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 : Evolution
Related people (7)
Initially trained in evolutionary and environmental sciences, I studied population genetics and micro-evolutionary processes in a number of postdoctoral research projects. I recently joined the C3BI-Hub at the Institut Pasteur, where I work on various aspects involving Biostatistics and the analysis of genetic data.
Association studiesGenomicsGenotypingBiostatisticsGeneticsEvolutionPopulation genetics
BacteriaParasiteHumanInsect or arthropodOther animal
As a computational biologist I have been involved in various projects seeking to answer different biological questions. Those projects have allowed me to define my main research interest, namely the evolutionary study of the emergence, storage and modulation of information in biological systems assisted by computational methods. During my research career I have acquired extensive experience in the analysis of sequence data at the DNA and protein level. I’m trained both in NGS bioinformatic protocols (ChIP-seq, ATAC-seq, RNA-seq, genome assembly) and fine detail sequence analysis. Most importantly, I have gained proficiency in the use of the statistical models that are at the basis of the quantitative analysis of low and high throughput sequence data. Additionally, my experience as a lecturer and instructor has taught me that training researchers about the formal basis of bioinformatic methodologies is the key for a successful collaboration between wet and dry lab. Likewise, I have gained valuable skills by working within two international consortia (TARA Oceans project and TRANSNET): the ability to collaborate with multidisciplinary groups and to coordinate younger researchers.
AlgorithmicsGenomicsSequence analysisTranscriptomicsGenome analysisGeneticsEvolutionInteractomics
- fliC locus of Y. pestis(Mara CARLONI - Yersinia) - In Progress
- Mechanisms defining functional heterogeneity of anatomically distinct myogenic populations: insights from single nuclei-ATAC-seq data(Glenda COMAI - Department of Developmental and Stem Cell Biology) - In Progress
- basic alignment/visualisation pipeline(Pablo NAVARRO - Epigenetics of Stem Cells) - In Progress
| 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
- Comparative genomics analysis of cyclic-di-GMP metabolism across the Leptospira genus(Roman THIBEAUX - Leptospirosis,Other) - In Progress
- Fast and accurate identification of the medoid of a set of genomes(Olivier CHESNEAU - Collection of the Institut Pasteur (CIP)) - Awaiting Publication
- Quick phage data mining(Quentin LAMY-BESNIER - Bacteriophage, Bacterium, Host) - Closed
After a PhD in Microbiology on bacterial toxin-antitoxin systems at the Free University of Brussels, I joined the Institut Pasteur for a 3 years postdoc in Eduardo Rocha’s lab. During this period, I performed comparative genomics and pylogenetic analysis on bacterial conjugation and type IV secretion systems. Then, I worked 2 years in Olivier Tenaillon’s team on the modelling and evolution of organismal complexity. I joined the HUB in 2015, and I am involved in phylogenetic and comparative genomics projects.
GenomicsPhylogeneticsSequence analysisGenome analysisGeneticsEvolutionPopulation genetics
- Centrosome and basal body function in human parasites(Philippe BASTIN - Trypanosome Cell Biology) - New
- Evaluation of the mutation rate per site and dN/dS in the genomes of Yersinia enterocolitica(Cyril SAVIN - Yersinia) - Awaiting Publication
- Phylogenetic analysis of HHD-PDZ containing proteins(Nicolas WOLFF - Channel Receptors) - Closed
After a PhD in Biology in 2011 on population genetics and phylogeography on amazing little amphipods (Crangonyx, Crymostygius) at the University of Reykjavik (Iceland), I pursued my interest in Bioinformatics and Evolutionary Biology in various post-docs in Spain (MNCN Madrid, UB Barcelona). During this time, I investigated transcriptomic landscapes for various non-model species (groups Conus, Junco and Caecilians) using de novo assemblies and participated in the development of TRUFA, a web platform for de novo RNA-seq analysis. In July 2016, I integrated the Revive Consortium and the Epigenetic Regulation unit at Pasteur Institute, where my main focus were transcriptomic and epigenetic analyses on various thematics using short and long reads technologies, with a special interest in alternative splicing events detection. I joined the Bioinformatics and Biostatistics Hub in January 2018. My latest interests are long reads technologies, alternative splicing and achieving reproducibility in Bioinformatics using workflow managers, container technologies and literate programming.
Data managementData VisualizationSequence analysisTranscriptomicsWeb developmentGenome analysisProgram developmentExploratory data analysisSofware development and engineeringGeneticsEvolutionRead mappingWorkflow and pipeline developmentPopulation geneticsMotifs and patterns detectionGrid and cloud computing
HumanInsect or arthropodOther animalAnopheles gambiae (African malaria mosquito)Mouse
- Build a software to decipher Gephyrin alternative transcripts obtained with long read sequencing(allemand ERIC - Epigenetic Regulation) - Closed
- Transcriptomics of Anopheles – Plasmodium vivax interactions towards identification of malaria transmission blocking targets(Catherine BOURGOUIN - Functional Genetics of Infectious Diseases) - Closed
- Mapping of Enhancers from transcriptome data(Christian MUCHARDT - Epigenetic Regulation) - 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
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) - Closed
- Measles virus protein C interplay with cellular apoptotic pathways; applications for cancer treatment(Alice MEIGNIÉ - Viral Genomics and Vaccination) - Closed
- Diffusion des mutations de résistance du VIH : modèles et méthodes d’estimation(Olivier GASCUEL - Evolutionary Bioinformatics) - Closed
Related projects (4)
Comparison of Microsatellites and Multi Locus Sequences Typing approaches. Fungi: Pneumocytis jirovecii
Bacteria exposed to bacteriophages deploy several defence systems that we wished to identify by genomes sequencing of bacteriophage-resistant isolates
The LeiSHield-MATI consortium: Investigating genomic adaptation of Leishmania parasites in endemic areas
Leishmania causes devastating human diseases – leishmaniases - representing an important public health problem in the Mediterranean basin and declared as emerging diseases in the EU due to climate change and population displacement. The LeiSHield-MATI consortium will for the first time investigate in an integrative fashion the complex parasite-vector-host interplay in cutaneous leishmaniasis affecting Morocco, Algeria, Tunisia, and Iran (MATI), using field isolates and human clinical samples. The ultimate goal of our project is to identify genetic factors selected during natural infection and to understand how the complex parasite-vector-animal interaction impacts clinical outcome in infected patients. This goal will be achieved through a highly ambitious secondment plan between all partners, and the organization of courses and workshops to train the next generation of scientists generating a long-term impact on the research capacities in endemic areas. Capitalizing on complementary infrastructures of its EU, African and Asian partners and their expertise in molecular parasitology, epidemiology, systems level analyses, bioinformatics, computational biology, immunology, dermatology, field studies, and public health, our project will drive important innovation in clinical research, strengthen capacities in disease endemic regions, inform authorities on control measures, and raise awareness in all partner countries on this emerging EU public health problem. The highly inter-disciplinary and inter-sectorial structure of LeiSHield-MATI, and its powerful integrative and comparative approach is novel in parasitic systems and will drive a unique bio-marker discovery pipeline for the future development of new prognostic and diagnostic tools, as well as novel preventive and therapeutic measures that will ensure long-term collaboration, promote scientific and commercial self-sustainability of its partners, and will have an important impact to improve public health.
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.