I am a PhD student since 2019 at the LBBE, under the supervision of Eric Tannier and Vincent Daubin

Research interest

I am interested in the construction of probabilistic models and methods for phylogeny. My main subject is phylogenetic reconciliation, that I try to extend to encompass both host/symbiont and gene/species frameworks in a single integrative model.

I am also interested in more theoretical properties of reconciliation, as a computer scientist, and on the other side of the spectrum, I take a special interest toward Helicobacter pylori a bacteria that is said to have coevolve with humans showing diversification patterns similar to the one of human early migrations.

Teaching

I teach computer science and statistics at the biology department of IUT Lyon 1.

Publications

S. Penel, H. Menet, T. Tricou, V. Daubin, E. Tannier, Thirdkind: displaying phylogenetic encounters beyond 2-level reconciliation, Bioinformatics, 2022

H. Menet, V. Daubin, E. Tannier, Phylogenetic reconciliation, preprint, HAL, 2021

Softwares

TALE : Three level Amalgamated Likelihood Estimation, implementation of our model and inference method for 3-level reconciliation, integrating host, symbionts and genes.

Thirdkind : software developped by Simon Penel for graphical visualization of reconciliations, creating a svg from a recphyloxml input.