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Reverse Engineering of Metazoan Gene Regulatory Networks Bart Deplancke Institute of Bioengineering, School of Life Sciences, EPFL, Switzerland Gene regulatory networks play a vital role in metazoan development and function. The protein-DNA interactions (PDIs) that form the basis of these networks have however been poorly characterized. The recent availability of the human genome sequence, as well as genomic resources for other organisms, has permitted the development of novel methodologies that probe regulatory networks at a systems level rather than at the individual gene level. Most of these methods are transcription factor (TF)-centered, in that they use the TF as the experimental starting point, and inquire what the respective binding site or target genes are. We have developed a gene-centered high-throughput PDI detection method as a powerful alternative to TF-centered approaches. The latter method has so-far only been applied in C. elegans, but efforts are underway to adapt the technology for use in Drosophila and mammalian organisms as welI. The ultimate goal is to achieve a quantitative understanding of the gene regulatory networks that control metazoan differential gene expression through analysis of their composition, structure, function, and dynamic properties.