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 : Orthology and paralogy analysis
Related people (4)
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
- Comparative genomics of Listeria monocytogenes isolates(Marc LECUIT - Biology of Infection) - Awaiting Publication
- Duplications in bacteriophage genomes.(Luisa DE SORDI - Molecular Biology of Gene in Extremophiles) - Closed
- De novo sequencing and analysis of three unassigned species of non tuberculous mycobacteria.(RIM GHARBI - Integrated Mycobacterial Pathogenomics) - Closed
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
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
- Virulence and natural anti-sense RNA in Entamoeba histolytica, the agent of human amoebiasis(Nancy GUILLEN - Bioimage Analysis,Biology of Host-parasite Interactions) - In Progress
- Setup of bioinformatic pipelines for paleo(meta)genomics(Nicolás RASCOVAN - Department of Genomes and Genetics) - In Progress
- Multiparametric immunophenotyping of whole blood in IFN-treated multiple sclerosis patients(Priyanka DEVI - Cytokine Signaling) - Closed
Najwa has been a postdoctoral fellow funded by the PTR project OM-Nega of the Institut Pasteur. Since January 2018 she has become the permanent bioinformatician of the group as part of the Hub team C3BI of the Institut Pasteur.
GenomicsSequence analysisDatabaseGenome analysisEvolutionOrthology and paralogy analysis
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.
Proteomes of different cellular compartments of choanoflagellates will be compared to omic datasets from other species to gain insights into the evolution of animal cellular phenotypes.
Finely tuned sensory systems enable bacteria to sense and respond to fluctuating environments, coordinating adaptive changes in metabolic pathways and physiological outputs. For pathogenic Leptospira, signaling pathways allow a timely expression of virulence factors during the successive steps of infection of a mammal host. As the bacteria is excreted by its host, signaling pathways enable switching the expression towards factors promoting survival in the environment. A unifying theme across bacterial species is that biofilm formation coincides with the synthesis of the cellular signaling molecule bis-(3?-5?)-cyclic dimeric guanosine monophosphate (c-di-GMP) and this feature seems to be conserved in Leptospira. Our current work shows that the c-di-GMP regulation pathway is a major regulatory network involved in biofilm formation, virulence and motility in the pathogen Leptospira interrogans. Biofilm production and virulence expression is quite variable across the leptospira genus (highly virulent species, low virulent species and saprophytes species showing increase biofilm production). We would like to explore how the c-di-GMP metabolism, and the many genes associated with its synthesis, and degradation have evolved across the leptospira genus. We believe that understanding the evolutionary relationship of the c-di-GMP metabolism genes in the Leptospira genus would help us to understand the contribution of this second messenger to pathogenesis and biofilm formation in the Leptospira genus