Francesco Musella

Decoding single-cell replication states from imaging data reveals locus-specific subnuclear position dependencies of replication initiation

The paper introduces RepTile, a framework to infer single-cell replication states from imaging data, revealing locus-specific dependencies of replication initiation on subnuclear position.

Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes

The paper identifies a nuclear subcompartment in mouse cerebellum formed by long enhancers and genes, and shows Etv1's role in their compartmentalization and expression.

Specialised super-enhancer networks in stem cells and neurons

The paper compares super-enhancer networks in embryonic stem cells and dopaminergic neurons, revealing their structural differences and functional roles in transcriptional regulation.

Prediction of single-cell chromatin compartments from single-cell chromosome structures by MaxComp

This paper introduces MaxComp, an unsupervised method to predict single-cell chromatin compartments from 3D chromosome structures, showing that compartment annotations can be derived from geometric considerations alone.

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

The paper investigates cell-type specific 3D chromatin structures in the brain using immunoGAM, finding TAD melting, neuron-specific contacts, and compartmentalization patterns related to gene expression and neurodegenerative diseases.