A Monte Carlo method for in silico modeling and visualization of Waddington's epigenetic landscape with intermediate details.

A Monte Carlo method for in silico modeling and visualization of Waddington's epigenetic landscape with intermediate details. Biosystems. 2020 Oct 17;:104275 Authors: Zhang X, Chong KH, Zhu L, Zheng J Abstract Waddington's epigenetic landscape is a classic metaphor for describing the cellular dynamics during the development modulated by gene regulation. Quantifying Waddington's epigenetic landscape by mathematical modeling would be useful for understanding the mechanisms of cell fate determination. A few computational methods have been proposed for quantitative modeling of landscape; however, to model and visualize the landscape of a high dimensional gene regulatory system with realistic details is still challenging. Here, we propose a Monte Carlo method for modeling the Waddington's epigenetic landscape of a gene regulatory network (GRN). The method estimates the probability distribution of cellular states by collecting a large number of time-course simulations with random initial conditions. By projecting all the trajectories into a 2-dimensional plane of dimensions i and j, we can approximately calculate the quasi-potential U(xi,xj,∗)=-ln P(xi,xj,∗), where P(xi,xj,∗) is the estimated probability of an equilibrium steady state or a non-equilibrium state. Compared to the state-of-the-art methods, our Monte Carlo method can quantify the global potential landscape (or emergence behavior) of GRN for a high dimensional system. The...
Source: Biosystems - Category: Biotechnology Authors: Tags: Biosystems Source Type: research