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Reconstruction of gene regulatory networks (GRN) plays an important role in understanding the complexity, functionality and pathways of biological systems, which could support the design of new drugs for diseases. Because differential equation models are flexible and strong, these models have been utilized to identify biochemical reactions and gene regulatory networks. This paper investigates the differential equation models for reverse engineering gene regulatory networks. We introduce three kinds of differential equation models, including ordinary differential equation (ODE), time-delayed differential equation (TDDE) and stochastic differential equation (SDE). ODE models include linear ODE, nonlinear ODE and S-system model. We also discuss the evolutionary algorithms, which are utilized to search the optimal structures and parameters of differential equation models. This investigation could provide a comprehensive understanding of differential equation models, and lead to the discovery of novel differential equation models.
This article was published in the following journal.
Name: Current protein & peptide science
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Methods of studying differential GENE EXPRESSION of especially low-abundance, tissue-specific gene transcripts.
Any of the processes by which cytoplasmic factors influence the differential control of gene action in viruses.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.
Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in archaea.
Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control of gene action in plants.
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