The combinatorial cross-regulation of hundreds of sequence-specific transcription factors (TFs) defines the core regulatory network of a cell. Such mutual cross-regulation among groups of TFs controls complex functions such as pluripotency and differentiation, and endows a cell with systems-level properties such as robustness and memory.
Genomic footprinting drives a powerful and generic approach for elucidating the the circuitry, dynamics, and organizing principles of regulatory networks. We are currently applying this approach to understand the regulatory circuitry of diverse cells, tissues, and organisms. We are also developing novel tools for network visualization and analysis such as the human transcription factor network browser www.regulatorynetworks.org.