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 : Sequence homology analysis
Related people (4)
| work as a research engineer in the ßioinƒormatics and ßiostatistics HUß of the |nstitut Pasteur. Holder of a PhD in bioinƒormatics, my main interest is on ƒast but robust phylogenetic inƒerence algorithms and methods ƒrom large genome-scaled datasets. |n consequence, | am oƒten involved in related bioinƒormatics projects, such as perƒorming de novo or ab initio genome assemblies, designing and processing core genome †yping schemes, building and analysing phylogenomics datasets, or implementing and distributing novel tools and methods.
AlgorithmicsClusteringGenome assemblyGenomicsGenotypingPhylogeneticsTaxonomyGenome analysisProgram developmentEvolutionSequence homology analysis
- Séquençage à haut débit (NGS) et traitement de séquences ADN des domaines variables d’anticorps simple chaine d’alpaga (domaines VHH ou Nanobodies®)(Margarida GOMES - Antibody Engineering) - Pending
- Antimalarial drug resistance in Africa: A comprehensive molecular analysis of the emergence of artemisinin resistant parasites in Africa(Didier MENARD - Biology of Host-parasite Interactions) - In Progress
- Implémentation d’un algorithme rapide de génotypage cgMLST(Valérie BOUCHEZ - Molecular Prevention and Therapy of Human Diseases) - In Progress
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
- 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
- Environmental and human surveillance of polioviruses, VDPVs, and other enteroviruses in Madagascar and the impact during the switch from tOPV to bOPV(Patsy POLSTON - Biology of Enteric Viruses) - In Progress
2015 – . – Institut Pasteur, Paris, France – Unit : Bioinformatics and Biostatistics HUB 2012 – 2015 – Institut Pasteur, Paris, France – Unit : Molecular Genetics of Yeasts Supervisor : Prof. B. Dujon 2012 – Institut Pasteur, Paris, France – Unit : Integrated Mycobacterial Pathogenomics Supervisor: Dr. R. Brosch Education 2012– MSc. Bioinformatics – Université Paris Diderot (Paris VII)
Genome assemblySequence analysisGenome analysisOrthology and paralogy analysisRead mappingSequence homology analysisDNA structure analysisGenome rearrangementsMotifs and patterns detection
- Duplications in bacteriophage genomes.(Luisa DE SORDI - Molecular Biology of Gene in Extremophiles) - New
- De novo sequencing and analysis of three unassigned species of non tuberculous mycobacteria.(RIM GHARBI - Integrated Mycobacterial Pathogenomics) - Awaiting Publication
- Differentiation of Shigella species from Escherichia coli by MALDI-TOF mass spectrometry(Sophie LEFÈVRE - Enteric Bacterial Pathogens) - In Progress
Graduated in “Structural Genomics and Bioinformatics”, I mainly worked during almost 6 years at the Genoscope (CEA) in the LABGeM team, within the microbial annotation platform MicroScope. I specifically focused on functional annotation and microbial metabolic pathways prediction and reconstruction, through pipeline implementation, database modeling and web interface development. Broadly, interactions in the MicroScope platform allowed me to tackle the whole annotation process: from genome assembly and gene prediction to network reconstruction. I also performed several comparative genomics analyses. As a member of the “Hub team”, I now take part to various projects, linked to HTS data, on different subjects (lncRNAs and stem cells, HIV integration and DNA structure, Ribosomal protein genes and genome evolution, Natural Antisense Transcripts in compact genomes…).
Data managementGenomicsSequence analysisWeb developmentDatabaseGenome analysisDatabases and ontologiesOrthology and paralogy analysisRead mappingSequence homology analysisGene prediction
- Genomic DNA sequencing of Burkholderia ambifaria Q53 strain isolated from peanut rizospheric soil(Mathilde BEN ASSAYA - Structural Microbiology) - Pending
- Comparative genomics of Helicobacter pylori bismuth resistant strains(Hilde DE REUSE - Helicobacter Pathogenesis) - Pending
- Sequence analysis of Mycobacterium marinum mutants(Mena CIMINO - Department of Genomes and Genetics) - In Progress
Related projects (3)
The microbiota of the gastrointestinal tract is a diverse mixture different species and strains of bacteria. We aim to identify regions of dissimilarity between two different bacterial strains to be able to quantitate their relative abundance and thus obtain information about their ability to cohabitate a common environment. In addition, we are interested in assessing the surface localised protein repertoir of specific species through a combination bioinformatic analysis and proteomics.
Looking for DNMT (DNA methyltransferase) orthologs in Leishmania which could be potential targets of epigenetic inhibitors active against the parasite.
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