Johan Harmen Gibcus

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

UnionLoops improves chromatin loop detection across related Hi-C datasets by integrating information to enhance specificity, precision, and sensitivity.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

In DT40 cells, condensins displace extrusive cohesin, bypass cohesive cohesin and stall against each other while extruding ~1-3 kb/sec, yielding irregular helical chromatids of consecutive loops.

The paper uses polymer physics models to simulate and analyze the 3D structure of the LTN1 gene region, comparing results with Hi-C data to predict structural features for microscopy experiments.

The paper uses multi-omics analysis to compare malignant and normal uveal melanocytes, identifying genomic instability and a BAP1 promoter deletion as key features of uveal melanoma.

The paper reanalyzes sperm chromatin structure in mice, finding that prior studies were contaminated by cell-free chromatin, and identifies open loci associated with early development.

This study shows that cohesin-mediated loops in G1 phase determine the genomic location of replication origins in S phase by anchoring replication initiation zones.

This study evaluates 3C-based assays to understand how experimental parameters affect chromatin interaction detection and quantification, leading to the development of Hi-C 3.0.

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.

The paper shows mitotic chromosomes form through condensin-mediated disassembly of interphase chromatin and helical winding of loop arrays during prophase and prometaphase.

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

Hi-C 2.0 improves Hi-C protocol to achieve high-resolution mapping of chromatin interactions with better resolution and reduced noise.