PhD in Statistical Genomics / PhD in Statistical Genomics (female)

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 esteemed research institutes in Switzerland and Belgium. The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich, in conjunction with the Quantitative Genetics & Genomics group led by Dr. Tom Druet from the University of Liège, Belgium, focuses on investigating DNA variation in individual animal genomes as well as at the population scale. Our groups employ state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals using both long and short reads, applying bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We are offering two PhD positions at the intersection of computational and 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 a collaborative effort 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 explores how structural variants (SV) on sex chromosomes contribute to genetic variation in complex traits, particularly those associated with reproduction and meiosis.

The project aims to create a new cattle pangenome, encompassing nearly complete assemblies of sex chromosomes, and develop statistical methods to transfer information from pangenome variation panels to large mapping populations through imputation, facilitating association testing between complex traits and SVs.

This four-year project builds upon comprehensive research conducted by both the Animal Genomics group and the Quantitative Genetics & Genomics group. We have amassed considerable long-read sequencing data (PacBio HiFi) which will be utilized to construct genome assemblies and integrate them into pangenomes. This has allowed us to explore the distribution of structural variants in cattle and related species, construct diverse pangenome graphs, and identify trait-associated structural variants. Furthermore, we've developed imputation methodologies that yield accurate genotypes in pedigreed populations, alongside haplotype-based association testing strategies, specifically designed for sex chromosomes.

Job Description

We are seeking two enthusiastic and highly motivated candidates to actively engage in this groundbreaking project.

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

Close collaboration between both doctoral students is anticipated, with opportunities for research exchanges between the two groups. Prior experience with genomic data analysis on high-performance computing clusters, along with strong communication skills, is highly 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.
• Affiliation to computational genomics, bioinformatics, or statistics is essential.
• The ability to write scientific papers and actively participate in international conferences requires proficiency in English.

Workplace

We provide an inspiring, supportive, and team-oriented research environment that promotes seamless integration into an ambitious research project. Our team is composed of a vibrant, international group of researchers committed to making significant contributions to high-level academic research in the broad field of animal genomics. Our team boasts a remarkable track record of publications in leading multidisciplinary journals.

We Offer

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

We Value Diversity and Sustainability

ETH Zurich is committed to fostering an inclusive culture, promoting equality of opportunity, and valuing diversity while nurturing a respectful working and learning environment for all staff and students. Explore our Equal Opportunities and Diversity website to understand how we maintain a fair environment for growth and development. Sustainability is a fundamental value for us, and we strive toward 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). Some data necessary for conducting the research are already collected, allowing for 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.

About ETH Zurich

ETH Zurich is one of the world’s leading universities specializing in science and technology. Renowned for its excellent education, cutting-edge research, and the direct transfer of new knowledge to society, our university consists of over 30,000 individuals from more than 120 countries who thrive in an environment that encourages independent thinking and excellence. Located in the heart of Europe, we collaborate globally to develop solutions for contemporary and future challenges.