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 : Comparative metagenomics
Related people (4)
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
- Evaluation of a novel mouse model for Primary Antibody Deficiency (PAD)(Lise HUNAULT - Antibodies in Therapy and Pathology) - In Progress
- Measles virus type 1 infection disturbs the mitochondrial network leading to type I interferon production through the RNA polymerase III/RIG-I pathway(Jean-Pierre VARTANIAN - Department of Virology) - Pending
- Comparative analysis of choanoflagellate proteomic data(Thibaut BRUNET - Other) - Closed
I am seeking to apply my knowledge in computer science and statistics to understand real world data. I have interdisciplinary background spanning complex systems, Big Data, machine learning, biostatistics and genomics. I have completed a PhD in which I applied clustering and PCA to epigenomics data and discovered new insights on the coupling between replication and epigenetics. I worked at Dataiku, a dynamic start up in which I was actively engaged to help their clients to build their Big Data strategy and draw value from their data. I studied the human microbiota during two years at MetaGenoPolis (MGP), an innovative research center. We aim at improving human health by developing strategies (eg. nutritional, therapeutical, preventive…) to restore dysbiosed microbiota with our industrial and academical partners. I currently work in the statistical genetics group at the Pasteur Institut where I apply my software development and data science skills to quantify the impact of the human genome variation on diverse health parameters.
ClusteringData managementGenomicsGenome analysisExploratory data analysisGeneticsComparative metagenomicsDimensional reductionMultidimensional data analysis
I have been involved in genomic projects for prokaryotic and human genetic studies (GWAS) since 1998. Currently, I am working on novel visualization techniques to explore large and highly complex data sets. I have develop a web based graphical user interface, called SynTView (http://genopole.pasteur.fr/SynTView/) to visualize biological features in comparative genomic studies. The tool allows interactive visualization of microbial genomes to investigate massive amounts of information efficiently. The software is characterized by the presentation of synthetic organisations of microbial genomes and the visualization of polymorphism data. I am extending this work into designing novel dynamic views for comparative analysis of viruses in emerging disease.
Data VisualizationDatabaseSofware development and engineeringComparative metagenomicsOrthology and paralogy analysis
- Detection of newly produced NIRVS in mosquito persistently infected cells(Anna-Bella FAILLOUX - Arboviruses and Insect Vectors) - Pending
- Genetic diversity of arbovirus populations in Aedes aegypti mosquitoes from Colombia(Anna-Bella FAILLOUX - Arboviruses and Insect Vectors) - Pending
- Genetic diversity of yellow fever virus populations in mosquitoes(Anna-Bella FAILLOUX - Arboviruses and Insect Vectors) - Pending
After a PhD in bioinformatics at Inria/IRISA, Université de Rennes 1, Rennes (France), under the supervision of Dominique Lavenier and Pierre Peterlongo, I did a postdoc in bioinformatics at Laboratory of Ecology and Evolution of Plankton in Stazione Zoologica Anton Dohrn of Naples, Italy. Both my thesis and my postdoc were about the Tara Oceans projet and the development of new software to analyze huge quantities of raw reads coming from metagenomics sample. I am currently occupying a research engineer position at the Hub as leader of ALPS group and focus on several different computing problems including metagenomics, protein assembly and several short term developments.
AlgorithmicsData managementProteomicsDatabaseProgram developmentScientific computingSofware development and engineeringComparative metagenomics
- Analysis of neuronal population dynamics in rodents during virtual navigation(Christoph SCHMIDT-HIEBER - Neural circuits for spatial navigation and memory) - Closed
- Recombination among enteroviruses(Maël BESSAUD - Biology of Enteric Viruses) - Pending
- Identification of new or unexpected pathogens, including viruses, bacteria, fungi and parasites associated with acute or progressive diseases(Marc ELOIT - Biology of Infection) - In Progress
Related projects (3)
With an estimated 1031 particles on earth, bacteriophages are the most abundant genomic entities across all habitats and important drivers of microbial communities. Growing evidence suggest that they play roles in intestinal human microbiota homeostasis, and recent metagenomics studies on the viral fraction of this ecosystem have provided crucial information about their diversity and specificity. However, the bacterial hosts of this viral fraction, a necessary information to characterize further the balance of these ecosystems, remain poorly characterized. Here we unveil, using an enhanced metagenomic Hi-C approach, a large network of 6,651 host-phage relationships in the healthy human gut allowing to study in situ phage-host ratio. We notably found that half of these contigs appear to be sleeping prophages whereas ¼ exhibit a higher coverage than their associated MAG representing potentially active phages impacting the ecosystem. We also detect different candidate members of the crAss-like phage family as well as their bacterial hosts showing that these elusive phages infect different genus of Bacteroidetes. This work opens the door to single sample analysis and concomitant study of phages and bacteria in complex communities.
Immune responses are conditioned by host genetics as well as environmental stimuli that include disease-causing pathogens but also a diverse community of commensal micro-organisms (bacteria, fungi, viruses). However, we still have little information on how immune reactivity is regulated in normal healthy humans. Knowledge in this arena is critical since it could lead to experimental approaches that might impact on the amplitude and duration of immune responses against pathogenic infections. A better understanding of the regulation of mucosal responsiveness can have a major impact on the development and implementation of future vaccine candidates as well as the regulation of systemic diseases, including metabolic, allergic, autoimmune, and psychiatric disorders, which are now suggested to be associated with the perturbation of the normal commensal microbiota.
Gene conversion and allelic selection drives L. donovani genomic adaptation in experimental Sand fly infection
Leishmania genomic adaptation during sand fly infection is only poorly understood. In particular, the possibility of allelic selection in a given parasite population inside the insect vector has not been investigated, even though sexual recombination and the possibly of self-sex (selfing) can change allele frequencies and thus may be relevant for parasite transmission and virulence. We investigate this important open question conducting experimental sand fly infection with bona fide amastigotes isolated from infected hamster spleen, and derived promastigotes with different karyotypic profiles. Applying our genome instability pipeline (GIP) on sand fly-recovered parasites revealed a novel form of Leishmania genome instability inside the insect vector relying on gene conversion, which causes haplotype shuffling and likely allows for the selection of beneficial alleles.