Pouyet Fanny

Research

I am an assistant professor in the Bioinfo team at LISN – Université Paris-Saclay since 09/2020. As an evolutionary biologist I am particularly interested in deciphering selective from non-adaptive processes that drive the evolution of genome content. I use either phylogenetics, population genomics or comparative genetics approaches. 

Working projects

The origin of the genetic diversity at the population level in Saccharomyces cerevisiae, also known as the budding yeast. Yeast has been used by human societies for millenia for baking and distilling alcoholic beverages. Additionally, this species has served as a model organism for nearly a century to decipher the principles of eukaryotic  genetics. However, recent large-scale population genomics data have challenged our understanding of the canonical life cycle of the species as it is classically described in textbooks, thereby suggesting unanticipated levels of genetic complexity. We use ABC methods. I supervise Louis Ollivier in collaboration with Sorbonne University.

The impact of cultural transmission of reproductive success in humans. It has been previously shown in humans that children from large families tend to have a larger number of offsprings. We are elucidating how such a mecanism could interfere with demographic inferences or the estimates of polygenic selection. I supervise Ferdinand Petit in collaboration with the Musée de l’Homme and INRAe le Moulon.

The evolutionary and molecular origin of genes GC-content. A third project studies the start of most protein-coding genes in animals which is marked by a spike in GC-content. This GC- peak reaches its maximum ~70 nucleotides downstream of the transcriptional start site (TSS) and gradually slopes down. We are trying to figure out what are the molecular processes on top of natural selection that impact the long term genetic content of genes. I work in collaboration with Toronto University.

Published projects

As a postdoc, I showed that more than 95% of the human genomic diversity is affected by background selection and/or biased gene conversion towards GC (gBGC). I showed that these two mechanisms bias the population genetics inferences of demography. I also studied patterns of genetic diversity in regions of low recombination in humans and showed that associative pseudo-overdominance might counteract the effect of background selection. 

During my PhD (2013 – 2016), I developed a codon-based model that disentangle the role of mutational bias from synonymous codon preferences on the evolution of genes in bacterias. I also quantified the importance of both translational selection and gBGC on the evolution of codon usage (i.e. GC3) in humans.

The list of my published work is available on HAL.

Teaching

I am an Assistant Prof at Paris-Saclay University since September 2020. I teach informatics and bioinformatics in French such that the rest of the page is in french.

Projet de bioinformatique

Contenu: Préparation d’un fichier de génotypes/ Science des données en lien avec le changement climatique
Niveau: L3 Info
Volume horaire: 20h

Introduction aux Sciences des données

Contenu: Python, machine learning, image processing
Niveau: L1 Info
Volume horaire S2: 9h de CM + 18h de TP

Métagénomique et génétique des populations

Contenu: R, métagénomique, génétique des populations, théorie de coalescence
Niveau: M2 AMI2B
Volume horaire S3: 4h de CM + 6h de TP