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 (5)
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) - In Progress
- 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 + 1 project
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
- Characterization of the bacterial and fungal microbiota in Aedes aegypti natural breeding sites and larvae(Louis LAMBRECHTS - Insect-Virus Interactions) - Pending
- Targeted search of specific commensals in 16S databases(Pamela SCHNUPF - Molecular Microbial Pathogenesis) - In Progress
- Microbiota dysbiosis in human colon cancer(Iradj SOBHANI - Other) - 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 joined the Bioinformatics and Biostatistics HUB at Pasteur Institute and she’s detached to the Biomics Pole in C2RT, where she is in charge of the bioinformatics analyses for transcriptomics and epigenomics projects. She’s also involved in Long Reads (PacBio and Nanopore) developments with other bioinformaticians of Biomics Pole.
AlgorithmicsChIP-seqEpigenomicsNon coding RNATranscriptomicsGenome analysisProgram developmentScientific computingSofware development and engineeringIllumina HiSeqRead mappingSequencingWorkflow and pipeline developmentChromatin accessibility assaysPac BioRibosome profiling
BacteriaFungiParasiteHumanInsect or arthropodOther animal
- Genome-wide interactions between HP1g and RNA.(Christophe RACHEZ - Epigenetic Regulation) - In Progress
- Identification of eukaryotic 5'UTRs(Arnaud ECHARD - Membrane Traffic and Cell Division) - Closed
- Functional interactions between HP1 proteins and RNA.(Christophe RACHEZ - Epigenetic Regulation) - Closed
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
- Serpentine: a flexible 2D binning method for differential Hi-C analysis(Vittore SCOLARI - Spatial Regulation of Genomes) - In Progress
- The anti-IgE antibody Omalizumab induces adverse reactions through engagement of Fc gamma receptors(Bianca BALBINO - Antibodies in Therapy and Pathology) - In Progress
- LGP2 binds PACT to regulate RIG-I- and MDA5-mediated antiviral response(Anastassia KOMAROVA - Viral Genomics and Vaccination) - In Progress
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