Bin Yang* and Yuehui Chen
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.
Gene regulatory network, differential equation, gene expression data, time-delayed, S-system, reverse engineering
School of Information Science and Engineering, Zaozhuang University, Zaozhuang, 277160, School of Information Science and Engineering, University of Jinan, Jinan, 250022