PhD Candidate in Statistical Genomics / PhD Candidate in Computational Genomics

Two PhD Positions in Statistical Genomics / Computational Genomics

100%, Zurich, Fixed-Term

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 dedicated to investigating DNA variation in individual animal genomes and at the population scale. Our research teams utilize state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals using both long and short reads. We then apply bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We are excited to offer two PhD positions at the intersection of computational and statistical genomics, and bioinformatics.

Project Background

The project PangenomiX aims to assess the impacts of sex chromosomal structural variants on reproduction- and meiosis-related traits in cattle through pangenomes and advanced imputation and association methods. This joint initiative, co-developed by Dr. Tom Druet and Prof. Hubert Pausch, has recently received funding as a Weave project by the Fonds de la recherche scientifique (F.R.S.-FNRS) and the Swiss National Science Foundation.

PangenomiX seeks to explore 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 near-complete assemblies of the sex chromosomes, paired with the development of statistical methods for transferring information from the pangenome variation panel to large mapping populations through imputation, enabling association testing between complex traits and SVs.

This four-year project builds upon significant previous research by both the Animal Genomics group and the Quantitative Genetics & Genomics group. We have amassed extensive long-read sequencing data (PacBio HiFi) to create genome assemblies and integrate them into pangenomes, allowing us to investigate the distribution of structural variants in cattle and related species, construct pangenome graphs, and identify trait-associated structural variants. Furthermore, we have developed accurate imputation methods for pedigreed populations and haplotype-based association testing approaches, specifically designed for sex chromosomes.

PangenomiX will utilize large-scale long and short-read sequencing data from two cattle populations to characterize structural variant diversity on sex chromosomes and examine how these variants influence male fertility and recombination rates.

Job Description

We are seeking two enthusiastic and highly motivated candidates to contribute to this exciting project:

• First Candidate: This role involves building pangenomes from long read sequencing data collected from two cattle breeds. Existing PacBio HiFi sequencing data will be supplemented with ultra-long sequencing through ONT to construct near-complete assemblies for the sex chromosomes. This sub-project will be closely supervised by Prof. Hubert Pausch at ETH Zurich.
• Second Candidate: This role will focus on imputation and association testing. The candidate will develop methods to impute structural variants into large mapping cohorts with array- or short-read derived genotypes. The resulting genotypes will be tested for associations with complex traits using methodologies that account for the multi-allelic nature of the SVs. This sub-project will be closely supervised by Dr. Tom Druet at the University of Liège.

Collaboration between both doctoral students is anticipated, with research exchanges between the two groups expected.

Prior experience with genomic data analysis on a high-performance computing cluster, along with strong communication skills, is desirable.

Profile

• Research interest in statistical genomics, computational biology, computational genomics, or animal genomics.
• Experience with a programming language (e.g., Python, R) and a basic working knowledge of high-performance computing clusters is required.
• A MSc degree in genetics, genomics, computational biology, bioinformatics, animal sciences, or disciplines related to the PhD position.
• Affinity for computational genomics, bioinformatics, or statistics is essential.
• The ability to write scientific papers and actively participate in international conferences requires a good command of English.

Workplace

We offer an inspiring, supportive, and team-oriented research environment, facilitating seamless integration into an ambitious research project. Our team consists of a young, international group of researchers who share a common vision of contributing significantly to cutting-edge academic research in the broad field of animal genomics. The team boasts an excellent track record of publishing in leading multidisciplinary journals.

We Value Diversity and Sustainability

In line with our values, ETH Zurich fosters an inclusive culture. We promote equality of opportunity, value diversity, and nurture a working and learning environment where the rights and dignity of all staff and students are respected. We also prioritize sustainability as a core value, consistently working towards a climate-neutral future.

Curious? So Are We!

Both positions are fixed-term for four years, with an anticipated start date of September 1st, 2026 (negotiable). Elements of the data required for research have been collected, enabling potential earlier project initiation. You will join either 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. Only applications matching the job profile will be considered.