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Updated: Aug 27, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
Published on: December 7, 2021
A computational model of a class of gene networks with positive and negative controls
1Bachelor of Technology Programme, Faculty of Engineering, National University of Singapore, 10 Kent Ridge Crescent, Singapore 119260, Singapore. engchenp@nus.edu.sg
Abstract:
This article proposes a computational framework for modelling the logical behavior of a class of gene networks. We characterize the basic behavior of genes in terms of a state-and-transition structure, and model the individual genes as language-generating automata. We consider positive and negative controls as the interaction mechanisms among the genes, and treat such controls as constraints (also expressed in automata) imposed on the behavior of the gene network. By computing the intersection of the languages generated by the gene models and the constraints, we obtain the complete set of pathways in a gene network. Implications and possible improvement of this work are discussed.
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