Karolina Jodkowska

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.

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.

Three-dimensional connectivity and chromatin environment mediate the activation efficiency of mammalian DNA replication origins

The paper investigates how 3D chromatin structure and chromatin environment influence DNA replication origin activation efficiency in mouse embryonic stem cells under stress and control conditions.

Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells

The paper uses super-resolution microscopy to visualize a chromatin loop in human cells and validates the results with Hi-C data.