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We discuss the identification of genetic networks based on a class of boolean gene activation rules known as hierarchically canalizing functions. We introduce a class of kinetic models for the concentration of the proteins in the network built on a family ...
The last decade has witnessed a fundamental change in the role of network theory. Side by side with the increasing relevance of interdisciplinarity, this ensemble of mathematical tools and methods has known such a success and such a wide range of different ...
By considering the eigenratio of the Laplacian of the connection graph as a synchronizability measure, we propose a procedure for weighting dynamical networks to enhance their synchronizability. The method is based on node and edge betweenness centrality m ...
In this paper we investigate optimization of synchronization cost in undirected dynamical networks. To do so, proper weights are assigned to the networks’ edges considering node and edge betweenness centrality measures. The proposed method gives near-optim ...
Plasmodium falciparum is a deadly parasite that causes malaria in humans. This disease causes the death of one million people every year. To find new means to fight this parasite, it is important to learn more about its biology. As the pathways of protein ...
Motivation: Understanding gene regulation in biological processes and modeling the robustness of underlying regulatory networks is an important problem that is currently being addressed by computational systems biologists. Lately, there has been a renewed ...
Within systems biology there is an increasing interest in the stochastic behavior of biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous-time Markov chain (CTMC). S ...
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We discuss the identification of genetic networks based on a class of boolean gene activation rules known as hierarchically canalizing functions. We introduce a class of kinetic models for the concentration of the proteins in the network built on a family ...
Study of a metabolic network with respect to the sensitivity of the metabolite concentrations and the metabolic fluxes to genetic, biochemical, and environmental variations requires knowledge of the kinetic properties of the enzymes in the network. Experim ...
The large-scale structure of complex systems is intimately related to their functionality and evolution. In particular, global transport processes in flow networks rely on the presence of directed pathways from input to output nodes and edges, which organi ...