Biography
I’m a PhD student in population genetics at Université Paris Cité. I use statistical physics and bioinformatics to analyse patterns of mutation and model bacterial evolution.
My work focuses on the short and long term evolution of Escherichia coli, using 81,000 genomes to uncover mechanisms of patho-adaptation and acquisition of antibiotic resistance. I sometimes change scale from genetics to the dynamics of microbial communities in the human gut.
- Population genetics
- Microbiology & microbial ecology
- Computational biology
- Mathematical modelling
MSc in Life Sciences Engineering, 2020
EPFL (Lausanne 🇨🇭)
MSc in Life Sciences, 2019
École polytechnique (Paris 🇫🇷)
BSc in Maths & Physics, 2016
École polytechnique (Paris 🇫🇷)
Experience
Bacterial population genetics of Escherichia coli. Inference of mutation effect and epistatic interactions between mutations using Direct-Coupling Analysis. Organisation of 60,000 Escherichia coli strains into a database.
Side projects including analysis of DNA barcodes during experimental evolution using a bayesian statistical framework, microbiota 16S metagenomics analyses.
Main languages/softwares used: Python, SQL, Qiime.
Performance of alternative Bayesian estimation algorithms/softwares in Pharmacokinetics/Pharmacodynamic non-linear mixed effect models. Investigated the use of Hamiltonian Monte Carlo simulations in PKPD modelling. Compared performances with standard approaches. Investigated optimal design of clinical trials.
Main languages/softwares used: R, Stan, PopED, NONMEM.
Research project on comparative population genetics of the bacterial species Neisseria meningitidis and Neisseria gonorrhoeae, under the supervision of Pr. Adam Eyre-Walker. Re-implemented standard population genetics tests (Tajima’s D, Πn, Πs,…) and inferred recombination events.
Main languages used: Python, R.
Accomplishments
Skills
Contact
- [first name] . [last name without accent] @ inserm.fr
- DM Me