PhD in Statistical Genomics / PhD in Statistical 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 prestigious 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 led by Dr. Tom Druet at the University of Liège will investigate DNA variation in individual animal genomes and at the population scale. Our teams leverage state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals and employ advanced bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We are offering two PhD positions at the intersection of computational genomics, statistical genomics, and bioinformatics.

Project Background

The project titled "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 co-developed by Dr. Tom Druet and Prof. Hubert Pausch. Recently funded 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 on the sex chromosomes contribute to genetic variation in complex traits, particularly those related to reproduction and meiosis.

The project will establish a new cattle pangenome incorporating nearly complete assemblies of the sex chromosomes, and develop statistical methods to transfer information from the pangenome variation panel to large mapping populations through imputation. This will facilitate association testing between complex traits and structural variants.

This four-year project builds upon previous research conducted by both the Animal Genomics group and the Quantitative Genetics & Genomics group. We have amassed significant long-read sequencing data (PacBio HiFi) to construct genome assemblies and integrate them into pangenomes. This foundation will allow us to explore the distribution of structural variants in cattle, develop diverse pangenome graphs, and pinpoint trait-associated structural variants. Additionally, our team has developed accurate imputation methods for genotypes in pedigreed populations and haplotype-based association testing approaches for 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 assess how these variants affect male fertility and recombination rates.

Job Description

We are seeking two enthusiastic and highly motivated candidates to work on this exciting project.

• The first candidate will create pangenomes from long-read sequencing data collected from two cattle breeds. This sub-project will be closely supervised by Prof. Hubert Pausch at ETH Zurich.
• The second candidate will focus on imputation and association testing, developing methods to impute structural variants into large mapping cohorts with derived genotypes from arrays or short-read sequencing. The resulting genotypes will be tested for associations with complex traits, taking into account the multi-allelic nature of the structural variants. This sub-project will be closely supervised by Dr. Tom Druet at the University of Liège.

Close collaboration between both doctoral students is expected, and research exchanges between the groups are encouraged.

Prior experience with genomic data analysis on high-performance computing clusters, 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 related disciplines is essential.
• Affinity for computational genomics, bioinformatics, or statistics is a prerequisite.
• The ability to write scientific papers and actively participate in international conferences requires good proficiency in English.

Workplace

You will join a vibrant research environment that fosters innovation and collaboration. Our team consists of a young, international group of researchers dedicated to contributing significantly to high-level academic research in the field of animal genomics, with a proven track record of publication in leading multidisciplinary journals.

We Offer

• Integration into a dynamic research team with diverse backgrounds.
• Ownership within a fully funded four-year project.
• Flexibility in designing and pursuing individual research ideas within the project's scope.
• Collaboration opportunities with national and international partners.
• Competitive salary conditions in accordance with the respective funding agency's regulations.

We Value Diversity and Sustainability

ETH Zurich is committed to fostering an inclusive culture, promoting equality of opportunity, and respecting the rights and dignity of all staff and students. Sustainability is at the heart of our values, and we continually strive for 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). We look forward to receiving your online application, which can be submitted using the form below. Only applications matching the job profile will be considered.