I am CNRS researcher in the Computer Science Lab at Paris-Saclay University (LRI becoming LISN the interdisciplinary computer science lab Jan 1st 2021). I'm a member of BioInfo and associate member of TAU (ML and optimization).
Extracting information from genomic data
Development of methods extracting information from large genomic data in a supervised or unsupervised fashion.
B Yelmen, A Decelle, L Ongaro, D Marnetto, C Tallec, F Montinaro, C Furtlehner, L Pagani, F Jay (2021). Creating Artificial Human Genomes Using Generative Models.Paper
T Sanchez, J Cury, G Charpiat, F Jay (2020). Deep learning for population size history inference: design, comparison and combination with approximate Bayesian computation. Molecular Ecology Ressources DOI:10.1111/1755-0998.13224 Link
Demographic inference using ABC
- Find relevant statistics, suitable to whole-genome data
- Handle sequencing errors
- Identify recent human expansions related to lifestyle
F Jay, S Boitard, F Austerlitz (2019). An ABC method for whole-genome sequence data: inferring paleolithic and neolithic human expansions. Molecular Biology and Evolution, 36(7), 1565-1579. Link
L Lemaire, F Jay, I Lee, K Csilléry, MGB Blum Goodness-of-fit statistics for approximate Bayesian computation. arXiv:1601.04096. Link
S Boitard, W
Rodriguez, F Jay, S Mona, and F Austerlitz (2016). Inferring
population size history from large samples of genome-wide molecular
data-an approximate Bayesian computation approach. PLoS Genet 12, no. 3, e1005877 LinkAdmixture between archaic and modern Humans
JD Wall, MA Yang, F Jay, et al. Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics,
K Prüfer, F Racimo, N Patterson, F Jay, et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43–49. Link
Sex-biased gene flow
JA Cahill, RE Green, TL Fulton, M Stiller, F Jay, et al. (2013).
Genomic evidence for island population conversion resolves conflicting
theories of polar bear evolution. Plos Genetics, 9(3):e1003345. Link
Inbreeding and relatedness in ancient individuals
Meyer, M Kircher, M-T Gansauge, H Li, F Racimo, S Mallick, JG Schraiber, F Jay, et al. (2012). A High-Coverage Genome Sequence from an Archaic Denisovan Individual. Science, 338(6104), 222-226. Link
K Prüfer, F Racimo, N Patterson, F Jay, et al. (2014)
The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505: 43–49. Link
MD Martin, F Jay, S Castellano and M Slatkin (2017). Determination of genetic relatedness from low‐coverage human genome sequences using pedigree simulations. Molecular Ecology. Link
Geography and genetic variation
F Jay, P Sjödin, M Jakobsson, MGB Blum (2013). Anisotropic isolation by distance: the main orientations of human genetic differentiation. Molecular Biology and Evolution 30 (3): 513-525. Link
F Jay, O François, and MGB Blum (2011). Predictions of Native
American population structure using linguistic covariates in a hidden
regression framework. Plos One, 6(1): e16227. Link
Culture, geography and genes in Human population
CM Schlebusch, P Skoglund, P Sjödin, LM Gattepaille, D Hernandez, F Jay, et al. (2012). Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History. Science, 338(6105), 374-379. Link
F Jay, O François, and MGB Blum (2011). Predictions of Native
American population structure using linguistic covariates in a hidden
regression framework. Plos One, 6(1): e16227. Link
Population genetic structure, environment and climate change
F Jay, S Manel, N Alvarez, EY Durand, W Thuiller, R Holderegger, P
Taberlet, O François (2012). Forecasting changes in population genetic
structure of Alpine plants in response to global warming. Molecular Ecology, 21: 2354–2368. Link
Software development
PoPS: Predictions of Population Structure. Inferring population genetic structure and its relationships with
environmental variables. Predicting changes in population structure
PoPS webpage
F Jay, MGB Blum, E Frichot, O François (2011). Modèles à variables latentes en génétique des populations. Journal de la Société Française de Statistique, 152(3). Link
Models in epidemiology
M , et al. (2014). Insights into Persistence Mechanisms of a Zoonotic Virus in Bat Colonies Using a Multispecies Metapopulation Mode. Plos One. DOI: 10.1371/journal.pone.0095610. Link
