Exact Model Reduction of Combinatorial Reaction Networks

in BMC Systems Biology (2008), 2

Domain oriented model reduction of signal transduction models

Poster (2004, October)

Feedback Mechanisms in Intra-Cellular Dynamics

Conference (2003, May 29)

An approach for dividing models of biological reaction networks into functional units

in Simulation: Trans. Society for Modeling and Simulation International (2003), 79(12), 703-716

Biological reaction networks consist of many substances and reactions between them. Like many other biological systems, they have a modular structure. Therefore, a division of a biological reaction ... [more ▼]

Biological reaction networks consist of many substances and reactions between them. Like many other biological systems, they have a modular structure. Therefore, a division of a biological reaction network into smaller units highly facilitates its investigation. The authors propose an algorithm to divide an ordinary differential equation (ODE) model of a biological reaction network hierarchically into functional units. For every compound, an activity function dependent on concentration or concentration change rate is defined. After performing suitable simulations, distances between the compounds are computed by comparing the activities along the trajectories of the simulation. The distance information is used to generate a dendrogram revealing the internal structure of the reaction network. The algorithm identifies functional units in two models of different networks: catabolite repression in Escherichia coli and epidermal growth factor (EGF) signal transduction in mammalian cells. [less ▲]

Systems Biology - A Glossary from two perspectives

Poster (2002)

Biosystems Engineering: Applying methods from systems theory to biological systems

in Proc. of the 3rd International Conference on Systems Biology (2001, November)