Krzysztof H. Banecki

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.

ChromMovie: A Molecular Dynamics Approach for Simultaneous Modeling of Chromatin Conformation Changes from Multiple Single-Cell Hi-C Maps

ChromMovie models 3D chromatin structure changes across cellular trajectories using single-cell Hi-C data and cell cycle information.

Tri-omic mapping revealed concerted dynamics of 3D epigenome and transcriptome in brain cells

The paper introduces a tri-omic method to study 3D epigenome and transcriptome dynamics in brain cells across mouse lifespan, revealing distinct genomic mechanisms in neurons and non-neuronal cells.

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.