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  • Visiting Scientist
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  • Director of Center
  • Director of Department
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© Research

Projects

Project
Ongoing
2 Members

ERC-2017-COG Synarchic – Investigating the functional architecture of microbial genomes with synthetic approaches

Romain Koszul (PI)

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 […]
Project
Completed
2 Members

ERC-2010-StG Interaction dynamique entre chromosomes eucaryotes : impact sur la stabilité du génome (DICIG)

Romain Koszul (PI)

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 […]

Software

Software
Ongoing
6 Members

instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder

Romain Koszul (PI)

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 […]
Software
Ongoing
9 Members

Chromosight: A computer vision program for pattern detection in chromosome contact maps

Romain Koszul (PI)

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 […]
Software
Ongoing
5 Members

Serpentine: a flexible 2D binning method for differential Hi-C analysis

Romain Koszul (PI)

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 […]
Software
Completed
6 Members

GRAAL: genome assembly from chromosome contact frequencies

Christophe Zimmer (PI)

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 […]
Software
Ongoing
6 Members

META3C (MetaHiC), metaTOR

Romain Koszul (PI)

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 […]

Publications

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