Modeling gene expression with differential equations.

We propose a differential equation model for gene expression and provide two methods to construct the model from a set of temporal data. We model both transcription and translation by kinetic equations with feedback loops from translation products to transcription. Degradation of proteins and mRNAs is also incorporated. We study two methods to construct the model from experimental data: Minimum Weight Solutions to Linear Equations (MWSLE), which determines the regulation by solving under-determined linear equations, and Fourier Transform for Stable Systems (FTSS), which refines the model with cell cycle constraints. The results suggest that a minor set of temporal data may be sufficient to construct the model at the genome level. We also give a comprehensive discussion of other extended models: the RNA Model, the Protein Model, and the Time Delay Model.