systems Biology (WS 2008/09)
• Systems Theory in Systems Biology (SS 2008)
• Introduction to Systems Biology (WS 2007/08)
• Assistant for Nonlinear Control (WS 2006/07)
• Assistant for Regelungstechnik II (SS 2006)
• Assistant for Dynamics of nontechnical systems (WS 2005/06)
• Praktikum RT I, RT II, Mehrtankversuch (WS 2005/06 – SS 2007)

Thesis supervision

• Stabilitätsanalyse der MAPK Kaskade mit negativer Rückkopplung, Studienarbeit (2006)
• Modellierung und Simulation des fluidischen Verhaltens von biologischen Flüssigkeiten in Mikrokanälen, Diplomarbeit (2007)
• Numerische Bifurkationsanalyse mit Anwendungen in der Systembiologie, Studienarbeit (2007)
• Globale Sensitivitätsanalyse der TNF-induzierten antiapoptotischen Signaltransduktion mit semidefiniter Programmierung, Diplomarbeit (2008)
• Modelling and simulation of the mitochondrial electron transfer chain, Studienarbeit (2008)
• Analysis of dynamical behaviour in singularly perturbed Lure systems, Studienarbeit (2008)
• Statistical oscillations in biomolecular networks, Studienarbeit (2008)
• Parameteridentifikation des TNF-induzierten NF-kB Signalweg-Modelles, Studienarbeit (2008)
• Entrainment and synchronization of synthetic mammalian oscillators, Diplomarbeit (2009)
• A systems biology approach to insulin resistance in ICU patients resulting from medical treatment, Diplomarbeit (2009)
• Detection of bifurcations points in time-delay systems, Studienarbeit (2009)
• Modellreduktion für stochastische Modelle biochemischer Netzwerke, Studienarbeit (2010)
• Inverse Optimalität in der Regulation biochemischer Netzwerke, Studienarbeit (2010)
• Adaptation in Biochemical Reaction Networks under Kinetic Perturbations, Studienarbeit (2012)
• Stationäre Ausgangs-Robustheit biochemischer Netzwerke, Bachelorarbeit (2012)