publications

2022

1. ROSIE: RObust Sparse ensemble for outlIEr detection and gene selection in cancer omics data

   Antje Jensch, Marta B. Lopes, Susana Vinga, and 1 more author

   Statistical Methods in Medical Research 2022
2. Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns

   Sabrina Adam, Julia Bräcker, Viviane Klingel, and 5 more authors

   Communications Biology 2022

2021

1. SiCaSMA: An Alternative Stochastic Description via Concatenation of Markov Processes for a Class of Catalytic Systems

   Vincent Wagner, and Nicole Erika Radde

   Mathematics 2021

   Abs

   The Chemical Master Equation is a standard approach to model biochemical reaction networks. It consists of a system of linear differential equations, in which each state corresponds to a possible configuration of the reaction system, and the solution describes a time-dependent probability distribution over all configurations. The Stochastic Simulation Algorithm (SSA) is a method to simulate sample paths from this stochastic process. Both approaches are only applicable for small systems, characterized by few reactions and small numbers of molecules. For larger systems, the CME is computationally intractable due to a large number of possible configurations, and the SSA suffers from large reaction propensities. In our study, we focus on catalytic reaction systems, in which substrates are converted by catalytic molecules. We present an alternative description of these systems, called SiCaSMA, in which the full system is subdivided into smaller subsystems with one catalyst molecule each. These single catalyst subsystems can be analyzed individually, and their solutions are concatenated to give the solution of the full system. We show the validity of our approach by applying it to two test-bed reaction systems, a reversible switch of a molecule and methyltransferase-mediated DNA methylation.

2. Model-based robustness and bistability analysis for methylation-based, epigenetic memory systems

   V. Klingel, J. Kirch, T. Ullrich, and 3 more authors

   The FEBS Journal 2021
3. Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function

   Bruno Christ, Maximilian Collatz, Uta Dahmen, and 10 more authors

   Frontiers in Physiology 2021
4. SiCaSMA: An Alternative Stochastic Description via Concatenation of Markov Processes for a Class of Catalytic Systems

   V. Wagner, and N. Radde

   Mathematics 2021

2015

1. A computational model of PKD and CERT interactions at the trans-Golgi network of mammalian cells

   P. Weber, M. Hornjik, M. A. Olayioye, and 2 more authors

   BMC Sys. Biol. 2015
2. Bifurcation analysis for intracellular regulation networks based on their circuit structure

   N. Radde, and S. Klaus

   In Proc. 9th IFAC Symp. Biological and Medical Systems 2015

2010

1. A maximum likelihood estimator for parameter distributions in heterogeneous cell populations

   J. Hasenauer, S. Waldherr, N. Radde, and 3 more authors

   Procedia Computer Science 2010
2. Fixed point characterization of biological networks with complex graph topology

   N. Radde

   Bioinformatics 2010
3. Towards experimental design using a Bayesian framework for parameter identification in dynamic intracellular network models

   A. Kramer, and N. Radde

   In Procedia Comp. Sci. 2010
4. Computation of the posterior entropy in a Bayesian framework for parameter estimation in biological networks

   A. Kramer, J. Hasenauer, F. Allgöwer, and 1 more author

   In Proc. IEEE Int. Conf. Control Applications (CCA) 2010
5. Generic bifurcations in the dynamics of biochemical networks

   S. Waldherr, F. Allgöwer, and N. Radde

   In Proc. IEEE Int. Conf. Control Applications (CCA) 2010

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