Irene Farabella

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

This paper introduces COMET, a drift correction method for SMLM that improves resolution and temporal precision, and demonstrates its effectiveness across multiple SMLM techniques.

The paper uses ultra-deep Hi-C and a new computational method to fine-map nuclear compartments, revealing that active promoters and enhancers localize in the A compartment even when adjacent sequences are inactive.

This study examines 3D genome architecture changes during B cell differentiation and in B cell neoplasias using Hi-C and multi-omic data, revealing dynamic compartment shifts and tumor-specific chromatin reorganization.

This paper introduces a method to reconstruct 3D chromatin organization from sparse 3C-based data, achieving reliable results with as little as 2-3% of the interaction matrix.

TADpole identifies hierarchical chromatin domains in Hi-C data, revealing significant structural differences between wild-type and mutant mouse strains.

The paper links diabetes-associated enhancers with their target genes using 3D chromatin architecture in human pancreatic islets, revealing genetic variants that impact insulin secretion heritability.

The paper introduces TADdyn, a tool that simulates chromatin structural rearrangements during cell reprogramming using time-course 3C data and molecular dynamics, revealing a hit-and-stick mechanism for transcriptional stabilization.

The paper uses super-resolution imaging and integrative modeling to achieve 10 kb resolution of chromosome folding.

The paper introduces Proximity RNA-seq to study nuclear transcriptome organization, revealing bipartite compartments with distinct RNA density and transcription elongation rates.