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 […]
2022Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection-related chromatin reorganization., Genome Res 2022 Sep; (): .
2022Karyotype engineering reveals spatio-temporal control of replication firing and gene contacts., Cell Genom 2022 Aug; 2(8): None.
2022Smc3 acetylation, Pds5 and Scc2 control the translocase activity that establishes cohesin-dependent chromatin loops., Nat Struct Mol Biol 2022 Jun; 29(6): 575-585.
2022Metagenomes Binning Using Proximity-Ligation Data., Methods Mol Biol 2022 ; 2301(): 163-181.
2022Normalization of Chromosome Contact Maps: Matrix Balancing and Visualization., Methods Mol Biol 2022 ; 2301(): 1-15.
2021Cohesin regulates homology search during recombinational DNA repair., Nat Cell Biol 2021 Nov; 23(11): 1176-1186.
2021Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga., Sci Adv 2021 Oct; 7(41): eabg4216.
2021Generation of gene-level resolution chromosome contact maps in bacteria and archaea., STAR Protoc 2021 Jun; 2(2): 100512.
2021Closed and High-Quality Bacterial Genome Sequences of the Oligo-Mouse-Microbiota Community., Microbiol Resour Announc 2021 Apr; 10(17): .
2021MetaHiC phage-bacteria infection network reveals active cycling phages of the healthy human gut., Elife 2021 Feb; 10(): .
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