PhD Candidate in Computational Genomics / PhD Candidate in Computational Genomics

PhD Position in Computational Genomics

100%, Zurich, fixed-term

The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich investigates DNA variation within individual genomes and across populations. We employ long-read sequencing technologies to characterize animal genomes, utilizing bioinformatics and statistical genomics approaches to identify trait-associated sequence variations. We are pleased to announce a PhD position at the interface of computational and statistical genomics, and bioinformatics.

Cattle serve as an intriguing "model organism" to study inherited genetic variation and the molecular-genetic foundations of complex traits and diseases. Whole-genome sequencing and extensive phenotyping data are available for tens of thousands of individuals, enabling us to explore the transmission of alleles and conduct powerful association testing to examine the genetic architecture of complex traits and diseases.

The project entitled “OPISCOW - Origin, Prevalence, and Impact of Complex Structural Variation in a Large Mammalian Genome Discovered Through Genome Assembly at the Population Scale” is a four-year initiative recently funded by the Swiss National Science Foundation (SNSF). OPISCOW aims to investigate the de novo mutation rate of structural variants in a large cattle pedigree using highly accurate long reads and nearly complete assemblies.

This project builds on previous research conducted by the Animal Genomics group, which explored the presence of structural variants in the bovine genome. We have amassed large datasets of long read sequencing data (PacBio HiFi) to construct genome assemblies and integrate them into pangenomes. This research has enabled us to examine the distribution of structural variants in cattle and related species, build various pangenome graphs, and identify trait-associated structural variants.

Job Description

We are seeking an enthusiastic and highly motivated candidate responsible for investigating long read sequencing data collected from a large cattle pedigree. HiFi data will be available for 50 trios (mother, father, offspring). The incoming PhD student will:

• Map these reads against a recently built T2T assembly
• Create haplotype resolved assemblies for the offspring animals

Both the read alignments and assemblies will be analyzed to identify variants in the offspring that are absent in both parental genomes, allowing for investigations into the rate of various types of variants occurring de novo. There is also an opportunity to contribute to our ongoing effort to establish a comprehensive bovine pangenome.

Prior experience with workflow management software (e.g., Snakemake or Nextflow) and 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 genomics, computational biology, bioinformatics, genetics, animal sciences, or related disciplines
• Affinity to computational genomics, bioinformatics, or statistics is a prerequisite
• The ability to write scientific papers and actively participate in international conferences requires good knowledge of English

Workplace

We offer 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 making significant contributions to the highest-level academic research in the broad field of animal genomics. The team boasts an excellent track record of publications in leading multidisciplinary journals.

We Offer

• Integration into a young and dynamic research team with diverse backgrounds
• Responsibility to conduct research within a fully funded four-year project
• High level of support throughout the PhD journey
• Flexibility in designing and pursuing personal research ideas within the scope of the overall project
• Collaboration with national and international partners to develop a scientific network
• Participation in international conferences and seminars
• Competitive salary conditions according to ETH regulations

We Value Diversity

In line with our values, ETH Zurich promotes an inclusive culture. We encourage 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 find out 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 October 1st, 2025 (negotiable). Part of the data required for conducting the research has already been collected, which may allow for an earlier start date. You will join the Animal Genomics group led by Hubert Pausch.

We look forward to receiving your online application 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 the direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find our university to be a place that promotes independent thinking and inspires excellence. Located in the heart of Europe yet forging connections all over the world, we work together to develop solutions for the global challenges of today and tomorrow.