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Full-Text Articles in Mathematics
Boolean Modeling Of Biochemical Networks, Tomáš Helikar, Naomi Kochi, John Konvalina, Jim A. Rogers
Boolean Modeling Of Biochemical Networks, Tomáš Helikar, Naomi Kochi, John Konvalina, Jim A. Rogers
Mathematics Faculty Publications
The use of modeling to observe and analyze the mechanisms of complex biochemical network function is becoming an important methodological tool in the systems biology era. Number of different approaches to model these networks have been utilized-- they range from analysis of static connection graphs to dynamical models based on kinetic interaction data. Dynamical models have a distinct appeal in that they make it possible to observe these networks in action, but they also pose a distinct challenge in that they require detailed information describing how the individual components of these networks interact in living cells. Because this level of …
Emergent Decision-Making In Biological Signal Transduction Networks, Tomáš Helikar, Jack Heidel, Jim A. Rogers, Jimmy Rogers
Emergent Decision-Making In Biological Signal Transduction Networks, Tomáš Helikar, Jack Heidel, Jim A. Rogers, Jimmy Rogers
Mathematics Faculty Publications
The complexity of biochemical intracellular signal transduction networks has led to speculation that the high degree of interconnectivity that exists in these networks transforms them into an information processing network. To test this hypothesis directly, a large scale model was created with the logical mechanism of each node described completely to allow simulation and dynamical analysis. Exposing the network to tens of thousands of random combinations of inputs and analyzing the combined dynamics of multiple outputs revealed a robust system capable of clustering widely varying input combinations into equivalence classes of biologically relevant cellular responses. This capability was nontrivial in …