Hub members Have many expertise, covering most of the fields in bioinformatics and biostatistics. You'll find below a non-exhaustive list of these expertise
Searched keyword : Cytometry
Related people (1)
Bernd Jagla received his PhD in bioinformatics (department of Biology, Chemistry, and Parmacy) from the Free University in Berlin, Germany in 1999. Before joining the Institut Pasteur, he worked for almost ten years in New York City, including as an associate research scientist in the Joint Centers for System Biology (Columbia University) and at the Columbia University Screening Center led by Dr J.E. Rothman. He joined the Institut Pasteur in 2009 to take charge of the bioinformatic needs at the Transcriptome et Epigenome platform, focusing on Next Generation Sequencing. As of 2016 he is member of the C3BI – HUB Team detached to the Human immunology center (CIH) and provides support for cytometry, next generation sequencing, and microarray data analysis. His areas of interest include the quality assurance and data analysis and visualization at the facility. He also has strong expertise in developing algorithms for function prediction from sequence data, image analysis, analysis of mass spectrometry data, workflow management systems. While at Pasteur he developed: KNIME extensions for Next Generation Sequencing (Link) Post Alignment Visualization and Characterization of High-Throughput Sequencing Experiments (Link) Post Alignment statistics of Illumina reads (Link)
AlgorithmicsChIP-seqData managementData VisualizationImage analysisMachine learningSequence analysisDatabaseGenome analysisBiostatisticsProgram developmentScientific computingData and text miningIllumina HiSeqGraphics and Image ProcessingIllumina MiSeqHigh Throughput ScreeningFlow cytometry/cell sortingPac Bio
Related projects (2)
Nous avons créer un programme sous R pur l'analyse non supervisé de fichier de cytométrie et nous avons besoin d'aide pour optimiser ce programme. Nous avons également besoin de conseils pour optimiser le clustering. Nous avons déjà rencontré Hugo Varet.
Invasion of human intestinal epithelial cells by Shigella flexneri is secondary to the delivery of bacterial effectors into the host cell cytoplasm via a type III secretion system (T3SS). By using a beta-lactamase reporter tool we observed that in contrast to the epithelium, human lymphocytes are mainly targeted by injection of T3SS effectors not resulting in subsequent cell invasion (Pinaud et al., 2017). Furthermore, we observed that the targeting process, in form of successful injection of effectors into the host cell, is dependent on glycan-glycan interactions between bacterial and host cell surfaces rendering the targeting process to be dependent on the activation state of the host cell (Belotserkovsky et al., 2018). CyTOF technology is a research tool used for phenotypic analysis of complex cell population allowing for the simultaneous labelling of up to 40 different surface and intracellular marker without issues of compensation as present in regular flow cytometry (van Unen et al., 2016). Using CyTOF technology and the beta-lactamase reporter tool, we will perform a detailed analysis of Shigella targeting in a complex cell population using human lamina propria mononuclear cells (LPMCs), isolated from human colon explants. Analysis will address the question if specific cellular subsets are preferentially targeted in the intestinal environment and if this differs from targeting of peripheral blood mononuclear cells (PBMCs) diverging in their immune phenotypes and cellular activation.