Cells efficiently carry out organic synthesis, energy transduction, and signal processing across a range of environmental conditions and at nanometer scales-rivaling any engineered system. In the cell, these processes are orchestrated by gene networks, which we define broadly as networks of interacting genes, proteins, and metabolites. Understanding how the dynamics of gene networks give rise to cellular functions is a principal challenge in biology, and identifying their structure is the first step towards their control. This knowledge has applications ranging from the improvement of antibiotics, the engineering of microbes for environmental remediation, and the creation of biologically-derived energy sources. In this review, we discuss several methods for the identification of gene networks. (c) 2005 Elsevier Ltd. All rights reserved.