Romain Koszul

Origins and dynamics of oral dysbiosis associated with environmental enteric dysfunction. Preventive intervention in Central African infants. Objectives and research hypothesis Considering that the presence of oropharyngeal pathobionts in the duodenum and the gut […]

The folding of eukaryotic and prokaryotic chromosomes consists of an assortment of intertwined structural features. The resulting complex networks of contacts is highly dynamic and interacts functionally with, or regulates metabolic processes ranging from […]

Ce projet vise à comprendre les interactions fonctionnelles et mécaniques entre chromosomes, périphérie nucléaire et cytosquelette, ainsi que leur influence sur la stabilité génomique, à travers des approches in vivo et in vitro chez […]

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data structures, […]

https://github.com/koszullab/instaGRAAL Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of data, we developed […]

Chromosomes of all species studied so far display a variety of higher-order organizational features such as domains, loops, or compartments. Many of these structures have been characterized from the genome-wide contact maps generated by […]

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320618/ Motivation: Hi-C contact maps reflect the relative contact frequencies between pairs of genomic loci, quantified through deep sequencing. Differential analyses of these maps enable downstream biological interpretations. However, the multi-fractal nature of the […]

A software to reconstruct 1D genome structures from 3D contact data obtained from Hi-C experiments. This movie shows the iterative assembly by GRAAL of the Trichoderma reesei genome (right) using contact frequencies determined by […]

https://github.com/koszullab/metaTOR We have pushed further our analysis about the potential of 3D contact data to solve genomics limitations and problems. We have developed meta3C, a metagenomic chromosome conformation capture approach that allows characterizing individual […]