Kevin LEBRIGAND – IPMC

Recherche

Intranet

Thème

Nathalie LEROUDIER

Michel LAZDUNSKI

Présentation

Head of the Computational Biology & Omics Data Analysis (CoBiODA) Bioinformatics Hub at the Institute of Molecular and Cellular Pharmacology of the CNRS in Nice-Sophia-Antipolis. Expert in bioinformatics omics data analysis using R and Python statistical workflows. Since 2015, Kévin Lebrigand has focused his expertise on methodological developments for single cell and spatial transcriptomics, using 10x Genomics Chromium and Visium libraries sequenced on Oxford Nanopore Technology PromethION long-read sequencer to perform isoform-level profiling at single cell spatial resolution. In the last 2 years, his work has mainly been dedicated to data analysis of highly multiplexed RNA in situ hybridisation assays performed on Merscope (Vizgen) and Xenium (10xGenomics) commercial platforms using state-of-the-art statistical workflows (Seurat, Scanpy, Squidpy, SpatialData).

Projets

Omics Data Integration Network (ODIN)

The volume of data from biological experiments is constantly increasing. The storage, access and exploitation of this highly heterogeneous heterogeneous […]

Publications

Lebrigand K, Bergenstråhle J, Thrane K, Mollbrink A, Meletis K, Barbry P, Waldmann R, Lundeberg J, The spatial landscape of gene expression isoforms in tissue sections., Nucleic Acids Res 2023 May; 51(8): e47.

Lebrigand K, Magnone V, Barbry P, Waldmann R, High throughput error corrected Nanopore single cell transcriptome sequencing., Nat Commun 2020 Aug; 11(1): 4025.

Baranek T, Lebrigand K, de Amat Herbozo C, Gonzalez L, Bogard G, Dietrich C, Magnone V, Boisseau C, Jouan Y, Trottein F, Si-Tahar M, Leite-de-Moraes M, Mallevaey T, Paget C, High Dimensional Single-Cell Analysis Reveals iNKT Cell Developmental Trajectories and Effector Fate Decision., Cell Rep 2020 Sep; 32(10): 108116.

Arguel MJ, LeBrigand K, Paquet A, Ruiz García S, Zaragosi LE, Barbry P, Waldmann R, A cost effective 5΄ selective single cell transcriptome profiling approach with improved UMI design., Nucleic Acids Res 2017 Apr; 45(7): e48.

Lebrigand K, He LD, Thakur N, Arguel MJ, Polanowska J, Henrissat B, Record E, Magdelenat G, Barbe V, Raffaele S, Barbry P, Ewbank JJ, Comparative Genomic Analysis of Drechmeria coniospora Reveals Core and Specific Genetic Requirements for Fungal Endoparasitism of Nematodes., PLoS Genet 2016 May; 12(5): e1006017.

Popa A, Lebrigand K, Barbry P, Waldmann R, Pateamine A-sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells., BMC Genomics 2016 Jan; 17(): 52.

Popa A, Lebrigand K, Paquet A, Nottet N, Robbe-Sermesant K, Waldmann R, Barbry P, RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing., F1000Res 2016 ; 5(): 1309.

Le Brigand K, Robbe-Sermesant K, Mari B, Barbry P, MiRonTop: mining microRNAs targets across large scale gene expression studies., Bioinformatics 2010 Dec; 26(24): 3131-2.

Le Brigand K, Barbry P, Mediante: a web-based microarray data manager., Bioinformatics 2007 May; 23(10): 1304-6.

Le Brigand K, Russell R, Moreilhon C, Rouillard JM, Jost B, Amiot F, Magnone V, Bole-Feysot C, Rostagno P, Virolle V, Defamie V, Dessen P, Williams G, Lyons P, Rios G, Mari B, Gulari E, Kastner P, Gidrol X, Freeman TC, Barbry P, An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes., Nucleic Acids Res 2006 Jul; 34(12): e87.