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Intracellular Fate of FGFRs with BioAmbients

Maria Vigliotti, Steffen van Bakel, John Heath

Spatial 2009 - Overcoming Distance in Signaling Networks.

Reactions in signaling pathways can vary according to the location of components. A typical example of this kind of pathway is the receptor-mediated endocytotic pathway. To faithfully model these pathways, there is a need to explicitly represent different compartments of the cell to finely describe the relocation of components. In our work, we consider a spatial model for different sorting of receptors of Fibroblast Growth Factor via the endocytotic pathway.

For computational model, we use the stochastic version of BioAmbients, a process calculus that allows to model both signaling pathways and the spatial distributions of signaling. The stochastic simulation is carried out using BAM (BioAmbient Machine), a Java implementation of BioAmbients via a spatial version of the Gillespie Algorithm. Our model, and the associated results of the simulations, confirm known experimental data. Our work [4] sheds light on different mechanisms that influence the spatial distribution of the different components in the pathway.

Computational Bioinformatics
Theory of Computational Systems
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