Giancarlo Bonora

The paper investigates how CTCF-mediated chromatin insulation and structure regulate escape from X chromosome inactivation in mouse cells, showing that CTCF binding and domain organization are critical for maintaining XCI.

This study investigates how 3D chromatin organization changes during human endothelial cell differentiation and links these changes to gene expression and transcriptional regulation.

The paper integrates single-cell RNA-seq, ATAC-seq, and Hi-C data to study nuclear configuration and gene expression changes during stem cell differentiation and X inactivation, revealing discrete structural changes and delayed chromatin compaction.

ACE integrates clustering and marker gene selection into a single deep learning workflow to identify discriminative and nonredundant gene panels.

This study shows that Firre RNA has trans-acting effects on the inactive X chromosome, affecting histone modifications, PRC2 complex components, and chromatin structure.

This paper applies and extends MMD-MA to align single-cell transcriptome and chromatin accessibility data from ~2000 cells, demonstrating its scalability and accuracy.

This study uses topic modeling on scHi-C data to identify cell type-specific chromatin structural patterns and compartment structures.

The paper studies how nuclear architecture changes during human heart development using Hi-C, RNA-seq, and ATAC-seq, revealing dynamic chromosomal organization and gene regulation.

The paper introduces MREBS, a method for DNA methylation estimation that reduces sequencing costs while improving coverage compared to existing methods.

The paper shows Dxz4 orientation controls long-range contacts on the inactive X chromosome, maintaining its bipartite structure through CTCF motif direction.

This study compares OSKM reprogramming factor binding in human and mouse fibroblasts, finding conserved mechanisms and species-specific differences in target sites and regulatory networks.