Florian GILBERT

En résumé

Entreprises

• Chu Bordeaux - BioInformatics Engineer

  Talence 2017 - maintenant Team of the Strokes observatory (Observatoires des AVC) :
  As a member of the strokes observatory, I'm in charge of the analysis of the practice and the medical care of the patient through the Aquitaine and now New Aquitaine regions. More precisely, the different centers (hospitals, clinics) of the region give us the information about how they are dealing with the strokes coming in and for each hospital and territory we analyse their practice (delay response, what kind of drugs, how much, which technics...). The goal of this observatory is to have an idea of the practice in the region and inform back the centers to show them their practice and other practice to have a more efficient response and medical care of the patient.
  Because time is important in the way of treating strokes and improve every part of the medical care can help patient, recovery and save lifes.
  
  As part of the project, a study about the post effects and recovery of strokes is also realized to improve the post strokes medical care.
  
  Programming and tools :
  R, Talend

• Centre de BioInformatique de Bordeaux - Ingénieur d'étude

  2016 - 2016 Beacon Project :
  For the Elixir project, development and deployment of the Beacon service for the platform in Bordeaux. Beacon is defined as a simple public web service designed to accept a query like "Do you have any genomes with an 'A' at position 100,735 on chromosome 3" and responds like "Yes"/"No.".
  To facilitate access to large volumes of data, it's necessary to develop standards for interoperability that enable sharing across a federated network. This demonstrating the willingness of international organizations to work together to define standards for genomic data sharing. Beacon demonstrate the viability of a global federated model for genomics data discovery and sharing through a simple and securable technical protocol.
  Development of the API, Web Interface and related databases.
  
  Data Analysis :
  NGS data analysis for others teams in contact with the center for the treatment of their data.
  Analysis of PCR data from AIDS (Quality Control, Clustering...).
  
  Other :
  Tools development and deployment on Galaxy.
  
  Programming:
  R, Bash, Python, PostGreSQL, PHP, Javascript, HTML, Perl, Java.

• CNRS - Ingénieur de recherche

  Paris 2014 - 2015 Néri Team, CNRS UMR8256 Biology of Adaptation and Aging.
  Huntington’s Disease Study, modeling study of the molecular dynamics of Huntington's disease.
  
  Network analysis :
  Network and neighbor comparative analysis using graph theory in the Huntington disease and other CAG repeat disorders. Recomputation of STRING links scores.
  Neighbor analysis to see the modifications and the effects in those networks (STRING, MouseNet). Neighbor map and relative distance comparisons between original network and computed disease network. Statistical analysis to identify if the mutated proteins (Htt and various Ataxines) have a significant effect on the network rearrangement (response).
  
  Spectral Analysis:
  Analysis of a collection of genomic/tanscriptomic data (MicroArray, RNAseq) in different model (Human, Mouse, Worm). Spectral analysis performed with a pipeline which use a Fourier analysis to create module depending of the network (STRING, MouseNet, WormNet...) and the genes expression. Integration and annotation of all this modules across datasets and models intra-species and inter-species. Comparison between models to see preserved and deregulated regions and annotations in response of the mutated protein.
  
  Pathway analysis :
  Using previous results of the spectral and network analysis with fourier module, apply the network pipeline to a pathway environment to see if and which pathways undergoes effects and modifications of mutated proteins.
  
  Databases management :
  Creation and databases management.
  
  Server :
  Installation and management of different servers for the team.
  
  Web interface:
  Development and management of a web interface to browse all the result present in the different databases.
  
  Programming :
  R, Python, MySQL, Shell, PostGreSQL, Perl.

• Inserm - Ingénieur d'Etude

  PARIS 13 2013 - 2014 Néri Team- INSERM U894.
  Huntington’s Disease Study
  
  Network analysis :
  Network and neighbor comparative analysis using graph theory in the Huntington disease and other CAG repeat disorders.
  Neighbor analysis to see the modifications and the effects in those networks (STRING, MouseNet). Neighbor map and relative distance comparisons between original network and computed disease network. Statistical analysis to identify if the mutated proteins (Htt and various Ataxines) have a significant effect on the network rearrangement (response).
  
  Databases management :
  Creation and databases management.
  
  Programming :
  Python, MySQL, Shell, PostGreSQL.

• Ecole Polytechnique Fédérale de Lausanne (EPFL) - BioInformatics Internship

  91128 PALAISEAU Cedex 2012 - 2012 Internship in collaboration between Gisou Van der Goot lab and Jacques Fellay lab.
  
  NGS Data Analysis :
  Data collection for the DHHC family enzyme (23 genes) extracted from the GWAS : 1000 Genomes Project. Comparative genes family analysis performed leads to an identification and a mapping of those variants.
  Annotation and characterization of the detected SNPs in the population for a better understanding of the impact of these SNPs on the genes and proteins functions.
  Statistical analysis to define the presence of polymorphism region.
  
  Phylogeny Analysis :
  Phylogeny analysis of the DHHC6 enzyme to visualize the evolutionary pressures on this gene and identify positive selection site.
  
  Tools used:
  VAAST, GATK, PALM.
  
  Programming Skills :
  Python, Shell, JAVA.

Formations

• Université Bordeaux 1 Sciences Et Technologies

  Talence 2010 - 2012 Masters Degree
  
  Master Biology and Health, BioInformatics major
  Honors
  Programmation for biology
  Informatics(Programming, Databases, Algorithm)
  Language : Python, Shell, R, Java, C++, MySQL...
  Genomoics-Statistics

• Université Bordeaux 1 Sciences Et Technologies

  Talence 2007 - 2010 Bachelors Degree
  
  Bachelor in Cellular and Physiological Biology
  Option Neuroscience
  Honors, Merit Scolarship
  Cellular-Molecular Biology, Biochemistry
  Immunology, Microbiology
  Genetics, Neurosciences

Réseau

• Antoine LELEU

• Association AQUIDOC

• Emmanuel DUSAUTOIR

• France PERRIN

• Kamel KACI

• Lucas MARMIESSE

• Marie BEURTON

• Quang Phi-Vu VU

• Salvatore CONTE

• Sciencepro47 SCIENCES