title: A primer on thermodynamic-based models for deciphering transcriptional regulatory logic.
abstract: A rigorous analysis of transcriptional regulation at the DNA level is crucial to the understanding of many biological systems. Mathematical modeling has offered researchers a new approach to understanding this central process. In particular, thermodynamic-based modeling represents the most biophysically informed approach aimed at connecting DNA level regulatory sequences to the expression of specific genes. The goal of this review is to give biologists a thorough description of the steps involved in building, analyzing, and implementing a thermodynamic-based model of transcriptional regulation. The data requirements for this modeling approach are described, the derivation for a specific regulatory region is shown, and the challenges and future directions for the quantitative modeling of gene regulation are discussed.
authors: Department of Mathematics, Harvey Mudd College, Claremont, CA 91711, USA. dreschja@msu.edu
authors: Jacqueline M
authors: JM
authors: Dresch
authors: Megan
authors: M
authors: Richards
authors: Ahmet
authors: A
authors: Ay
mesh_terms: D005786:Gene Expression Regulation; D008957:Models, Genetic; D013816:Thermodynamics; D014158:Transcription, Genetic
keywords: Enhancer; Parameter estimation; Sensitivity analysis; Thermodynamic modeling; Transcriptional regulation