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
- exploiting information from horizontal gene transfers to date species phylogenies (e.g. see this manuscript and the associated recommendation by PCI Evol Biol)
- detecting directional selection at the sequence level, notably to study convergent genomic evolution (collaboration with Louis Duchemin and Philippe Veber)
I have recently broadened my interests in a variety of directions, which led me to study
- wheat yields, and how they depend on meteorological conditions (collaboration with Louis Duchemin and Philippe Veber)
- the occurrence of massive synchronized fruiting in oak trees, known as masting, and how this phenomenon depends on meteorological conditions (collaboration with Emilie Fleurot, Marie-Claude et Samuel Venner de l'équipe "Ecologie Quantitative et Evolutive des Communautés")
- 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)
- whether machine learning approaches can help in the fields of phylogenetic reconstruction and molecular evolution (collaboration with Johanna Trost, Luca Nesterenko, Philippe Veber and Laurent Jacob)
In terms of teaching, I have been involved in teaching Bayesian statistics, Computational Molecular Evolution, Genomics.
I also taught about the environmental footprint of our food systems as part of the course "Climat et transitions" taught at Université Lyon 1.
Display of 1 to 30 publications on 60 in total
Adaptation to host cell environment during experimental evolution of Zika virus
Communications Biology . 5 ( 1 ) : 1115
Evaluation of methods to detect shifts in directional selection at the genome scale
Polymorphism‐aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes
Methods in Ecology and Evolution . 13 ( 11 ) : 2339-2346
Relative Time Constraints Improve Molecular Dating
Systematic Biology . 71 ( 4 ) : 797-809
Phyloformer: towards fast and accurate phylogeny estimation with self-attention networks
Bayesian investigation of SARS-CoV-2-related mortality in France
Peer Community Journal . 2 ( e6 )
Predicted effects of summer holidays and seasonality on the SARS-Cov-2 epidemic in France
medRxiv : the preprint server for health sciences .
Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824
Reconciling Gene trees with Species Trees
Phylogenetics in the Genomic Era . : 3.2:1--3.2:23
Tracing Human Ancestral Migrations Using Symbiotic Bacteria
Groupe des Méthodes Pluridisciplinaires Contribuant à l'Archéologie (GMPCA) .
CAARS: comparative assembly and annotation of RNA-Seq data
Bioinformatics . 35 ( 13 ) : 2199-2207
Detecting adaptive convergent amino acid evolution
Philosophical Transactions of the Royal Society B: Biological Sciences . 374 ( 1777 ) : 1-11
Gene transfers can date the tree of life
Nature Ecology & Evolution . 2 ( 5 ) : 904-909
RecPhyloXML: a format for reconciled gene trees
Bioinformatics . 34 ( 21 ) : 3646-3652
Biodiversité, évolution et fonctionnement des écosystèmes
Les Cahiers des prospectives . hors série : 25-33.
MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers
Integrative 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
Dating with transfers
Journées Ouvertes Biologie Informatique Mathématiques .
Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated
Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310
Efficient gene tree correction guided by genome evolution
PLoS ONE . 11 ( 8 ) : e0159559 (22 pages)
RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language
Systematic Biology . 65 : 726-36
Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree
Science . 350 ( 6257 ) : 171-171
The inference of gene trees with species trees
Systematic Biology . 64 ( 1 ) : e42-e62
Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
PLoS ONE . 10 ( 6 ) : e0129183
Assessing Approaches for Inferring Species Trees from Multi-Copy Genes
Systematic Biology . 64 ( 2 ) : 325-339
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi
Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 370 : 20140335 (11 pages)