Christophe Zimmer

Antimicrobial resistance (AMR) is one of the most pressing global health problems of our times. To counteract AMR, we urgently need new antibiotics, particularly with novel modes of action (MoA). However, while typical antibiotic […]

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 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 […]

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 […]

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 […]

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 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/

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.

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 […]

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 […]

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 […]

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 […]