Teaching :
I teach mathematics, modelling in biology and computer science in Licence and Masters BEE@Lyon and Bioinfo@Lyon .
Mostly, I write programming courses for biologists, in R and Python, in the form of a tutorials, to give students practical experience, where they develop simulation programs of simple biological models (genetics and population dynamics) in individual-centered mode. This allows them to discover this type of modelling and awakens their in/erest in the role of computational tools in biology. On the modelling part, I design Markov modelling tutorials in R (HMM, phylogeny) in which the students start from the mathematical model and work their way up to data analysis. In math&meth, beyond usual linear algebra, I am interested into teaching data analysis techniques, such as clustering methods & Singular Value Decomposition.
Research:
I work on molecular modeling in evolution, mostly in phylogeny. I currently work on methods and models that focus on branch specific estimates of selection and of other evolutive features (such as GC bias), and also on the inclusion of polymorphism information in phylogenetic scale analysis.
An essential part of my research activity consists of developing the Bio++ suite of libraries (see on Github ), in collaboration with Julien Dutheil (Max Planck Institute for Evolutionary Biology , Plön). Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. Bio++ is Object Oriented and is designed to be both easy to use and computer efficient. Bio++ intends to help programmers to write computer expensive programs, by providing them a set of re-usable tools.
Using these libraries, many softwares are available for maximum likelihood inference, ancestral reconstruction, sequence simulation, in BppSuite , and substitution mapping,branch clustering in TestNH .
I maintain the DGINN pipeline, developed by Léa Picard, a PhD student under my supervision and that of Lucie ÉTIENNE (CIRI, ENS Lyon). DGINN is dedicated to find signs of innovation in a gene family, performing automatically all the process from a sequence to positive selection detection, through homologous sequence retrieval, curation, alignment, reconciliation, recombination detection and finally phylogenetic analysis.
Publications
Affichage des publications 1 à 30 sur 40 au total
SAMD9L acts as an antiviral factor against HIV-1 and primate lentiviruses by restricting viral and cellular translation
PLoS Biology . 22 ( 7 ) : e3002696
Article dans une revue
voir la publicationCalculs d’inférence dans les arbres phylogénétiques
Modèles et méthodes pour l’évolution biologique . 9781789480696 : 177-202
Chapitre d'ouvrage
voir la publicationDistinct evolutionary trajectories of SARS-CoV-2-interacting proteins in bats and primates identify important host determinants of COVID-19
Proceedings of the National Academy of Sciences of the United States of America . 119 ( 35 )
Article dans une revue
voir la publicationExtreme mitochondrial DNA divergence underlies genetic conflict over sex determination
Current Biology - CB . 32 ( 10 ) : 2325-2333.e1-e6
Article dans une revue
voir la publicationComparison of developmental genome expression in rodent molars reveals extensive developmental system drift
Pré-publication
voir la publicationA Codon Model for Associating Phenotypic Traits with Altered Selective Patterns of Sequence Evolution
Systematic Biology . 70 ( 3 ) : 608-622
Article dans une revue
voir la publicationAncestral Genome Organization as a Diagnosis Tool for Phylogenomics
Phylogenetics in the Genomic Era . : 2.5:1--2.5:19
Chapitre d'ouvrage
voir la publicationTreerecs: an integrated phylogenetic tool, from sequences to reconciliations.
Bioinformatics . 36 ( 18 ) : 4822-4824
Article dans une revue
voir la publicationDGINN, an automated and highly-flexible pipeline for the detection of genetic innovations on protein-coding genes
Nucleic Acids Research . 48 ( 18 ) : e103-e103
DOI: 10.1093/nar/gkaa680
Article dans une revue
voir la publicationGC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes
Genome Biology . 20 ( 1 )
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 publicationUnbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition
Molecular Biology and Evolution . 35 ( 3 ) : 734-742
Article dans une revue
voir la publicationLife History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods
Molecular Biology and Evolution . 35 ( 12 ) : 2900-2912
Article dans une revue
voir la publicationMareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps
Genome Biology and Evolution . 9 ( 10 ) : 2506-2509
DOI: 10.1093/gbe/evx178
Article dans une revue
voir la publicationTranscriptomic signatures shaped by cell proportions shed light on comparative developmental biology
Genome Biology . 18 : 29
Article dans une revue
voir la publicationAncestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium
Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431
DOI: 10.1093/gbe/evx255
Article dans une revue
voir la publicationLess effective selection leads to larger genomes
Genome Research . 27 : 1016-1028
Article dans une revue
voir la publicationSENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage
Genome Biology and Evolution . 8 : 2427-41
DOI: 10.1093/gbe/evw165
Article dans une revue
voir la publicationBreaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation
Genome Biology and Evolution . 8 ( 5 ) : 1427-1439
DOI: 10.1093/gbe/evw083
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 publicationMoments of genome evolution by Double Cut-and-Join
BMC Bioinformatics . 16 ( Suppl 14 ) : S7
Article dans une revue
voir la publicationProbabilistic modeling of the evolution of gene synteny within reconciled phylogenies
BMC Bioinformatics . 16 ( Suppl 14 ) : S5
Article dans une revue
voir la publicationDuplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later
Models and Algorithms for Genome Evolution . 19 : 47-62
Chapitre d'ouvrage
voir la publicationBio++ : Efficient Extensible Libraries and Tools for Computational Molecular Evolution
Molecular Biology and Evolution . 30 ( 8 ) : 1745 - 1750
Article dans une revue
voir la publicationAccurate Estimation of Substitution Rates with Neighbor-Dependent Models in a Phylogenetic Context
Systematic Biology . 61 ( 3 ) : 510-521
Article dans une revue
voir la publicationGenomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens
Genome Biology and Evolution . 3 ( 3 ) : 762-781
DOI: 10.1093/gbe/evr070
Article dans une revue
voir la publicationIdentification de fonctions « spécifiques d'espèce » impliquées dans l'individualisation en écovar de l’espèce G8 du complexe Agrobacterium tumefaciens
Journées des Microbiologistes de l'INRA .
Acte de congrès
voir la publicationLa notion d'espèce en écologie microbienne
1er Colloque National d'Ecologie Scientifique .
Acte de congrès
voir la publicationToward an ecological concept for bacterial species in Agrobacterium
12th International Conference on Plant Pathogenic Bacteria .
Acte de congrès
voir la publicationComputing the likelihood of sequence segmentation under Markov modelling
Pré-publication
voir la publication