Prof. Dr. rer. nat.

# Nicole Radde

Systems Theory in Systems Biology

Institute for Systems Theory and Automatic Control

## Contact

+49 711 685-67729

+49 711 685-67735

Email

Pfaffenwaldring 9

70569
Stuttgart

Germany

Room: 2.243

## Office Hours

Tuesdays, 1 to 2 pm

## Subject

Systems Theory in Systems Biology

My research focuses on the modeling and analysis of intracellular regulation processes. The ultimate goal is the development and application of mathematical methods to facilitate a better systemic understanding of these processes for particular subsystems and the organization of molecular regulation mechanisms in general. My group works in close collaboration with partners from molecular and cellular biology. I focus in particular on the following topics:

- Dynamic modeling of intracellular regulation processes
- Statistical sampling-based approaches for parameter estimation and predictions
- Analysis methods for intracellular regulation networs based on their network topology

I am a member of the Excellence Cluster 'Simulation Technology', which is funded by the German Research Foundation (EXC 310/1), and the 'Stuttgart Research Center Systems Biology'.

## Gender Equality Officer

Prof. Nicole Radde is the university's gender equality officer. To contact her in that function, go to her officer's profile.

### article

- A. Jensch
*et al.*, “The tumor suppressor protein DLC1 maintains protein kinase D activity and Golgi secretory function,”*J.\ Biol.\ Chem.*, vol. 293, no. 37, pp. 14407–14416, 2018. - A. Jensch, C. Thomaseth, and N. E. Radde, “Sampling-based Bayesian approaches reveal the importance of quasi-bistable behavior in cellular decision processes on the example of the MAPK signaling pathway in PC-12 cell lines,”
*BMC Sys. Biol.*, vol. 11, no. 1, p. 11, Jan. 2017. - C. Thomaseth, K. Kuritz, F. Allgoewer, and R. N., “The circuit-breaking algorithm for monotone systems,”
*Mathematical Biosciences*, vol. 284, pp. 80–91, 2017. - N. Radde and M.-T. Hütt, “The Physics behind Systems Biology,”
*Eur. Phys. J. Nonlin. Biomed. Phys.*, vol. 4, no. 1, 2016. - J. Kirch, C. Thomaseth, A. Jensch, and N. Radde, “The effect of model rescaling and normalization on sensitivity analysis on an example of a MAPK pathway model,”
*Eur. Phys. J. Nonlin. Biomed. Phys.*, vol. 4, no. 3, 2016. - P. Weber, M. Hornjik, M. A. Olayioye, A. Hausser, and N. Radde, “A computational model of PKD and CERT interactions at the trans-Golgi network of mammalian cells,”
*BMC Sys. Biol.*, vol. 9, no. 1, p. 147, 2015. - A. Kramer, V. Stathopoulus, M. Girolami, and N. Radde, “MCMC_CLIB: An advanced MCMC sampling package for ode models.,”
*Bioinformatics*, vol. 30, no. 20, pp. 2991–2992, 2014. - S. Heinrich
*et al.*, “Determinants of robustness in spindle assembly checkpoint signalling,”*Nat. Cell. Biol.*, vol. 15, no. 11, pp. 1328–1339, 2014. - A. Kramer, B. Calderhead, and N. Radde, “Hamiltonian Monte Carlo Methods for Efficient Parameter Estimation in Steady State Dynamical Systems,”
*BMC Bioinf.*, vol. 15, p. 253, 2014. - N. Radde and J. Offtermatt, “Convergence of posteriors for structurally non-identified problems using results from the theory of inverse problems,”
*J Inverse Ill-Pose P*, vol. 22, no. 2, pp. 251–276, 2014. - C. Thomaseth, P. Weber, T. Hamm, K. Kashima, and R. N., “Modeling sphingomyelin synthase 1 driven reaction at the Golgi apparatus can explain data by inclusion of a positive feedback mechanism,”
*J. Theor. Biol.*, vol. 337, pp. 174–180, 2013. - N. Radde, “Analyzing fixed points of intracellular regulation networks with complex feedback topology,”
*BMC Sys. Biol.*, vol. 6, no. 57, 2012. - J. Hasenauer, S. Waldherr, M. Doszczak, N. Radde, P. Scheurich, and F. Allgöwer, “Analysis of heterogeneous cell populations: A density-based modeling and identification framework,”
*J. Proc. Contr.*, vol. 21, no. 10, pp. 1417–1425, 2011. - 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 Bioinf.*, vol. 12, p. 125, 2011. - N. Radde, “The role of feedback mechanisms in biological network models - A tutorial,”
*Asian J. Control*, vol. 13, no. 5, pp. 1–14, 2011. - N. Radde, “Fixed point characterization of biological networks with complex graph topology,”
*Bioinformatics*, vol. 26, no. 22, pp. 2874–2880, 2010. - J. Hasenauer, S. Waldherr, N. Radde, M. Doszczak, P. Scheurich, and F. Allgöwer, “A maximum likelihood estimator for parameter distributions in heterogeneous cell populations,”
*Procedia Computer Science*, vol. 1, no. 1, pp. 1649–1657, 2010. - N. Radde, “The impact of time-delays on the robustness of biological oscillators and the effect of bifurcations on the inverse problem,”
*Eurasip Journal on Bioinformatics and Systems Biology*, vol. 2009, 2009. - J. Gebert, N. Radde, U. Faigle, J. Strösser, and A. Burkovski, “Modeling and simulation of nitrogen regulation in Corynebacterium glutamicum,”
*Discrete Appl. Math.*, 2009. - N. Radde, N. S. Bar, and M. Banaji, “Graphical methods for analysing feedback in biological networks - A survey -,”
*Int. J. Systems Science*, 2009. - N. Radde, J. Gebert, U. Faigle, R. Schrader, and K. Schnetz, “Modeling feedback loops in the H-NS-mediated regulation of the Escherichia coli bgl operon.,”
*Journal of Theoretical Biology*, vol. 250, no. 2, 2008. - N. Radde and L. Kaderali, “Inference of an oscillatory model for the yeast cell cycle,”
*Discrete Appl. Math.*, vol. doi:10.1016/j.dam.2008.06.036, 2008. - N. Radde, “The effect of time scale differences and time-delays on the structural stability of oscillations in a two-gene network,”
*Adv. Complex. Syst.*, vol. 11, no. 3, pp. 471–483, 2008. - J. Gebert, N. Radde, and G.-W. Weber, “Modeling gene regulatory networks with piecewise linear differential equations,”
*European Journal of Operational Research*, vol. 181, no. 3, pp. 1148–1165, 2007. - N. Radde, J. Gebert, and C. V. Forst, “Systematic component selection for gene-network refinement,”
*Bioinformatics*, vol. 22, no. 21, pp. 2674–2680, 2006.

### inbook

- N. Radde and L. Kaderali, “A Bayes Regularized ODE Model for the Inference of Gene Regulatory Networks,” S. Das, D. Caragea, W. H. Hsu, and S. M. Welch, Eds. IGI Global, 2009.
- L. Kaderali and N. Radde, “Inferring gene regulatory networks from expression data,” in
*Studies in Computational Intelligence*, vol. 1, Springer, 2007.

### inproceedings

- D. Paul and N. Radde, “Robustness and filtering properties of ubiquitous signaling network motifs,” in
*Proc. 6th Foundations of Systems Biology in Engineering (FOSBE)*, Magdeburg, Germany, 2016. - N. Radde and S. Klaus, “Bifurcation analysis for intracellular regulation networks based on their circuit structure,” in
*Proc. 9th IFAC Symp. Biological and Medical Systems*, Berlin, Germany, 2015, vol. 48, no. 20, pp. 165–170. - N. Radde, “Identification of feedback circuits that are connected to multiple fixed points in biological networks,” in
*Proc. 8th Int. Workshop on Computational Systems Biology (WCSB)*, Ulm, Germany, 2012, pp. 59–62. - P. Weber, J. Hasenauer, F. Allgöwer, and N. Radde, “Parameter estimation and identifiability of biological networks using relative data,” in
*Proc. 18th IFAC World Congress*, Milano, Italy, 2011, pp. 11648–11653. - J. Hasenauer, S. Waldherr, M. Doszczak, N. Radde, P. Scheurich, and F. Allgöwer, “Parameter estimation and uncertainty analysis for models of heterogeneous cell populations,” in
*Proc. 12th Int. Conf. Systems Biology (ICSB)*, Heidelberg/Mannheim, Germany, 2011. - A. Kramer, J. Hasenauer, F. Allgöwer, and N. Radde, “Computation of the posterior entropy in a Bayesian framework for parameter estimation in biological networks,” in
*Proc. IEEE Int. Conf. Control Applications (CCA)*, Yokohama, Japan, 2010, pp. 493–498. - S. Waldherr, F. Allgöwer, and N. Radde, “Generic bifurcations in the dynamics of biochemical networks,” in
*Proc. IEEE Int. Conf. Control Applications (CCA)*, Yokohama, Japan, 2010, pp. 135--141. - A. Kramer and N. Radde, “Towards experimental design using a Bayesian framework for parameter identification in dynamic intracellular network models,” in
*Procedia Comp. Sci.*, 2010, vol. 1, no. 1, pp. 1639--1647. - A. Kramer and N. Radde, “A Stochastic Framework for Noise Separation in Dynamic Models of Intracellular Networks,” in
*Proc. CASYS’09*, 2009, no. 9, pp. 68–73. - N. Radde, N. S. Bar, and A. Tresch, “A comparison of likelihoods for dynamic stochastic models of biological networks,” in
*WCSB Conference proceedings*, 2009. - N. Radde and L. Kaderali, “Bayesian inference of gene regulatory networks using gene expression time series data,” in
*Bioinformatics Research and Development, BIRD07*, 2007, vol. 4414. - J. Gebert and N. Radde, “A new approach for modeling prokaryotic biochemical networks with differential equations,” in
*AIP Conference Proceedings of 7th International Conference on Computing Anticipatory Systems (CASYS05)*, 2006, vol. 839.

### misc

- C. Thomaseth and N. Radde, “Normalization of Western blot data affects the statistics of estimators.” 2016.
- C. Thomaseth, A. Jensch, and N. @ARTICLEist:thomaseth17. Radde author =. Thomaseth, C. and Kuritz, K. and Allgoewer, F. and Radde N. .. title =. The circuit-breaking algorithm for monotone systems, journal =. Mathematical Biosciences, year =. 2017, volume =. 284, pages =. 80-91 @ARTICLEist:thomaseth17a, author =. Thomaseth, C. and Kuritz, K. and Allgoewer, F. and Radde N. .. title =. The circuit-breaking algorithm for monotone systems, journal =. Mathematical Biosciences, year =. 2017, volume =. 284, pages =. 80-91, “Positive and negative feedback-endowed pathways show robustness against biological heterogeneity and stochastic fluctuations.” 2015.
- C. Thomaseth and N. Radde, “Model calibration: the statistical effects of data normalization.” 2015.
- A. Jensch, C. Thomaseth, and N. Radde, “Sampling-Based Analysis of Feedback in a Model of the MAP Kinase Pathway.” 2015.
- C. Thomaseth, P. Weber, T. Hamm, K. Kashima, and N. Radde, “Modeling sphingomyelin synthase 1 driven reaction at the Golgi apparatus can explain data by inclusion of a positive feedback mechanism.” 2013.
- K. Kuritz, N. Radde, and M. Olayioye, “Multi-scale modeling reveals membrane domain variations as mechanism behind augmented ErbB receptor activation.” 2013.
- J. Hasenauer, S. Waldherr, M. Doszczak, P. Scheurich, N. Radde, and F. Allgöwer, “From single-cell models to mechanicstic population descriptions - A modeling, simulation, and analysis framework.” 2011.

My teaching activities are associated to the study programs Engineering Cybernetics, Technical Biology and Simulation Technology. Currently I teach the following courses:

Summer term 2019:

Winter term 2018/2019

- Dynamik biologischer Systeme
- Wahrscheinlichkeitstheorie und Statistik I
- Statistische Lernverfahren und stochastische Regelung
- Grundlagen der Systembiologie/Systembiologie II

My complete teaching history inlcuding evaluation results and supervised student projects can be seen here.

- Since 2015 Professor for Systems Theory in Systems Biology at the Institute for Systems Theory and Automatic Control (IST) at the University of Stuttgart.
- 2008 - 2015 Junior Professor for Systems Theory in Systems Biology at the Institute for Systems Theory and Automatic Control (IST) at the University of Stuttgart.
- 2007 - 2008 Postdoc at the Institute for Medical Informatics, Statistics and Epidemiology (IMISE) of the University Leipzig in Korbinian Strimmer's group 'Statistics and Computational Biology'.
- 2007 PhD thesis 'Modeling Non-Linear Dynamic Phenomena in Biochemical Networks', Center for Applied Computer Science (ZAIK) at the University of Cologne, Prof. Ulrich Faigle
- 2003 - 2007 PhD student at the Center for Applied Computer Science (ZAIK) at the University of Cologne
- 2002 'Erstes Staatsexamen' (First State Examination) in Physics and Mathematics, Technical University Darmstadt
- 2002 Diploma in Phyiscs, Technical University Darmstadt, thesis title 'Neutrino Transport in Proto-Neutronensternen', 'Nuclei, Hadrons and Quarks (NHQ) group', Prof. Jochen Wambach
- 1997 - 2002 Studies in Physics, TU Darmstadt
- 1996 - 2002 'Lehramt' Mathematics and Physics, TU Darmstadt