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 : Sequencing
Related people (6)
I obtained an engineering degree in Biomedical engineering from Université de Technologie de Compiègne (UTC) in 1989, a master degree in Control of Complex Systems from UTC in 1990, a PhD in Control of Complex Systems from UTC in 1993, a University Degree in Human Genetics from The University of Rennes 1 in 2001 and a master degree in Functional Genomics from University Paris Diderot (Paris 7) in 2002. I worked as a statistician at the Transcriptome and Epigenome Platform from 2002 to 2017, where I was responsible for the statistical analyses of the data and had an important training activity (on the campus and outside). Since 2015 I have been co-head of the Bioinformatics and Biostatistics Hub within the Center of Bioinformatics, Biostatistics and Integrative Biology (C3BI). I am co-director of the Pasteur course Introduction to Data Analysis and co-organiser of the sincellTE summer school (a school dedicated to single cell transcriptome and epigenome data analysis). I am also co-managing the StatOmique group which gathers more than 60 statisticians from France.
RNA-seqStatistical inferenceTranscriptomicsBiostatisticsApplication of mathematics in sciencesExploratory data analysisIllumina HiSeqStatistical experiment designSequencing
- Biomarqueurs d’identification précoce du sepsis aux urgences (BIPS)(Jean-Marc CAVAILLON - Cytokines and Inflammation) - Awaiting Publication
- Study of the early pathogenesis during Lassa fever in cynomolgus monkeys and its correlation with the outcome(Sylvain BAIZE - Biology of Viral Emerging Infections) - In Progress
- Host microbiota modification by the pathogen Listeria monocytogenes(Javier PIZARRO-CERDA - Bacteria-Cell Interactions) - Closed
After a PhD in informatics on graph analysis (metabolic networks and sRNA-mRNA interaction graphs) at the LaBRI (Université de Bordeaux), I joined the DSIMB team (INTS) for a post-doc on structural modeling. Then, I performed a second post-doc at Metagenopolis – INRA Jouy-en-Josas, where I was initiated to the analysis of metagenomic data. I was recruited at the HUB in 2015, and since I pursue the development of methods dedicated to the treatment of metagenomic data by combining either the treatment of sequencing data, the statistics, the protein structural modeling and the graph analysis.
AlgorithmicsClusteringGenome assemblyGenomicsMetabolomicsModelingNon coding RNASequence analysisStructural bioinformaticsTargeted metagenomicsDatabaseGenome analysisBiostatisticsProgram developmentScientific computingDatabases and ontologiesExploratory data analysisData and text miningIllumina HiSeqComparative metagenomicsRead mappingIllumina MiSeqSequence homology analysisGene predictionMultidimensional data analysisSequencingShotgun metagenomics
- Regulation of nasopharyngeal microbiome in normal healthy individuals(James DI SANTO - Innate Immunity) - Pending
- Changes in cellular pathways during SARS-CoV-2 infection upon drug treatment(Bjoern MEYER - Viral Populations and Pathogenesis) - In Progress
- Identification, structural and functional analyses of peptides from SARS-Cov2 binding with high affinity to MHC-E and impact on NK cell responses in SARS-Cov2 infection(Huot NICOLAS - HIV, Inflammation and Persistence) - Pending
Rachel Legendre is a bioinformatics engineer. She completed her master degree in apprenticeship for two years at INRA in Jouy-en-Josas in the Genetic Animal department. She was involved in a project aiming at the detection and the expression analysis of micro-RNA involved in an equine disease. In 2012, she joined the Genomic, Structure and Translation Team at Paris-Sud (Paris XI) university. She worked principally on Ribosome Profiling data analysis, a new technique that allows to identify the position of the ribosome on the mRNA at the nucleotide level. Since november 2015, she worked at Institut Pasteur. During 4 years, she was detached to the Biomics Platform, where she was in charge of the bioinformatics analyses for transcriptomics and epigenomics projects. She was also involved in Long Reads (PacBio and Nanopore) developments with other bioinformaticians of Biomics. Since november 2019, she has joined the Hub of Bioinformatics and Biostatistics, et more precisely the Genome Organization Regulation and Expression group.
AlgorithmicsChIP-seqEpigenomicsNon coding RNATranscriptomicsGenome analysisProgram developmentScientific computingSofware development and engineeringIllumina HiSeqRead mappingSequencingWorkflow and pipeline developmentChromatin accessibility assaysPac BioRibosome profiling
BacteriaFungiParasiteHumanInsect or arthropodOther animal
- The master regulator of virulence gene expression in Group B Streptococcus(Arnaud FIRON - Biology of Gram-Positive Pathogens) - Pending
- Transcriptional analysis of injured skeletal muscle(Eleonora ROSSI - Stroma, Inflammation and Tissue Repair) - Closed
- Small RNA signature on RIG-I like receptors(Anastasia KOMAROVA - Molecular Genetics of RNA Viruses) - In Progress
After a Master degree in bioinformatics and biostatistics, I did a PhD in computer science / bioinformatics at University Paris-Sud (now in University Paris-Saclay), where I worked on integration and analysis of comparative genomics data. After a postdoc in Lausanne, Switzerland where I worked on small-RNA sequencing data, I joined GenoSplice where I was responsible for the development of bioinformatics projects related to next generation sequencing. I joined Institut Pasteur in Nov. 2015, to work in the Evolutionary Bioinformatics Unit and participate in the development of new tools and algorithms that are able to tackle efficiently the ever increasing amount of sequencing data.
AlgorithmicsData managementPhylogeneticsSequence analysisDatabaseGenome analysisProgram developmentScientific computingDatabases and ontologiesSequencingWorkflow and pipeline development
Image analysisStatistical inferenceBiostatisticsGeneticsSequencingDiagnostic tools
- Analysis of genes transcription profiles in E.coli after expression of the T4 phage protein Ndd(Foutel-Rodier THÉO - Spatial Regulation of Genomes) - In Progress
- Single-cell characterization of autoreactive IgG-secreting cells in Immune thrombocytopenia(Pablo CANALES HERRERIAS - Antibodies in Therapy and Pathology) - In Progress
- Phages - bacteria interactions network of the healthy human gut(Martial MARBOUTY - Spatial Regulation of Genomes) - Awaiting Publication
- A cost-effective molecular Tool for Strengthening Antimalarial drug Resistance surveillance in Africa (TSARA)(Didier MENARD - Group : Malaria Genetic and Resistance) - In Progress
- Study of the deficiency in lactose utilization by Shigella strains(Claude PARSOT - Enteric Bacterial Pathogens) - Closed
- A cost-effective molecular Tool for Strengthening Antimalarial drug Resistance surveillance in Africa (TSARA)(Didier MENARD - Group : Malaria Genetic and Resistance) - Closed
Related project (1)
Séquençage à haut débit (NGS) et traitement de séquences ADN des domaines variables d’anticorps simple chaine d’alpaga (domaines VHH ou Nanobodies®)
Dans notre laboratoire nous nous intéressons à la conception et construction de banques d’anticorps simple chaine issus du répertoire immunitaire des alpagas. Ces banques immunes, sont constituées d’u