Accurate reconstruction of the regulatory networks that control gene expression is one of the
key current challenges in molecular biology. Although gene expression and chromatin state
dynamics are ultimately encoded by constellations of binding sites recognized by regulators
such as transcriptions factors (TFs) and microRNAs (miRNAs), our understanding of this
regulatory code and its context-dependent read-out remains very limited. Given that there
are thousands of potential regulators in mammals, it is not practical to use direct …

… We developed a methodology that models gene expression or chromatin modifications in
terms of genome-wide predictions of regulatory sites and completely automated it into a web-based
tool called ISMARA (Integrated System for Motif Activity Response Analysis). Given only gene
expression or chromatin state data across a set of samples as input, … Here we present
ISMARA (Integrated System for Motif Activity Response Analysis), a completely automated
computational tool that aims to make the computational reconstruction of regulatory circuitry …