Mathematical modeling of gene expression: a guide for the perplexed biologist.

The detailed analysis of transcriptional networks holds a key for understanding central biological processes, and interest in this field has exploded due to new large-scale data acquisition techniques. Mathematical modeling can provide essential insights, but the diversity of modeling approaches can be a daunting prospect to investigators new to this area. For those interested in beginning a transcriptional mathematical modeling project, we provide here an overview of major types of models and their applications to transcriptional networks. In this discussion of recent literature on thermodynamic, Boolean, and differential equation models, we focus on considerations critical for choosing and validating a modeling approach that will be useful for quantitative understanding of biological systems.