This is a unique opportunity for two doctoral students to participate in an international collaboration between two research institutes in Switzerland and Belgium. The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich and the Quantitative Genetics & Genomics group of Dr. Tom Druet from the University of Liège are investigating DNA variation in individual animal genomes and at the population scale. Our groups apply state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals using both long and short reads, along with bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We offer two PhD positions at the interface of computational and statistical genomics, and bioinformatics.
The project "PangenomiX - Assessing impacts of sex chromosomal structural variants on reproduction- and meiosis-related traits in cattle through pangenomes and advanced imputation and association methods" is a joint endeavor co-developed by Dr. Tom Druet and Prof. Hubert Pausch. PangenomiX has recently secured funding as a Weave project by the Fonds de la recherche scientifique (F.R.S.-FNRS) and the Swiss National Science Foundation.
PangenomiX aims to study how structural variants (SV) on the sex chromosomes contribute to genetic variation in complex traits, particularly those related to reproduction and meiosis. To achieve this, we will generate a new cattle pangenome that includes nearly complete assemblies of the sex chromosomes while developing statistical methods to transfer information from the pangenome variation panel to large mapping populations through imputation, allowing for association testing between complex traits and SVs.
This four-year project builds upon previous research conducted by the Animal Genomics group and the Quantitative Genetics & Genomics group. We have amassed large datasets of long-read sequencing data (PacBio HiFi) to create genome assemblies integrated into pangenomes. This has enabled us to investigate the distribution of structural variants in cattle and related species, construct various pangenome graphs, and identify trait-associated structural variants. Furthermore, we have developed imputation methods that provide accurate genotypes in pedigreed populations and haplotype-based association testing approaches, including several specifically designed for the sex chromosomes.
PangenomiX will utilize large-scale long and short read sequencing data from two cattle populations to characterize structural variant diversity on the sex chromosomes and investigate how these variants influence male fertility and recombination rates.
We are looking for two enthusiastic and highly motivated candidates to work on this project:
Both doctoral students are expected to collaborate closely, with research exchanges anticipated between the two groups. Prior experience with genomic data analysis on a high-performance computing cluster, along with strong communication skills, is desirable.
We offer an inspiring, supportive, and team-based research environment to facilitate seamless integration into an ambitious research project. Our team consists of a young and international group of researchers who share a common vision of contributing significantly to high-level academic research in the broad field of animal genomics. The team boasts an excellent track record of publishing in leading multidisciplinary journals.
In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity, and nurture a working and learning environment that respects the rights and dignity of all our staff and students. Visit our Equal Opportunities and Diversity website to learn how we ensure a fair and open environment that allows everyone to grow and flourish. Sustainability is a core value for us; we are actively working towards a climate-neutral future.
Both positions are fixed-term for four years, with an anticipated start date of September 1st, 2026 (negotiable). Some data required for research have been collected, allowing for potentially earlier project commencement. You will either join the Animal Genomics group led by Hubert Pausch or the Quantitative Genetics & Genomics group led by Dr. Tom Druet.
Apply online using the form below. Please note that only applications matching the job profile will be considered.
If you have any questions, further information about the Animal Genomics group can be found on this website. For further inquiries concerning the Quantitative Genetics group, please refer to this website. You may also contact Prof. Hubert Pausch at hubert.pausch@usys.ethz.ch (no applications) or Dr. Tom Druet at Tom.Druet@uliege.be (no applications).
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Location : Zürich
Country : Switzerland