INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Inception 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. Inception program uses Integrative Biology, Social Science […]
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 […]
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 […]
2018ZOLA-3D allows flexible 3D localization microscopy over an adjustable axial range, Nat Commun 2018 Jun;9(1):2409.
2018Chromatin mobility upon DNA damage: state of the art and remaining questions, Curr. Genet. 2018 Jun;.
2018Visualization of Arenavirus RNA Species in Individual Cells by Single-Molecule Fluorescence Hybridization Suggests a Model of Cyclical Infection and Clearance during Persistence, J. Virol. 2018 06;92(12).
2018Deep learning massively accelerates super-resolution localization microscopy, Nat. Biotechnol. 2018 Jun;36(5):460-468.
2018From dynamic chromatin architecture to DNA damage repair and back, Nucleus 2018 Jan;9(1):161-170.
2017GPI-anchored proteins are confined in subdiffraction clusters at the apical surface of polarized epithelial cells, Biochem. J. 2017 12;474(24):4075-4090.
2017Functional organization of cytoplasmic inclusion bodies in cells infected by respiratory syncytial virus, Nat Commun 2017 09;8(1):563.
2017Chromatin stiffening underlies enhanced locus mobility after DNA damage in budding yeast, EMBO J. 2017 09;36(17):2595-2608.
2017Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme, Opt Express 2017 Jun;25(12):13668-13683.
2017Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations, Genome Biol. 2017 05;18(1):81.
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