GENETIC "CODE": Representations and Dynamical Models of Genetic Components and Networks

• Published in: Annual review of genomics and human genetics Vol. 3; no. 1; pp. 341 - 369
• Main Authors: Gilman, Alex, Arkin, Adam P
• Format: Journal Article
• Language: English
• Published: Palo Alto, CA 94303-0139 Annual Reviews 01.01.2002; 4139 El Camino Way, P.O. Box 10139; USA
• Subjects: Animals; Escherichia coli - genetics; gene expression; Gene Expression Regulation; Lac Operon - genetics; mathematical models; Models, Genetic; Models, Theoretical; Operon - genetics; regulation; Signal Transduction; transcription; Transcription, Genetic; translation
• ISSN: 1527-8204; 1545-293X
• DOI: 10.1146/annurev.genom.3.030502.111004

Dynamical modeling of biological systems is becoming increasingly widespread as people attempt to grasp biological phenomena in their full complexity and make sense of an accelerating stream of experimental data. We review a number of recent modeling studies that focus on systems specifically involving gene expression and regulation. These systems include bacterial metabolic operons and phase-variable piliation, bacteriophages T7 and λ, and interacting networks of eukaryotic developmental genes. A wide range of conceptual and mathematical representations of genetic components and phenomena appears in these works. We discuss these representations in depth and give an overview of the tools currently available for creating and exploring dynamical models. We argue that for modeling to realize its full potential as a mainstream biological research technique the tools must become more general and flexible, and formal, standardized representations of biological knowledge and data must be developed.