Junior research scientist in modelling for genomic prediction using complex data
CR26-GA-1 - You will join the Genetics, Physiology and Livestock Systems (GenPhyse, about 150 permanent staff) joint research unit, where researchers aim to contribute to the agroecological transition of livestock systems through better understanding of livestock biology, genetic bases of traits, and selection schemes to achieve resilient populations. The unit brings together skills in biology, physiology, genomics, genetics, statistics, and bioinformatics. Within the unit, you will join the Chamade team (Characterization and management of genetic diversity) of the Diversity and Selection group comprising methodologists in quantitative genetics (genomic prediction, selection and evolution) and population genomics, as well as statisticians. Within your research team, you will be in charge of developing a new research programme in applied statistics to integrate high-throughput, heterogenous, and multiscale data into genetic and genomic evaluation methods. You will conduct your research to improve genomic prediction models by integrating new information relative to genome function (e.g. functional annotation), molecular phenotypes (e.g. transcriptomics, methylation), and high-throughput or intermediate phenotypes (e.g. longitudinal data, high throughput sensors).To integrate different types of data into current genomic prediction models, you will draw on a variety of statistical modelling, for example modelling SNP effects according to their functional annotation category, or including random effects capturing the inter-individual covariance for intermediate phenotypes. The modelling could draw, for example, on hierarchical models, meta-analysis methods, mediation analysis or machine learning, possibly simulation-based. In addition, as new high-throughput data may not necessarily be available on the same individuals as traditional data, their integration will require the implementation of suitable statistical techniques. The predictive performance of the developed models will be evaluated using numerical simulations, for instance based on real breeding programmes. The models will also be tested on real data from experimental and commercial programmes of livestock species. These data will be available through existing projects and partnerships within the unit and the division to initiate your research project. Computational efficiency must be taken into consideration in your developments to ultimately ensure their practical use in genetic and genomic evaluation. To develop your research, you will benefit from the proximity of experts in statistics, computer science, quantitative, molecular and population genetics within GenPhySE. In accordance with INRAE's policy for open science, in addition to scientific publications, you will promote your work by distributing free software implementing the new methods developed to ensure their wide dissemination to the international community.
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![Comic: Holes. Elevation is to scale relative to sea level and ground level. Land shapes and horizontal distances are not to scale. [Lines for every 1k meters starting from -12k up to +4k: Bingham Canyon Mine (US), Veryovkina Cave (Georgia), MPONENG Gold Mine (South Africa), Sanford Laboratory (US), Giant Crystal Cave (Mexico), Derinkugo Underground City (Turkey), WIPP (US), Restof Salt Mine, with an arrow pointing at the bottom that reads “oops” (US), San Andreas Fault Observatory Borehole (US) CFB North Bay (Canada), Woodingdean Water Well (dug by hand) (United Kingdom), Diefen-Bunker (Canada), Deep Underground Command Center (Canceled in 1965) (US), Lake Peigneu, with another oops arrow next to it (US), Sydney Opera House Parking (Australia), Onkalo Spent Nuclear Fuel Repository (Finland), Hudson River, Delaware Aqueduct (US), Raven Rock (US), Wieliczka and Bochina Salt Mines (Poland), Atchison Storage Facility (US), Snolab (Canada), Detroit Salt Mine (US), Hongyancun Subway Station (China), Nuclear Test Shafts (North Korea), Super Kamiokande Neutrino Detector (Japan), Gran Sasso Laboratory (Italy), Peak above Gran Sasso, Modane Laboratory (France), Peak above Modane Laboratory, Gotthard Tunnel (Switzerland), Peak above Cheyenne Bunker and Gotthard Tunnel, Cheyenne Mountain Bunker (US), Kola Superdeep Borehole (Russia) - deepest artificial point below surface at -11917m, Lake Baikal (Russia), sediments under Lake Baikal, IDDP-2 Borehole (Iceland), Dead Sea (multiple countries), Ryfylke Tunnel (Norway), Pantal Remis Mine with another oops arrow (Malaysia), Great Blue Hole (Belize), Joides Resolution Expedition 307 (Atlantic Ocean), Deepwater Horizon Borehole (Gulf of Mexico) - deepest artificial point below sea level at -11944m, Glomar Challenger Hole 504B (Pacific Ocean), Mohole (Pacific Ocean), Joides Resolution Expedition 329 (Pacific Ocean), Mariana Trench (Pacific Ocean)]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreia43wl3gwyqydc47yse5gbdzybk2edtcibxdtr5jf4gqorc676ap4)
