Nicole Radde

Journal Articles

Hasenauer J., Waldherr S., Doszczak M., Scheurich P., Radde N. and Allgöwer F. Analysis of heterogeneous cell populations: A density-based modeling and identification framework. Journal of Process Control, in press, doi:10.1016/j.jprocont.2011.06.020.
Hasenauer J., Waldherr S., Doszczak M., Radde N., Scheurich P. and Allgöwer F. Identification of models of heterogeneous cell populations from population snapshot data. BMC Bioinf. 2011, 12:125, doi:10.1186/1471-2105-12-125.
Radde N.. The role of feedback mechanisms in biological network models - A tutorial. Asian Journal of Control 13(5), 597-610, doi:10.1002/asjc.376.
Radde N., 2010. Fixed point characterization of biological networks with complex graph topology. Bioinformatics 26(22), 2874-2880.
Bar N.S., Radde N., 2009. Long-term prediction of fish growth under varying ambient temperature using a multi-scale dynamic model. BMC Syst Biol 3:107, doi:10.1186/1752-0509-3-107.
Radde N., Bar N.S., Banaji M., 2009. Graphical methods for analysing feedback in biological networks - A survey - Int J Syst Sci., vol. 41, issue 1, 35.
Radde N., 2008. The impact of time-delays on the robustness of biological oscillators and the effect of bifurcations on the inverse problem. Eurasip J Bioinf Syst Biol, vol. 2009, article ID 327503, doi:10.1155/2009/327503.
Radde N., 2008. The effect of time scale differences and time-delays on the structural stability of oscillations in a two-gene network. Adv. Complex Syst. 11(3), 471-83. [Abstract]
Radde N., Gebert J., Faigle U., Schrader R., Schnetz K., 2008. Modeling feedback loops in the H-NS-mediated regulation of the Escherichia coli bgl operon. J. Theor. Biol. 250(2), 298-306. [Abstract]
Radde N., Kaderali L., 2008. Inference of an oscillating model for the yeast cell cycle. Discrete Appl. Math. 157 (10), 2285-2295, doi:10.1016/j.dam.2008.06.036. [Abstract]
Gebert J., Radde N., Faigle U., Strösser, J., Burkovski, A., 2008. Modelling and simulation of nitrogen regulation in Corynebacterium glutamicum. Discrete Appl. Math. 157 (10), doi:10.1016/j.dam.2008.06.055. advance online access [Abstract]
Gebert J., Radde N., Weber G.-W., 2007. Modelling gene regulatory networks with piecewise linear differential equations. Special issue `Challenges of Continuous Optimization in Theory and Applications', European Journal of Operational Research 18(3). [Abstract]
Radde N., Gebert J., Forst C.V., 2006. Systematic component selection for gene-network refinement. Bioinformatics 22(21), 2674-2680. [Abstract]
Ergenc T., Pickl S.W., Radde N., Weber G.-W., 2005. Generalized semi-infinite optimization and anticipatory systems. International Journal of Computing Anticipatory Systems 15, CHAOS, 3-30. [Abstract]
Gebert J., Öktem H., Pickl S.W., Radde N., Weber G.-W., Yilmaz F.B., 2004. Inference of gene expression patterns by using a hybrid system formulation - an algorithmic approach to local state transition matrices. Anticipative & Predictive Models in Systems Science 1, G.E. Lasker, D.M. Dubois (eds.), Canada, 63-66. [Abstract]

Further refereed publications

Weber P., Hasenauer J., Allgöwer F. and Radde N., 2011. Parameter Estimation and Identifiability of Biological Networks Using Relative Data. accepted for publication in Conf. Proc. of the 18th World Congress of the International Federation of Automatic Control (IFAC 2011), August 28 - September 1 2011, Milano, Italy.
Waldherr S., Allgöwer F. and Radde N., 2010. Generic bifurcations in the dynamics of biochemical networks. IEEE Multi-Conference on Systems and Control (MCS 2010), 135-141, September 8-10, Yokohama, Japan.
Kramer A., Hasenauer J., Radde N., 2010. Computation of the posterior entropy in a Bayesian framework for parameter estimation in biological networks. IEEE Multi-Conference on Systems and Control (MCS 2010), 493-498, September 8-10, Yokohama, Japan.
Hasenauer J., Waldherr S., Radde N., Doszczak M., Scheurich P. and Allgöwer F, 2010. A maximum likelihood estimator for parameter distributions in heterogeneous cell populations. Procedia Computer Science 1(1):1649-1657.
Kramer A. and Radde N., 2010. Towards experimental design using a Bayesian framework for parameter identification in dynamic intracellular network models. Procedia Comput Sci 1(1), 1639-1647, International Conference on Computational Systems (ICCS2010).
Hasenauer J., Waldherr S., Radde N., Doszczak M., Scheurich P., Allgöwer F., 2010. A maximum likelihood estimator for parameter distributions in heterogeneous cell populations. Procedia Comput Sci 1(1), 1659-1667, International Conference on Computational Systems (ICCS2010).
Kramer A.,Radde N., 2009. A statistical framework for noise separation in dynamical models of intracellular networks. accepted for Proceeedings of 9th International Conference on Computing Anticipatory Systems (Casys09), August 3-9, Liege, Belgium.
Radde N., Bar N.S., Tresch A., 2009. A comparison of likelihoods for dynamic stochastic models of biological networks. Proceedings of Workshop of Computational Biology (WCSB09), Aarhus, Denmark, 131-134.
Radde N., Kaderali L., 2007. Bayesian inference of gene regulatory networks using gene expression time series data. Lecture Notes in Bioinformatics (LNBI) 4414, Bird07, Springer Verlag, 1-15. [Abstract]
Gebert J., Radde N., 2006. A new approach for modeling prokaryotic biochemical networks with differential equations. Conference Proceedings of 7th International Conference on Computing Anticipatory Systems (CASYS'05), Liege, Belgium, 526-533. [Abstract]
Gebert J., Lätsch M., Pickl S.W., Radde N., Weber G.-W., Wünschiers R., 2004. Genetic networks and anticipation of gene expression patterns. AIP Conference Proceedings of Computing Anticipatory Systems (CASYS'03), 718, 474-485. [Abstract]

Miscellaneous

Radde N., 2009. Fixed point analysis in biological networks of coupled feedback Oberwolfach reports 11/2009, doi:10.4171/OWR/2009/11.

Book Contributions

Ahdesmäki M., Strimmer K., Radde N., Rahnenführer J., Klemm K., Lähdesmäki H., and Yli-Harja O. (eds), 2008. Proceedings of the 5th International Workshop on Computational Systems Biology, WCSB 2008, June 11-13, 2008, Leipzig, Germany (reprint).
Kaderali L., Radde N., 2007. Inferring Gene Regulatory Networks from Gene Expression Data. In 'Computational Intelligence in Bioinformatics', Chapter 2, Studies in Computational Intelligence (SCI) series, Springer-Verlag, Berlin. [Abstract]
Radde N., Kaderali L., 2010. A Bayes Regularized ODE Model for the Inference of Gene Regulatory Networks. In: Das S., Caragea D., Hsu W.H., Welch S.M. (eds.), 'Computational Methods in Gene Regulatory Networks', IGI Global, Chapter 6, pp. 139-168.

Theses

Radde, N., 2007. Modeling non-linear dynamic phenomena in biochemical networks. Ph.D. thesis in applied mathematics, Center of Applied Computer Science, University of Cologne (pdf).
Radde, N., 2002. Neutrino-Transport in Proto-Neutronen-Sternen. Diploma thesis in physics, Department of Nuclear Physics, Technical University Darmstadt (ps-File).

Conference Contributions / Workshops (Talks)

Radde N (2011). The role of protein kinase D in the balance between lipid homeostasis and secretory activity in mammalian cells: A systemic approach. Invited talk at Böhringer Ingelheim, Biberach a.d. Riss, Dec 13.
Radde N (2011). Vorstellung des Zentrums für Systembiologie. Tag der industriellen Biotechnologie am Zentrum für Bioverfahrenstechnik, University of Stuttgart, Nov 25.
Radde N (2011). New SimTech vision 'Integrated overall human model'. SimTech Statusseminar in Bad Boll, Nov 21-23.
Kramer A, Radde N (2011). Systems Biology investigates the properties of biochemical reaction networks. Joint Workshop 'Statistical and dynamical models in biology and medicine' of the GmdS/IBS working groups 'Statistical methods in bioinformatics' and 'Mathematical models in medicine', October 27-28, Göttingen, Germany.
Radde N., 2011. Fixed point characterization of biological networks with complex graph topology.Institute for Automatic Control, February 1, ETH Zürich, Switzerland.
Radde N., 2011. Fixed point characterization of biological networks with complex graph topology.B-IT Kolloquium 'Algorithmic Bioinformatics' at the Bonn-Aachen International Center for Information Technology, January 27, University of Bonn, Germany.
Radde N., 2011. A systemic modeling approach towards understanding the protein kinase D-mediated balance between lipid homeostasis and secretory activity in mammalian cells. Workshop 'Systembiologie zwischen Forschung und Anwendung' jointly organized by DECHEMA and Vereinigung deutscher Biotechnologie-Unternehmen (VBU), January 18-19, Frankfurt am Main, Germany.
Radde N., 2010. A statistical Bayesian framework for identification of biological networks from perturbation experiments.European Conference on Computational Biology, September 26-29, Ghent, Belgium.
Radde N., 2010. Generic bifurcations in the dynamics of biochemical networks. IEEE Multi-Conference on Systems and Control (MCS 2010), September 8-10, Yokohama, Japan.
Radde N., 2010. Computation of the posterior entropy in a Bayesian framework for parameter estimation in biological networks. IEEE Multi-Conference on Systems and Control (MCS 2010), September 8-10, Yokohama, Japan.
Kramer A. and Radde N., Towards optimal experimental design using a Bayesian framework for parameter identification in dynamic intracellular network models International Conference on Computational Systems (ICCS2010), Amsterdam, 29.5.-31.5.2010.
Kramer, A. and Radde, N., Optimal Experimental Design Using a Bayesian Framework for the Identification of Dynamic Intracellular Network Models DAGStat 2010, 2. gemeinsame Tagung der Deutschen Arbeitsgemeinschaft Statistik 'Statistik unter einem Dach', Dortmund, 23.3.-26.3.2010.
Radde, N., Analyse von Feedback-Mechanismen in biologischen Netzwerken 6. Elgersburg Workshop, Elgersburg, Thüringen, 1.-4.3.2010.
Radde, N., Systems Biology - A New Application Field in Systems Theory Kolloquium des Exzellenzclusters 'Simulation Technology', Universität Stuttgart, 22.12.2009.
Radde, N., Statistical approaches for the inference of biological networks GmdS Jahrestagung, Essen, 7.-10.9.2009.
Radde, N., A statistical framework for noise separation in dynamic models of intracellular networks 9th International Conference on Anticipatory Systems, Liege, Belgium, 3.-7.8.2009.
Radde, N., Systemtheoretische Ansaetze zur Untersuchung von Feedback-Mechanismen in biologischen Netzwerken Seminar an der Universität Hohenheim, 15.7.2009.
Radde, N., Statistical aprpoaches for the inference of biological networks Seminar am MPI Magdeburg, 26.6.2009.
Radde, N., A comparison of likelihood functions for dynamic stochastic models of biological networks Seminar an der Universität Magdeburg, 25.6.2009.

A comparison of likelihood functions for dynamic stochastic models of biological networks

Radde, N., Systemtheoretische Ansätze zur Analyse komplexer biologischer Systeme Workshop 'System und Komplexität: Kulturalistische vs. Naturalistische Aspekte, Universität Stuttgart, 29.5.2009.
Radde, N., Antrittsvorlesung: Warum sind Zellen komplex? Universität Stuttgart, 30.4.2009.
Radde, N., Fixed point analysis in biological networks of coupled feedback Oberwolfach Workshop: Control Theory: On the Way to New Application Fields, Oberwolfach, 22.2. - 28.2.2009.
Radde, N., Statistical Bayesian approaches for dynamic network inference Workshop on Computational Approaches to Stem Cell Biology, Leipzig, 12.1. - 14.1.2009.
Radde, N., Fixed point analysis in biological networks with interlocked feedback circuits Workshop on Gene Regulatory Network Inference, Jena, 25.9.-26.9.2008.
Radde, N., Fixed point analysis in biological networks with interlocked feedback circuits European Conference on Mathematical and Theoretical Biology, Edinburgh, 29.6.-4.7.2008.
Radde, N., Inference of oscillating regulatory networks using time series data. Invited talk on the Workshop on integrative network analysis: Network structure and biological function - reconstruction, modelling and statistical approaches, Potsdam, 10.4.-11.4.2008.
Radde N., Robustness of Oscillations in Biological Networks. Annual Conference of the Working Group 'Statistical Bioinformatics', München, 22.11.-23.11.2007.
Radde N., Bayesian Inference of Gene Regulatory Networks using Gene Expression Time Series Data. BioInformatics Research and Development (BIRD07), Berlin, 12.03.-14.03.2007.
Radde N., Hierarchical Bayesian Inference of Oscillating Gene Regulatory Networks. International Conference on Molecular Systems Biology (ICMSB06), Munich, 31.07.-04.08.2006.
Radde N., Ein Bayessches Lernverfahren für genregulatorische Netze. Kolloquium über Parallelverarbeitung in technisch-naturwissenschaftlichen Anwendungen, Jülich, 15.05.2006.
Radde N., Hierarchical Bayesian Inference of Gene Regulatory Networks. 30. Annual Conference of the German Classification Society (GfKl06), Berlin, 8.-10.3.2006.
Radde N., Graph Theory Applied to Biological Networks.Cologne-Twente Workshop (CTW) on Graphs and Combinatorial Optimization, Cologne, 18.-20.5.2005.

Selected Poster Presentations

Hasenauer J, Waldherr S, Schittler D, Breindl C, Weber P, Kramer A, Radde N, Allgöwer F. Systemtheorie in der Systembiologie CSB Symposium, Universität Stuttgart, 2010.
Kramer A. and Radde N., Systemtheorie in der Systembiologie - Analyse gekoppelter Feedback-Mechanismen Tag der offenen Tür, Universität Stuttgart, 2009.
Gebert J., Radde N. and Forst C.V., Systematic Refinement of a Dynamic Gene Network Model. International Conference on Molecular Systems Biology (ICMSB06), Munich, 2006.
Radde N. and Kaderali L., Reconstructing Oscillating Gene Regulatory Networks using Bayesian regulated Differential Equations. German Conference on Bioinformatics (GCB06), Tübingen, 2006.
Kaderali L. and Radde N., Reconstructing Gene Regulatory Networks using a Hierarchical Bayesian Approach. German Conference on Bioinformatics (GCB05), Hamburg, 2005.
Gebert J., Radde N. and Forst C.V., A dynamic response network model of Mtb DNA repair. 6th International Conference on Systems Biology (ICSB05), Boston, 2005.
Gebert J. and Radde N., Öktem H., Weber G.-W., Modelling Gene Regulatory Networks with Piecewise Linear Differential Equations. German Conference on Bioinformatics (GCB04), Bielefeld, 2004.