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The interactions between transcription factors (TFs) and their DNA binding sites are an integral part of gene regulatory networks within cells. We study these interactions in the yeast S. cerevisiae, the fruit fly D. melanogaster, mouse and human. For these studies, we develop and apply high-throughput genomic and proteomic technologies, as well as computational methods. The resulting data have permitted us to identify novel TFs and their DNA binding site motifs, predict the target genes and condition-specific regulatory roles of TFs, predict tissue-specific transcriptional enhancers, investigate functional divergence of paralogous TFs within a TF family, investigate the molecular determinants of TF-DNA ‘recognition’ specificity, and distinguish direct versus indirect TF-DNA interactions in vivo.
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