Francesco Ferrari

Biochemical properties of chromatin domains define genome compartmentalization

The paper develops 4f-SAMMY-seq to map euchromatin and heterochromatin based on accessibility and solubility, and reconstructs their 3D compartmentalization in one experiment.

CHD8 Suppression Impacts on Histone H3 Lysine 36 Trimethylation and Alters RNA Alternative Splicing.

This study shows that CHD8 suppression reduces H3K36me3 levels and alters alternative splicing of ~2000 genes, linking CHD8 to RNA processing and ASD.

Leveraging three-dimensional chromatin architecture for effective reconstruction of enhancer-target gene regulatory network

This paper introduces a statistical framework integrating 3D chromatin architecture to improve enhancer-target gene pairing and benchmark it against existing methods.

Early Polycomb-target deregulations in Hutchinson-Gilford Progeria Syndrome revealed by heterochromatin analysis

The paper identifies early chromatin structural changes in HGPS using a new method, showing Polycomb target gene deregulation linked to lamin-associated domain disruption.

A ChIC solution for ChIP-seq quality assessment

The paper introduces ChIC, a ChIP-seq quality assessment framework that evaluates enrichment profile shape, providing a reliable score for data quality.