Nezar A. Abdennur

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

This study proposes that cohesin bridging, not spatial proximity, mediates enhancer-promoter communication and develops a model to validate this mechanism through engineered cell systems.

This study shows cohesin-mediated chromatin remodeling is essential for dendritic cell differentiation and function, particularly antigen cross-presentation and IL-12 secretion.

The paper introduces a framework to jointly decompose Hi-C maps across tissues and development, revealing distinct nuclear architecture patterns and improving gene expression prediction.

Bigtools provides a high-performance library for generating and querying BigWig and BigBed files in Rust, with Python bindings and cross-platform support.

Pairtools processes sequencing data into contact pairs for 3C+ analysis, offering high-performance and flexible tools for various protocols.

Cooltools provides scalable and flexible analysis tools for high-resolution Hi-C data, addressing challenges in storage, memory, and customization.

Bioframe provides a Python library for efficient genomic interval operations using pandas dataframes, extending the data science stack for computational genomics.

This study uses tunable DNMT1 degradation to investigate DNA methylation dynamics and genome organization, revealing cooperative roles of DNMT1 and DNMT3B and their impact on heterochromatin and cell fitness.

The paper identifies three inactive chromatin states in HCT116 cells and shows how H3K9me3-HP1/β heterochromatin influences genome compartmentalization and loop extrusion barriers through DNA methylation.

The paper introduces the 4DN Data Portal, a resource for searching and visualizing curated nucleomics data, including Hi-C and other chromosome architecture datasets.

This study improves chromosome architecture mapping by using Micro-C to achieve nucleosome-resolution insights in human cells, revealing new looping interactions and structural patterns.

A haplotype-resolved Hi-C approach reveals structured homolog pairing in early Drosophila embryos, correlated with Zelda-mediated chromatin accessibility.

Cooler provides a scalable storage format for multidimensional genomic datasets, enabling efficient compression and random access for analysis.

This study shows that deleting Ncaph2 in mouse hepatocytes does not alter chromatin folding or gene expression, suggesting condensin II's role in interphase may be limited.

HiGlass, a web-based, containerized viewer, enables continuous multiscale navigation of Hi-C contact maps alongside genomic tracks using composable views linked by location and zoom.

This study shows that cohesin removal leads to loss of TADs and loops but preserves compartments, revealing two independent modes of chromosome organization.

This study shows CTCF is essential for TAD organization but not for genome compartmentalization, revealing distinct mechanisms for chromatin folding and insulation.

The paper reviews polymer models and experimental evidence supporting loop extrusion as a mechanism for chromosome folding, focusing on CTCF and cohesin perturbations in interphase.