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 31 à 60 sur 65 au total
Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree
Science . 350 ( 6257 ) : 171-171
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voir la publicationThe inference of gene trees with species trees
Systematic Biology . 64 ( 1 ) : e42-e62
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voir la publicationWeighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses
PLoS ONE . 10 ( 6 ) : e0129183
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voir la publicationAssessing Approaches for Inferring Species Trees from Multi-Copy Genes
Systematic Biology . 64 ( 2 ) : 325-339
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voir la publicationGenome-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)
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voir la publicationProbabilistic Graphical Model Representation in Phylogenetics
Systematic Biology . 63 ( 5 ) : 753-771
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voir la publicationWhole-genome analyses resolve early branches in the tree of life of modern birds.
Science . 346 ( 6215 ) : 1320-31
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voir la publicationEvidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition
Genome Biology . 15 : 549
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voir la publicationStatistical binning enables an accurate coalescent-based estimation of the avian tree
Science . 346 : 1250463
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voir la publicationStrepsiptera, Phylogenomics and the Long Branch Attraction Problem
PLoS ONE . 9 : e107709
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voir la publicationThe molecular signal for the adaptation to cold temperature during early life on Earth
Biology Letters . 9 ( 5 ) : 20130608
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voir la publicationEfficient Exploration of the Space of Reconciled Gene Trees.
Systematic Biology . 62 ( 6 ) : 901-912
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voir la publicationGenome-scale coestimation of species and gene trees.
Genome Research . 23 ( 2 ) : 323-330
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voir la publicationBio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution
Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750
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voir la publicationA Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences
Systematic Biology . 62 ( 4 ) : 523-538
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voir la publicationPhylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations.
Proceedings of the National Academy of Sciences of the United States of America . 109 ( 43 ) : 17513-17518
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voir la publicationFast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.
PLoS ONE . 7 ( 3 ) : e33852
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voir la publicationWhat genomes have to say about the evolution of the Earth
Gondwana Research . 21 : 483-494
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voir la publicationEfficient selection of branch-specific models of sequence evolution.
Molecular Biology and Evolution . 29 ( 7 ) : 1861-1874
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voir la publicationA Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
PLoS ONE . 7 : e48990
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voir la publicationEvolution of gene neighborhoods within reconciled phylogenies
Bioinformatics . 28 ( 18 ) : i382-i388
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voir la publicationDrift and Genome Complexity Revisited
PLoS Genetics . 7 : 1-5
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voir la publicationA Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies
Evolutionary Bioinformatics . 5 : 67-79
DOI: 10.4137/EBO.S2242
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voir la publicationGenomes as documents of evolutionary history
Trends in Ecology & Evolution . 1192 : 1-9
Article dans une revue
voir la publicationPhylogenetic Relationships Deduced from Whole Genome Comparisons
Encyclopedia of Life Sciences . : 1-8
The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event ?
BMC Evolutionary Biology . 8:336 : 1-19
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voir la publicationNon-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs
BMC Evolutionary Biology . 8:255 : 31-42
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voir la publicationMesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota.
Nature Reviews Microbiology . 6 ( 3 ) : 245-252
DOI: 10.1038/nrmicro1852
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voir la publicationAccounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria
BMC Evolutionary Biology . 8 : 272-272
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voir la publication