PhD Candidate in Statistical Genomics / PhD Candidate 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 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 utilize state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals, applying bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We are excited to offer two PhD positions at the interface of computational and statistical genomics, and bioinformatics.

Project Background

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 collaborative effort co-developed by Dr. Tom Druet and Prof. Hubert Pausch. PangenomiX has recently been 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 (SV) on the sex chromosomes contribute to genetic variation in complex traits, particularly those related to reproduction and meiosis. A new cattle pangenome that includes nearly complete assemblies of the sex chromosomes will be generated, and statistical methods will be developed to transfer information from the pangenome variation panel to large mapping populations via imputation. This will ultimately enable association testing between complex traits and SVs.

This 4-year project builds on previous research conducted by the Animal Genomics group and the Quantitative Genetics & Genomics group. We have amassed large amounts of long-read sequencing data (PacBio HiFi) to build genome assemblies and integrate them into pangenomes, allowing us to investigate the distribution of structural variants in cattle and related species, construct diverse pangenome graphs, and identify trait-associated structural variants. Moreover, we have developed imputation methods that yield accurate genotypes in pedigreed populations as well as haplotype-based association testing approaches tailored specifically for the sex chromosomes.

PangenomiX will leverage extensive long and short-read sequencing data from two cattle populations to characterize structural variant diversity on the sex chromosomes and explore how these variants influence male fertility and recombination rates.

Job Description

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

• The first candidate will build pangenomes from long-read sequencing data collected from two cattle breeds. Existing PacBio HiFi sequencing data will be augmented with ultra-long sequencing using ONT to create near-complete assemblies for the sex chromosomes. This sub-project will be closely supervised by Prof. Hubert Pausch at ETH Zurich.
• The second candidate will concentrate on imputation and association testing. The successful candidate will develop approaches to impute structural variants into large mapping cohorts that have array- or short-read sequencing-derived genotypes. The resulting genotypes will be tested for associations with complex traits using methods that accommodate the multi-allelic nature of the SVs. This sub-project will be supervised closely by Dr. Tom Druet at the University of Liège.

Close collaboration between both doctoral students is expected, with research exchanges between both groups anticipated. Prior experience with genomic data analysis on a high-performance computing cluster, along with strong communication skills, is desirable.

Profile

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

We Offer

We provide 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 significantly contributing to top-tier academic research in the field of animal genomics. Our group has an excellent track record of publishing in leading multidisciplinary journals.

Specifically, we offer:

• Integration into a young and dynamic research team with diverse backgrounds.
• Independence within a fully funded 4-year project.
• Flexibility to design and pursue your own research ideas within the scope of the overall project.
• Collaboration with national and international partners.
• Competitive salary conditions based on the regulations of the respective funding agency.

Workplace

ETH Zurich fosters an inclusive culture that promotes equality of opportunity, values diversity, and nurtures a working and learning environment in which the rights and dignity of all staff and students are respected. Visit our Equal Opportunities and Diversity website to learn how we maintain a fair and open environment that allows everyone to thrive. Sustainability is a core value for us, and we are committed to working towards a climate-neutral future.

Curious? So Are We!

Both positions are fixed-term for 4 years, with an anticipated start date of September 1st, 2026 (negotiable). Part of the data required to conduct the research has already been collected, allowing for the possibility of an earlier project start date. 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. Please note that only applications matching the job profile will be considered.