187 citations · 579 across the 36 of their papers we have counts for
19 papers · 1 filter
Qualitative dynamics of chemical reaction networks: an investigation using partial tropical equilibrations
Aurélien Desoeuvres, Peter Szmolyan, Ovidiu Radulescu
We discuss a method to describe the qualitative dynamics of chemical reaction networks in terms of symbolic dynamics. The method, that can be applied to mass-action reaction networ…
ODEbase: A Repository of ODE Systems for Systems Biology
Christoph Lüders, Thomas Sturm, Ovidiu Radulescu
Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symb…
Algorithmic Reduction of Biological Networks With Multiple Time Scales
Niclas Kruff, Christoph Lüders, Ovidiu Radulescu +2
We present a symbolic algorithmic approach that allows to compute invariant manifolds and corresponding reduced systems for differential equations modeling biological networks whic…
Effective computational methods for hybrid stochastic gene networks
Guilherme C. P. Innocentini, Fernando Antoneli, Arran Hodgkinson +1
At the scale of the individual cell, protein production is a stochastic process with multiple time scales, combining quick and slow random steps with discontinuous and smooth varia…
Maximal switchability of centralized networks
Sergei Vakulenko, Ivan Morozov, Ovidiu Radulescu
We consider continuous time Hopfield-like recurrent networks as dynamical models for gene regulation and neural networks. We are interested in networks that contain n high-degree n…
Geometric analysis of pathways dynamics: application to versatility of TGF-β receptors
Satya Swarup Samal, Aurélien Naldi, Dima Grigoriev +3
We propose a new geometric approach to describe the qualitative dynamics of chemical reactions networks. By this method we identify metastable regimes, defined as low dimensional r…