ERC-2017-COG Synarchic – Investigating the functional architecture of microbial genomes with synthetic approaches
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 […]
ERC-2010-StG Interaction dynamique entre chromosomes eucaryotes : impact sur la stabilité du génome (DICIG)
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 […]
instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder
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 […]
Chromosight: A computer vision program for pattern detection in chromosome contact maps
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 […]
Serpentine: a flexible 2D binning method for differential Hi-C analysis
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 […]
GRAAL: genome assembly from chromosome contact frequencies
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 […]
META3C (MetaHiC), metaTOR
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 […]
2020instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder., Genome Biol. 2020 Jun; 21(1): 148.
2020Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum., Nat Commun 2020 Mar; 11(1): 1485.
2020Regulation of Cohesin-Mediated Chromosome Folding by Eco1 and Other Partners, Mol. Cell 2020 Jan;.
2019Perspectives on Chromosome Organization, J. Mol. Biol. 2019 Dec;.
2019FACT mediates cohesin function on chromatin, Nat. Struct. Mol. Biol. 2019 Oct;26(10):970-979.
2019MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries, Front Genet 2019;10:753.
2019Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis, Mol. Cell 2019 07;75(1):131-144.e3.
2019Dynamic Processing of Displacement Loops during Recombinational DNA Repair, Mol. Cell 2019 03;73(6):1255-1266.e4.
2018Tridimensional infiltration of DNA viruses into the host genome shows preferential contact with active chromatin, Nat Commun 2018 Oct;9(1):4268.
2018Generation of a Metagenomics Proximity Ligation 3C Library of a Mammalian Gut Microbiota, Meth. Enzymol. 2018;612:183-195.
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