The combinatorial interplay among regulators, such as transcription factors (TFs) and RNA binding proteins (RBPs), is an essential mechanism for achieving precise control of mRNA level (Jiang et al., Microrna 2012). To comprehensively understand the regulatory cooperativity, I developed a computational framework CCAT (Combinatorial Code Analysis Tool) for predicting genome-wide co-binding between regulators and applied it to Drosophila to uncover cooperativity among TFs during embryo development (Jiang et al., Nucleic Acids Res 2014). I also used CCAT to analyze the cooperativity between RBPs and microRNAs in transcript decay control and found the binding of RBP Pumilio can release nearby microRNA binding sites from secondary structures in a sequence-dependent manner (Jiang et al., PLoS Comput Biol 2013).
- Link to CCAT website
- Link to miRNA-RBP analysis page