Sevastianos Korsak

The paper describes a project from the 4D Nucleome Hackathon aimed at developing a workflow for comparing and validating chromatin models, identifying challenges in model comparison and software development.

The paper introduces RepliSage, a framework that dynamically integrates replication timing, loop extrusion, and compartmentalization to simulate chromatin architecture during the cell cycle.

The paper introduces MultiMM, a 3D chromatin simulation model that generates genome-wide structures from nucleosome data using energy minimization.

The paper introduces an improved cohesin HiChIP protocol and analysis pipeline to enhance detection of chromatin loops and stripes.

LoopSage simulates chromatin loop extrusion using a Monte Carlo method, showing significant correlation with ChIA-PET data and phase transitions in chromatin structure.

The paper models chromatin folding using explosive percolation theory and shows that 80% of loops are needed for 3D condensation across cell lines.