Overview
We are interested in understanding gene expression regulation at different levels, mainly transcriptional and post-transcriptional, and the integration of the different types of regulations in regulatory circuits and regulatory networks. A main topic in the lab involves post-transcriptional regulation of gene expression in bacteria by both small RNAs (sRNAs) and RNases. We developed RIL-seq (Melamed et al, 2016), an experimental-computational methodology to decipher the sRNA-target network of a bacterium at a transcriptome-wide scale. RIL-seq was applied first to Escherichia coli and opened many research directions in the lab, such as the discovery of novel sRNAs processed from 3’ UTR of protein-coding genes, involvement of sRNAs in virulence pathways of pathogenic bacteria, and integration of regulation by sRNAs with cleavage by RNases. Most of our studies are large-scale, generating extensive amounts of data, presenting ample opportunities to process these data in original ways and find hidden jewels. This way, we were excited to discover novel mechanisms of transcription termination and involvement of premature termination in regulation of gene expression, inferred from sequencing data per se.
Our laboratory is interdisciplinary, combining state-of-the-art wet-lab experiments with advanced computational analyses. The projects in the lab are conducted either by lab members with interdisciplinary background in computer science and life sciences, or by fruitful collaborations between lab members with complementary backgrounds in life sciences, medical sciences, computer science, and physics.