Ageing & Longevity
According to the WHO, the global percentage of people aged of more than 60 years will double from 11 to 22% between 2000 and 2050. Nowadays most of the elderly die of non-transmissible diseases […]
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
IINCEPTION Goal The Inception’s goal is to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in a range of health issues (Official website here : https://www.inception-program.fr/en). Inception program […]
Diagnosing SARS-CoV-2 infections early, quickly, and reliably is critical to isolate patients and slow down transmission. Current RT-PCR based diagnostic tests are insufficiently accessible, time consuming and have suboptimal sensitivity. We propose to develop […]
Deep learning for biology
Deep learning methods use artificial neural networks to learn complex mappings between raw numeric input data and higher order semantic outputs. These computational techniques are at the heart of recent advances in artificial intelligence, with breakthrough […]
Fluorescence microscopy is a defining technology in cellular biology but the diffraction of light limits the resolution of standard microscopes to ~200 nm, thus preventing detailed analyses of molecular structures. We are actively interested […]
Nuclear architecture and function
The one-dimensional sequence of the genome is carried by long polymers (chromosomes), which fold in the three dimensional volume of the nucleus. How this folding occurs and what it implies for genome function remains […]
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 […]
Imjoy – open access platform for deep learning methods
Imjoy is a web-based computing platform for deploying advanced image analysis tools such as deep learning (Ouyang et al., 2019). The door to Imjoy is here: https://imjoy.io/
ZOLA-3D Zernike Optimized Localization approach
This software allows to reconstruct 3D super-resolution microscopy images obtained using optically engineered point spread functions. See Aristov et al. 2018. Available at: https://github.com/imodpasteur/ZOLA-3D.
This software allows to vastly reduce the acquisition time of super-resolution localization microscopy. See https://annapalm.pasteur.fr/#/. The method is described in detail in Ouyang et al. 2018.
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 […]
FISH-quant: automatically counting transcripts in RNA-FISH images
A free Matlab-based toolbox to detect and count individual mRNA transcripts in single cells by automatic analysis of 3D RNA-FISH images. Software is available freely together with extensive instructions at : https://code.google.com/p/fish-quant/. The […]
QuickPALM: Reconstruction of PALM/STORM super-resolution microscopy images
A free and fast ImageJ plugin for reconstructing super-resolution 3D images in PALM/STORM microscopy is available freely for download at : http://code.google.com/p/quickpalm/This website also offers tutorials about using the software and practical information on […]
Nucloc: mapping gene territories in the yeast nucleus
We have developed a series of software tools to compute and analyze the positions of genomic loci from thousands of yeast cells observed in fluorescence microscopy. These tools are available freely to academic and […]
2021Single-molecule localization microscopy, 1 (1), 1-27.
2021Super-resolution visualization and modeling of human chromosomal regions reveals cohesin-dependent loop structures., Genome Biol 2021 May; 22(1): 150.
2021Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages., EMBO J 2021 Jan; 40(1): e105247.
2021Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH, bioRxiv.
2020A Dual Protein-mRNA Localization Screen Reveals Compartmentalized Translation and Widespread Co-translational RNA Targeting., Dev Cell 2020 Sep; 54(6): 773-791.e5.
2020instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder., Genome Biol 2020 06; 21(1): 148.
2019ImJoy: an open-source computational platform for the deep learning era, Nat. Methods 2019 Dec;16(12):1199-1200.
2019How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization, Annu Rev Biophys 2019 May;48:231-253.
2018A computational framework to study sub-cellular RNA localization, Nat Commun 2018 Nov;9(1):4584.
2018ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range, Nat Commun 2018 Jun;9(1):2409.
+View full list of publications