Genomic Engineering Group / InteLAB
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Wednesday, 27 May 2020
Regulatory Networks

A central issue of post-genomic studies is to understand (and eventually control) how gene expression is regulated. Gene expression at a particular time and space is a delicate balance that obeys well established biochemical, i.e., physico-chemical rules, in a dynamic fashion, sustained away but not far from thermodynamic equilibrium conditions. Although genome-wide genetic circuitry is important in the establishment of how genes are expressed in response to environmental and internal variations (Remember: genes are commonly expressed in groups, or waves, also in response to internal gradients), state-of-the-art does not yet allow extensively study of more than a few genes interacting simultaneously. Typically, genes are expressed continuously, but on-off approaches are usually good enough to support biological hypothesis. We have used Petri net methodology to study regulatory-metabolic networks, in conjunction with logistic (discrete) models. As to our knowledge this was the first time Petri nets were used to study regulatory+metabolic networks. A case study modeling tryptophan biosynthesis in E. coli has been used to successfully test the methodology.

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Petri Nets
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