Sevastianos Korsak

The challenge of chromatin model comparison and validation a project from the first international 4D Nucleome Hackathon

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.

Chromatin as a Coevolutionary Graph: Modeling the Interplay of Replication with Chromatin Dynamics

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

Multiscale Molecular Modelling of Chromatin with MultiMM: From Nucleosomes to the Whole Genome

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

Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes

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

LoopSage: An Energy-Based Monte Carlo approach for the Loop Extrusion Modelling of Chromatin

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

Multi-scale phase separation by explosive percolation with single chromatin loop resolution

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