Publications


Not peer-reviewed / under review

  • Szatkownik, A., Planche, L., Demeulle, M., Chambe, T., Avila Arcos, M., Huerta-Sanchez, E., Furtlehner, C., Charpiat, G., Jay*, F. & Yelmen*, B. (2024). Diffusion-based artificial genomes and their usefulness for local ancestry inference. bioRxiv, 2024-10. Link
  • Yelmen, B., Alver, M., Estonian Resarch Biobank Team, Jay, F., & Milani, L. (2024). Interpreting artificial neural networks to detect genome-wide association signals for complex traits. arXiv preprint arXiv:2407.18811 Link
  • Szatkownik, A., Furtlehner, C., Charpiat, G., Yelmen*, B., & Jay*, F. (2024). Latent generative modeling of long genetic sequences with GANs. bioRxiv, 2024-08. Link
  • Koptekin, D., Aydogan, A., Karamurat, C., Altinisik, N. E., Vural, K. B., Kazanci, D. D., ... & Somel, M. (2024). Out-of-Anatolia: cultural and genetic interactions during the Neolithic expansion in the Aegean. bioRxiv, 2024-06. Link
  • Villanea, F. A., Peede, D., Kaufman, E. J., Anorve-Garibay, V., Dillon, K. E. W., Zeloni, R., ... & Huerta-Sanchez, E. (2023). The MUC19 gene in Denisovans, Neanderthals, and Modern Humans: An Evolutionary History of Recurrent Introgression and Natural Selection. bioRxiv, 2023-09. Link
  • L Lemaire, F Jay, I Lee, K Csilléry, MGB Blum. Goodness-of-fit statistics for approximate Bayesian computation. arXiv 2016 arXiv:1601.04096. Link   

Peer-reviewed conference/workshop with extended abstract or short paper

  • Szatkownik, A., Furtlehner, C., Charpiat, G., Yelmen, B., & Jay, F. (2024). Towards creating longer genetic sequences with GANs: Generation in principal component space. In Machine Learning in Computational Biology (pp. 110-122). PMLR. Conference paper with proceedings Link
  • J Cury, T Sanchez, E Bray, J Medina-Tretmanis, M Avila-Arcos, E Huerta-Sanchez, G Charpiat and F Jay (2022) Inferring effective population sizes of bacterial populations while accounting for unknown recombination and selection: a deep learning approach. Workshop Machine Learning for Microbial Genetics at ECML/PKDD, Sept 2022, Grenoble, short paper, no proceedings. Link

Peer-reviewed national and local conference/workshop with extended abstract or short paper

  • JB Lamy, F Jay. Combiner arbres phylogénétiques et visualisation d’ensembles. Atelier
    Visualisation d’informations, interaction et fouille de données, Jan 2020, Bruxelles, Belgique. hal-02968296
  • T Sanchez, G Charpiat, F Jay (2017). SPI-DNA: End-to-end Deep Learning Approach for Demographic History Inference. Paris-Saclay Junior Conference on Data Science and Engineering, Sep 2017, Orsay, France, hal-01679385, extended abstract [local conference]

Peer-reviewed journal papers

  •  Medina-Tretmanis, J., Jay*, F., Ávila-Arcos*, M. C., & Huerta-Sanchez*, E. (2024). Simulation-based benchmarking of ancient haplotype inference for detecting population structure. Human Population Genetics and Genomics, 4(1). https://doi.org/10.47248/hpgg2404010005
  • Lefeuvre, M., Martin, M. D., Jay, F., Marsolier, M. C., & Bon, C. (2024). GRUPS-rs, a high-performance ancient DNA genetic relatedness estimation software relying on pedigree simulations. Human Population Genetics and Genomics 2024;4(1):0001 | https://doi.org/10.47248/hpgg2404010001
  • B Yelmen, A Decelle, L Boulos, A Szatkownik, C Furtlehner, G Charpiat, and F Jay (2023). Deep convolutional and conditional neural networks for large-scale genomic data generation.PLoS Computational biology doi:10.1371/journal.pcbi.1011584
  • C Gain, Benedicte Rhone, P Cubry, I Salazar, F Forbes, Y Vigouroux, F Jay, and O François (2023). A quantitative theory for genomic offset statistics. Molecular Biology and Evolution, 40(6), msad140 Link
  • V Villa-Islas, A Izarraras-Gomez, M Larena, ... & Ávila-Arcos, M. C. (2023). Demographic history and genetic structure in pre-Hispanic Central Mexico. Science 380(6645), eadd6142. Link
  • B Yelmen and F Jay (2023). An overview of deep generative models in functional and evolutionary genomics. Annual Review of Biomedical Data Science, 6:173–89  Link
  •  J Guez, G Achaz, F Bienvenu, J Cury, B Toupance, E Heyer, F Jay°, F Austerlitz°. Cultural transmission of reproductive success impacts genomic diversity, coalescent tree topologies and demographic inferences. Genetics , 223(4), iyad007. Selected for April 2023 Highlights Link
  • T Sanchez*, EM Bray*, P Jobic, J Guez, A-C Letournel, G Charpiat, J Cury°, F Jay° (2023) Dnadna:  - A deep learning framework for population genetic inference. Bioinformatics  39(1), btac765. Link  Try dnadna!
  • I Overcast et al (2023) Toward a Genetic Theory of Island Biogeography: Inferring Processes from Multi-Dimensional Community-Scale Data. Global Ecology and Biogeography, 32(1), 4-23.
  • J Cury, B Haller, G Achaz, F Jay (2022). Simulation of bacterial populations with SLiM.   10.24072/pcjournal.72 - Peer Community Journal, Volume 2, article no. e7. (recommended by PCI EvolBiol in 2021) Paper ;  Simulator
  • 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. PLoS genetics, 17(2), e1009303. Paper ; repo
  • O François & F Jay (2020) Factor Analysis of Ancient Population Genomic Samples. Nature Communications 11(1), 1-11. Paper ; repo
  • V Pankratov, F Montinaro, A Kushniarevich, G Hudjashov, F Jay et al (2020). Differences in local population history at the finest level: the case of the Estonian population European Journal of Human Genetics, DOI:10.1038/s41431-020-0699-4. Link
  •  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 Paper ; repo ; pred notebook
  • 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. Paper ; sumstat code
  • K Caye, F Jay, O Michel, O Francois (2018). Fast Inference of Individual Admixture Coefficients Using Geographic Data. The Annals of Applied Statistics, 12(1), 586–608 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, 26 (16), 4145-4157. Paper ; repo
  •  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 Link ; repo
  • F Jay, O François, EY Durand, and MGB Blum (2015). POPS : A software for prediction of population genetic structure using latent regression models. Journal of Statistical Software, 68(9).  DOI: 10.18637/jss.v068.i09. Paper ; software
  • Q Fu, H Li, P Moorjani, F Jay, et al. (2014). Genome sequence of a 45,000-year-old modern human from western Siberia. Nature, 514(7523), 445-449. Link
  • 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
     
  • K Prüfer, F Racimo, N Patterson, F Jay, S Sankararaman, et al. (2014) The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505(7481): 43–49. Link
  • JD Wall, MA Yang, F Jay, et al. (2013) Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics, 194(1), 199-209, doi: 10.1534/genetics.112.148213. Link
     
  • 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
     
  • 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   --   Front cover
     
  • M 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
     
  • 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, 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(10), 2354–2368.  Link
     
  • 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
     
  • 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 ; software
     
  • EY Durand, F Jay, G Gaggiotti, and O François (2009). Spatial inference of admixture proportions and secondary contact zones. Molecular Biology and Evolution, 26(9), 1963-1973. Link ; software 

 

My PhD 

  • F Jay. Bayesian methods for population genetics : relationships between genetic population structure and environment.   Link (in French)
     

Theses of PhD students I co-mentored

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