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 : Data integration
Related people (6)
Emna has joined the C3BI in 2016 and worked actively in the IGDA platform doing research and education. Now, she is also part of the Viral Populations and Pathogenesis Unit (PVP).
Genome assemblySequence analysisProgram developmentData integrationRead mappingLIMSParallel computingGene predictionShotgun metagenomics
Since September 2016, I am a research engineer in the Bioinformatics and Biostatistics HUB of the Institut Pasteur and detached in the Proteomics facility. I have a PhD in Signal Processing from the Ecole Nationale Supérieure des Télécommunications de Bretagne (Telecom Bretagne) and a Master in Mathematics with a specialty in Statistical Engineering from Rennes 1 University. After my PhD, I was a research and teaching assistant in Mathematics at the Institut National des Sciences Appliquées (INSA) of Rennes, then I worked as a consultant for public local authorities in the company Ressources Consultants Finances. I started working in the field of Proteomics in October 2014 in the EDyP laboratory located in Grenoble (http://www.edyp.fr/). I have been working on the improvement of statistical analysis of bottom-up proteomics data. Today, most of the projects I work on consist of detecting changes in protein abundances using discovery-driven mass spectrometry. I am interested in the development of new methodologies to optimize proteomics data analysis pipelines, from the identification of peptides/proteins to their quantification and the interpretation of results. For this purpose, I worked on several R packages which can be downloaded from the CRAN and Bioconductor: cp4p (https://cran.r-project.org/web/packages/cp4p/index.html), imp4p (https://cran.r-project.org/web/packages/imp4p/index.html), DAPAR (http://bioconductor.org/packages/release/bioc/html/DAPAR.html) and its GUI ProStar.
Machine learningModelingPathway AnalysisProteomicsStatistical inferenceBiostatisticsApplication of mathematics in sciencesData and text miningData integrationStatistical experiment designMultidimensional data analysis
After a Master degree in Genetics at Magistère Européen de Génétique, Paris Diderot, I did a second Master in bioinformatics at University of Nantes where I focused my work on the study of mapping strategy for allele specific analysis at the bioinformatics platform of Institut Curie. I then joined Institut Pasteur to work on an ELIXIR project related to the bio.tools registry through the development of a dedicated tool and the participation of several workshops and hackathons. As an engineer of the bioinformatics and Biostatistics Hub, I am involved in several projects from Differential Analysis of RNA-seq data to Metagenomics. I am also in charge of the maintenance of the Galaxy Pasteur instance.
ChIP-seqEpigenomicsGenomicsSequence analysisProgram developmentDatabases and ontologiesSofware development and engineeringGeneticsData integrationRead mappingWorkflow and pipeline developmentConfocal Microscopy
- Impact of gut microbiota on lipid metabolism(Grégoire CHEVALIER - Microenvironment and Immunity) - Closed
- Analysis of IFITM RNA levels in vraious cell types and tissues(Olivier SCHWARTZ - Virus and Immunity) - Awaiting Publication
- Channels in metagenomics data(Delarue MARC - Structural Dynamics of Macromolecules) - Closed + 1 project
Data managementData VisualizationWeb developmentDatabaseProgram developmentDatabases and ontologiesSofware development and engineeringData integrationWorkflow and pipeline development
- crispr.pasteur.fr(David BIKARD - Synthetic Biology) - Closed
- The Flemmingsome: the proteome of intact cytokinetic midbodies(NEETU GUPTA-ROSSI - Membrane Traffic and Cell Division) - Awaiting Publication
- Development of a Software tool to integrate Bottomp-up, Middle-down and Top-down proteomics data(Mariette MATONDO - Proteomics,Structural Mass Spectrometry and Proteomics) - Pending
After graduating from Paris VI University with a PhD in Genetics on the “Role of histone protein post-translational modifications in splicing regulation” that I performed in the Epigenetic Regulation unit at the Institut Pasteur, I carried out two post-doctoral experiences. I first worked for three years as a postdoctoral associate of the Whitehead Institute for Biomedical Research/MIT in Cambridge (USA). My main project consisted in the integration of genomic and epigenomic data in order to predict the transcription factors that are potentially at the core of the regulation of the cell-type specific gene expression programs. I then joined the Institut Curie where I deepened my experience in multi-omics data analyses and integration to identify non-coding RNAs involved in cancer progression. I have recently joined the HUB-C3BI of the Institut Pasteur where I am performing high-throughput data integration to better understand biological complexity and contribute to precision medicine development.
ATAC-seqChIP-seqEpigenomicsNon coding RNAPathway AnalysisRNA-seqSingle CellSystems BiologyTool DevelopmentTranscriptomicsData integrationGraph theory and analysisCell biology and developmental biology
A computer scientist by training, I am applying this knowledge to solve biological problems and am particularly interested in modelling of biological systems, knowledge inference, ontologies and data visualisation.
AlgorithmicsData VisualizationMetabolomicsModelingPathway AnalysisPhylogeneticsSystems BiologyTool DevelopmentDatabaseProgram developmentScientific computingDatabases and ontologiesApplication of mathematics in sciencesSofware development and engineeringData and text miningEvolutionData integrationGraph theory and analysisWorkflow and pipeline developmentDiscrete and numerical optimization
VirusHuman Immunodeficiency virus (HIV)
- Modeling mitochondrial metabolism dormant Cryptococcus neoformans(Benjamin HOMMEL - Molecular Mycology) - In Progress
- Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment(Alice MEIGNIÉ - Viral Genomics and Vaccination) - In Progress
- Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation(Olivier GASCUEL - Evolutionary Bioinformatics) - In Progress
Related projects (6)
Innate lymphoid cells (ILCs) are the most recently identified components of the innate immune system. ILCs colonize different tissue sites and react promptly to microenvironmental perturbations. Due to their high plasticity, ILCs can shape their functional output in response to local cues. As such, ILCs play roles under homeostatic conditions and in the context of infection, chronic inflammation, metabolic diseases and cancer. Diverse ILC subsets (NK cells, ILC2) have been shown to regulate the metabolic homeostasis. Metabolic states affect cellular functions and have been shown to play an important role in the regulation of adaptive immunity. In contrast, almost nothing is known about innate lymphocytes metabolism and the importance of energy regulation for ILC function. This project will study metabolic profiles in human ILC subsets under diverse environmental conditions. Enhancing or interfering with ILC activity could ultimately represent a novel useful therapy for chronic inflammatory diseases.
Insight into the Immune System: A bioresource and data-sharing platform to study chronic inflammatory diseases (IsIShare)
Chronic inflammatory systemic diseases (CIDs) are a burden to humans because of life-long debilitating illness, increased mortality and high therapy costs. CIDs’ increasing prevalence in western countries has indeed placed them at the third rank of morbi-mortality causes. Unfortunately, available treatments are poorly targeted and non-curative. That is partly linked to a complex and largely ununderstood pathophysiology. Genetic susceptibility clearly plays a role. Genes linked to the immune system have been identified, but causal genes remain mostly unknown and other factors such as intestinal microbiota have also been implicated. The complexity of CIDs’ pathophysiology suggests that a holistic approach is the most susceptible to help make significant progress. Our project intends to take advantage of recent technical progress and development of informatics tools to set up a transversal approach. High-resolution sequencing technology indeed quickly produces large amounts of accurate data. Besides, new integrative informatics tools allowing storage and integrative analysis of this resulting high amount of data are now available. We intend to set-up a CID’s network allowing the gathering and extensive analysis of data related to immuno-genetic determinants, immune repertoire and microbiota from individuals suffering from one of the three major interlinked CIDs, namely Hidradenitis Suppurativa (HS), Crohn’s disease (CD) and Spondyloarthropathy (SpA) as compared to healthy volunteers.
It has been shown that methylation can act as a kind of memory of the immune system. For patients with co-infections, it is of particular importance to know when to begin an anti-retroviral therapy, especially if they are already infected with tuberculosis. The goal of this study is to find hyper or hypo methylated loci related to the reaction of HIV patients (co-infected or not) to different kind of treatments.
Cellular senescence is a complex stress response that durable (yet not irreversibly) arrests cell proliferation and is accompanied by widespread changes in chromatin structure, metabolism and gene exp
Asymptomatic pathogen carriage in stunted and non-stunted children living in Antananarivo, Madagascar
This project is integrated in the analysis of the gut ecosystem of children implicated in the AFRIBIOTA project, a translational project performed within a consortium of researchers and medical doctor
Bacteriophages infect bacteria. One bacteriophage can infect several strains. Around the world, many labs have performed spot tests to determine the host range of bacteriophages but this information i