Foundations for modeling the dynamics of gene regulatory networks: a multilevel-perspective review.

摘要: A promising alternative for unraveling the principles under which dynamic interactions among genes lead to cellular phenotypes relies on mathematical and computational models at different levels of abstraction, from molecular level protein-DNA system functional relationships genes. This review article presents, a bottom–up perspective, hierarchy approaches modeling gene regulatory network dynamics, microscopic descriptions single-molecule in spatial context an individual cell macroscopic providing phenomenological population-average level. The reviewed include Molecular Dynamics, Particle-Based Brownian Master Equation approach, Ordinary Differential Equations, Boolean logic abstraction. Each these frameworks is motivated by particular biological nature insight being pursued. setting such involves assumptions artifacts often ignored non-specialist. aims entry point biologists new field computer scientists not acquainted with some recent biophysically-inspired regulation. connections promoting intuition between abstraction role that approximations play process are highlighted throughout paper.