Deriving gene regulatory network dynamics directly from DNA sequence information

Develop a systematic calculation that starts from genomic sequence information—such as transcription factor binding site sequences and enhancer architectures—and derives explicit dynamical regulatory equations for gene expression, including regulation functions and network parameters as in the Monod–Wyman–Changeux formulations and spatiotemporal dynamical models of gap gene networks.

Background

Advances in genome editing enable precise manipulation of transcription factor binding sites and enhancer sequences, but current theoretical frameworks lack a systematic way to translate sequence‑level information into quantitative regulatory dynamics.

Connecting DNA sequence to network parameterizations and dynamical equations would greatly enhance predictive models and interpretability of perturbation experiments in developmental systems.