Gene Regulatory Network Investigation Using Ordinary Differential Equations

Abstract

This chapter reviews mathematical models of gene regulation, either as "pure" gene regulatory networks, as signal transduction pathways or as combinations of these. The basic underlying methods are discussed from first principles, relying on rigorous mathematical concepts but with an aim to avoid technical details and focus on the intuitive aspects of this type of mathematical models. After reviewing the principles, some real biological examples are presented to illustrate the practice of modeling, using recent examples from the literature. The proposed examples all arise in the context of plant biology, either at the single cell scale, looking at auxin signaling, or at higher scales, looking at auxin active transport.

Keywords: Auxin signaling; Differential equations; Gene networks; Modeling; Root development.