Probabilistic Boolean Networks - The Modeling and Control of Gene Regulatory Networks
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Modeling gene regulatory networks: Classical models, optimal perturbation for identification of network
Deep understanding of molecular biology has allowed emergence of new technologies like DNA decryption. On the other hand, advancements of molecular biology have made manipulation of genetic systems simpler than ever; this promises extraordinary progress in biological, medical and biotechnological applications. This is not an unrealistic goal since genes which are regulated by gene regulatory ...
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Probabilistic Boolean Networks (PBNs) are useful models for modeling genetic regulatory networks. In this paper, we propose efficient algorithms for constructing a sparse probabilistic Boolean network when its transition probability matrix and a set of possible Boolean networks are given. This is an interesting inverse problem in network inference and it is important in the sense that most micr...
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Control of gene regulatory networks is one of the fundamental topics in systems biology. In the last decade, control theory of Boolean networks (BNs), which is well known as a model of gene regulatory networks, has been widely studied. In this review paper, our previously proposed methods on optimal control of probabilistic Boolean networks (PBNs) are introduced. First, the outline of PBNs is e...
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Mathematical and computational modeling of genetic regulatory networks promises to uncover the fundamental principles governing biological systems in an integrative and holistic manner. It also paves the way toward the development of systematic approaches for effective therapeutic intervention in disease. The central theme in this paper is the Boolean formalism as a building block for modeling ...
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We study the problem of finding optimal control policies for Probabilistic Boolean Networks (PBNs). Boolean Networks (BNs) and PBNs are effective tools for modeling genetic regulatory networks. A PBN is a collection of BNs driven by a Markov chain process. It is well-known that the control/intervention of a genetic regulatory network is useful for avoiding undesirable states associated with dis...
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