Artificial Intelligence at the Institut Pasteur
Institut Pasteur is actively engaged in the application of artificial intelligence methods in biomedical research. In 2018, the Institute has created a Department of Computational Biology to strengthen its expertise in the analysis of […]
Drug Discovery & Screening at Institut Pasteur
The Technological Targeted Action Drug Discovery and Screening (ATC-DDS) coordinates projects and collaborations at the Institut Pasteur Paris campus on therapeutic development. It raises awareness for DDS in basic research projects and stimulates intra-campus […]
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 aims to develop a core structure to mobilize data resources, numerical sciences, and fundamental experimental biology in various health issues (Official website here: https://www.inception-program.fr/en). The inception program uses Integrative Biology, […]
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 […]
FISH-quant v2: a scalable and modular tool for smFISH image analysis
Regulation of RNA abundance and localization is a key step in gene expression control. Single-molecule RNA fluorescence in situ hybridization (smFISH) is a widely used single-cell-single-molecule imaging technique enabling quantitative studies of gene expression […]
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 software […]
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 […]
2023A specific molecular signature in SARS-CoV-2-infected kidney biopsies., JCI Insight 2023 Mar; 8(5): .
2023Polymer simulations guide the detection and quantification of chromatin loop extrusion by imaging., Nucleic Acids Res 2023 Feb; (): .
2023Deep learning in image-based phenotypic drug discovery., Trends Cell Biol 2023 Jan; (): .
2022ShareLoc – an open platform for sharing localization microscopy data., Nat Methods 2022 Oct; (): .
2022FISH-quant v2: a scalable and modular tool for smFISH image analysis., RNA 2022 06; 28(6): 786-795.
2022Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH., Life Sci Alliance 2022 Apr; 5(4): .
2022Molecular organization and mechanics of single vimentin filaments revealed by super-resolution imaging., Sci Adv 2022 Feb; 8(8): eabm2696.
2022Versatile CRISPR-Based Method for Site-Specific Insertion of Repeat Arrays to Visualize Chromatin Loci in Living Cells., Methods Mol Biol 2022 ; 2532(): 275-290.
2021Listeriolysin S: A bacteriocin from Listeria monocytogenes that induces membrane permeabilization in a contact-dependent manner., Proc Natl Acad Sci U S A 2021 Oct; 118(40): .
2021Single-molecule localization microscopy, 1 (1), 1-27.
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