Ph.D. Program in Biomedical Sciences and Oncology

The research activity of the Computational Biology Unit focuses on gene regulation at the transcriptional and post-transcriptional levels. In particular we are currently investigating:

• The function, evolution and variation of regulatory regions in the human genome, with an approach based on Total Binding Affinity as a predictor of the binding of transcription factors to cis-regulatory regions. This approach naturally takes into account the contribution of weak binding sites and, from an evolutionary perspective, the phenomenon of binding site turnover. We are applying this approach to (a) the prediction of gene expression from sequence and chromatin data in human cell lines (b) the study of naturally occurring variation in gene expression in human populations, and the unraveling of its genetic origin (c) the evolution of cis-regulatory regions as a major determinant of anatomical and behavioral differences in humans and great apes
• The role of 3' UTRs in the post-transcriptional regulation of gene expression, in two related aspects: (a) competing endogenous RNAs, where the titration of microRNA abundance by their targets results in a regulatory cross-talk by targets of the same microRNAs that is wholly independent of their gene products (b) shortening of 3' UTR, in which proliferating cells escape regulation by microRNAs and other RNA-binding trans-acting factors by expressing shortened 3' UTR isoforms lacking binding sites for those factors.