PhD Candidate in Computational Genomics / PhD Candidate in Animal Genomics

PhD Position in Computational Genomics / Animal Genomics

100%, Zurich, fixed-term

The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich investigates DNA variation in individual genomes and at the population scale. Our group applies state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals and employs bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We are offering a PhD position at the interface of computational and statistical genomics, and bioinformatics.

Project Background

Cattle serve as an intriguing "model organism" for studying inherited genetic variation and the molecular-genetic underpinnings of complex traits and diseases. Whole-genome sequencing and dense phenotyping data are available for tens of thousands of individuals connected through familial relationships. These extensive datasets enable the examination of allele transmission and robust association testing to investigate the genetic architecture of complex traits and diseases.

The project titled “OPISCOW - Origin, prevalence, and impact of complex structural variation in a large mammalian genome discovered through genome assembly at the population scale” has recently received funding from the Swiss National Science Foundation (SNSF). This four-year project builds upon previous research conducted by the Animal Genomics group, which investigated the presence of structural variants in the bovine genome. We have amassed large quantities of long-read sequencing data (PacBio HiFi) to construct genome assemblies and integrate them into pangenomes. This approach allows us to investigate the distribution of structural variants in cattle and related species, create various pangenome graphs, and identify trait-associated structural variants.

OPISCOW aims to explore the *de novo* mutation rate of structural variants in a large cattle pedigree using highly accurate long reads and nearly complete assemblies.

Job Description

We are seeking an enthusiastic and highly motivated candidate to investigate long-read sequencing data collected from a large cattle pedigree. We will sequence 50 trios (mother, father, offspring) using PacBio HiFi reads, and (a) map these reads against a recently built T2T assembly, and (b) create haplotype-resolved assemblies for the offspring animals. Both the read alignments and assemblies will be examined to identify variants that do not exist in both parental genomes. This investigation will allow us to explore the occurrence rate of various types of *de novo* variants. There is also an opportunity to contribute to our ongoing effort to establish a comprehensive bovine pangenome.

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 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 a prerequisite.
• Proficient English skills are required for writing scientific papers and active participation in international conferences.

Workplace

An inspiring, supportive, and team-based research environment to facilitate seamless integration into an ambitious research project awaits you. 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 has an excellent track record of publishing in leading multidisciplinary journals.

We Offer

• Integration into a young and dynamic research team with diverse backgrounds.
• Ownership and responsibility within a fully funded four-year project.
• Flexibility in designing and pursuing individual research ideas within the scope of the overall project.
• Collaboration with national and international partners.
• Competitive salary conditions according to ETH regulations.

We Value Diversity

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 in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to learn how we ensure a fair and open environment that allows everyone to grow and flourish.

Curious? So Are We.

This is a fixed-term position for four years with an anticipated start date of September 1st, 2025 (negotiable). Some of the data required for conducting the research have already been collected, enabling an earlier start date for the project. You will join the Animal Genomics group led by Hubert Pausch.

Interested candidates are invited to apply online using the form below. 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. We are renowned for our excellent education, cutting-edge fundamental research, and direct transfer of knowledge into society. With over 30,000 individuals from more than 120 countries, our university encourages independent thinking within an inspiring environment. Strategically located in the heart of Europe, we work collaboratively to find solutions for today’s and tomorrow’s global challenges.