My past research has been focused on extracting information from genomes to better understand how they encode phenotypes. Extant living organisms are the result of an historical process that has unfolded over billions of years. Their genomes have accumulated footprints of past episodes of selection in response to interactions with their environment or with other species. I have developed computational methods based on probabilistic models to detect these footprints and interpret genomic data on a large scale.
In particular, I have used ancestral sequence reconstruction to study the lifestyles of organisms that lived billions of years ago, I have developed methods for reconstructing gene trees and species trees to better understand genome evolution, and I have developed and assessed methods to find examples of convergent genomic evolution.
My research in genomics these days mainly focuses on:
- using machine learning approaches to help in the fields of phylogenetic reconstruction and molecular evolution (collaboration with Johanna Trost, Luca Nesterenko, Philippe Veber and Laurent Jacob)
- detecting directional selection at the sequence level, notably to study convergent genomic evolution (collaboration with Louis Duchemin and Philippe Veber)
- exploiting information from horizontal gene transfers to date species phylogenies (e.g. see this manuscript and the associated recommendation by PCI Evol Biol)
I have recently broadened my interests in a variety of directions, which led me to study:
- how aphids, their predators, sugar beets and viruses interact, with the hope that a better understanding of this ecological network might help us avoid pesticides when growing sugar beets (collaboration with Baptiste Maucourt, Eric Tannier and Léo Girardin)
- wheat yields, and how they depend on meteorological conditions (collaboration with Louis Duchemin and Philippe Veber)
In terms of teaching, I have been involved in teaching Bayesian statistics, Computational Molecular Evolution, Genomics.
I also teach about the environmental footprint of our food systems as part of the course "Climat et transitions" at Université Lyon 1.
Publications
Affichage des publications 1 à 30 sur 63 au total
An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event
Pré-publication
voir la publicationEvaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale
Molecular Biology and Evolution . 40 ( 2 )
Article dans une revue
voir la publicationEndoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses
eLife . 12 : e85993
DOI: 10.7554/eLife.85993
Article dans une revue
voir la publicationEvaluation of methods to detect shifts in directional selection at the genome scale
Pré-publication
voir la publicationNucleotide Usage Biases Distort Inferences of the Species Tree
DOI: 10.1093/gbe/evab290
Pré-publication
voir la publicationPolymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes
Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346
Article dans une revue
voir la publicationRelative Time Constraints Improve Molecular Dating
Systematic Biology . 71 ( 4 ) : 797-809
Article dans une revue
voir la publicationAdaptation to host cell environment during experimental evolution of Zika virus
Communications Biology . 5 ( 1 ) : 1115
Article dans une revue
voir la publicationPhyloformer: towards fast and accurate phylogeny estimation with self-attention networks
Pré-publication
voir la publicationBayesian investigation of SARS-CoV-2-related mortality in France
Peer Community Journal . 2 ( e6 )
Article dans une revue
voir la publicationPredicted effects of summer holidays and seasonality on the SARS-Cov-2 epidemic in France
medRxiv : the preprint server for health sciences .
Pré-publication
voir la publicationTreerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824
Article dans une revue
voir la publicationReconciling Gene trees with Species Trees
Phylogenetics in the Genomic Era . : 3.2:1--3.2:23
Chapitre d'ouvrage
voir la publicationQuand les branches de l’arbre du vivant s’entremêlent
Pour la science .
DOI: 10.3917/pls.506.0056
Article dans une revue
voir la publicationTracing Human Ancestral Migrations Using Symbiotic Bacteria
Groupe des Méthodes Pluridisciplinaires Contribuant à l'Archéologie (GMPCA) .
Acte de congrès
voir la publicationCAARS: comparative assembly and annotation of RNA-Seq data
Bioinformatics . 35 ( 13 ) : 2199-2207
Article dans une revue
voir la publicationDetecting adaptive convergent amino acid evolution
Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11
Article dans une revue
voir la publicationGene transfers can date the tree of life
Nature Ecology & Evolution . 2 ( 5 ) : 904-909
Article dans une revue
voir la publicationRecPhyloXML: a format for reconciled gene trees
Bioinformatics . 34 ( 21 ) : 3646-3652
Article dans une revue
voir la publicationBiodiversité, évolution et fonctionnement des écosystèmes
Les Cahiers des prospectives . hors série : 25-33.
Chapitre d'ouvrage
voir la publicationMaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers
DOI: 10.1101/127548
Autre publication
voir la publicationIntegrative modeling of gene and genome evolution roots the archaeal tree of life
Proceedings of the National Academy of Sciences of the United States of America . 114 ( 23 ) : E4602-E4611
Article dans une revue
voir la publicationDating with transfers
Journées Ouvertes Biologie Informatique Mathématiques .
Acte de congrès
voir la publicationGene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated
Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310
Article dans une revue
voir la publicationEfficient gene tree correction guided by genome evolution
PLoS ONE . 11 ( 8 ) : e0159559 (22 pages)
Article dans une revue
voir la publicationRevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
Systematic Biology . 65 : 726-36
Article dans une revue
voir la publicationResponse to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree
Science . 350 ( 6257 ) : 171-171
Article dans une revue
voir la publicationThe inference of gene trees with species trees
Systematic Biology . 64 ( 1 ) : e42-e62
Article dans une revue
voir la publication