Gianluca Pegoraro

The paper identifies DNA replication machinery components as critical for TAD boundary re-establishment during DNA replication.

The paper investigates the relationship between TAD boundaries and gene activity using single-cell imaging, finding they are largely uncoupled.

The paper identifies molecular regulators of centromere distribution by screening nuclear proteins and shows that mitosis influences interphase genome organization.

The paper identifies that DUB inhibitors and RNF168-mediated ubiquitylation drive SLFN11 chromatin recruitment, particularly at promoters, and that this process is suppressed by TAK243.

This study shows that transcriptional specificity is achieved through kinetic proofreading, where promoters discriminate specific TF interactions based on dwell time rather than occupancy.

OptoLoop enables light-induced manipulation of chromatin contacts to study genome organization's role in gene regulation, showing looping-mediated repression of TERT.

MetaChrome automates metaphase chromosome analysis using deep learning, improving segmentation accuracy and enabling colocalization analysis of FISH signals and proteins.

The paper develops a framework to quantitatively analyze spatial centromere distribution patterns using clustering metrics and modeling techniques, identifying Ripleys K Score as the most accurate metric.

The paper develops an Optical Pooled Screen (OPS) assay using telomeric native DNA FISH to measure ALT pathway activity and identifies regulators of the ALT pathway.

This study identifies novel genes that modulate the ALT pathway using a high-throughput imaging screen, revealing both promoting and inhibiting factors and demonstrating pharmacological modulation potential.

The paper develops a method to prioritize enhancers linked to pancreas disease risk by integrating chromatin interactions, machine learning, and single-cell perturbation assays.

The paper develops high-throughput DNA/RNA FISH methods to visualize allele-level chromatin features and gene activity across cell populations.

HiTIPS provides a flexible, open-source platform for high-throughput image analysis in cell biology, supporting customization and integration of new algorithms for tasks like segmentation, tracking, and quantification.

The paper develops and validates hcHCR, a high-content imaging method for single-cell mRNA quantification in primary human immune cells, demonstrating its sensitivity, scalability, and multiplexing capability.

This study identifies CTCF as a barrier to 2C-like reprogramming in ESCs, showing its role in maintaining chromatin structure and that its depletion promotes totipotent-like state conversion.

This paper introduces HiHiMap, a high-throughput imaging technique to quantify histone and PTM levels across the cell cycle at the single-cell level, revealing differences in PTM behavior between normal, immortalized, and transformed cells.

This study investigates cell-to-cell and cell-intrinsic variability in genome organization using Hi-C and genome imaging in human fibroblasts, revealing extensive heterogeneity in chromatin conformations.

This study compares 2D and 3D distance measurements for analyzing spatial genome organization, finding 3D more accurate but noisier, and 2D preferable for comparative cell analyses.