Research overview

 Extracting information from genomic data

I am curious about all techniques that can be used/developed for extracting information from large genomic data in a supervised or unsupervised fashion.

 

 Demographic inference

Inferring demography from SNP data and full sequences using Approximate Bayesian Computation:
- Find relevant statistics, suitable to whole-genome data

- How to deal with ascertainment bias and sequencing errors
- Identify recent human expansions related to lifestyle

 Admixture 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



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, S, et al. (2014)
The complete genome sequence of a Neanderthal
from the Altai Mountains. Nature 505: 43–49. 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 program documentation
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 Pons-Salort, J Serra-Cobo, F Jay, 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