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 in individual genomes and at the population scale. We apply long read sequencing technologies to characterize animal genomes and utilize bioinformatics and statistical genomics approaches to identify trait-associated sequence variation. We offer a PhD position at the interface of computational and statistical genomics, and bioinformatics.

Cattle serve as an intriguing model organism for studying inherited genetic variation and the molecular-genetic foundations of complex traits and diseases. With access to whole-genome sequencing and dense phenotyping data for tens of thousands of individuals, we can examine allele transmission and perform powerful association tests to understand the genetic architecture of complex traits and diseases.

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

Job Description

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

• Mapping these reads against a recently built T2T assembly.
• Creating haplotype-resolved assemblies for the offspring animals.

Both the read alignments and assemblies will be examined to identify variants in the offspring that are absent in both parental genomes. This investigation will allow us to study the rate at which different types of variants occur de novo. Additionally, there is an opportunity to contribute to our ongoing efforts 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, in addition to 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 genomics, computational biology, bioinformatics, genetics, animal sciences, or related disciplines.
• Affinity for computational genomics, bioinformatics, or statistics is a prerequisite.
• Good command of English for writing scientific papers and active participation in international conferences.

Workplace

Join us in an inspiring and supportive research environment that promotes seamless integration into an ambitious research project. Our team comprises a young and international group of researchers unified by a common vision of making significant contributions to cutting-edge academic research in the broad field of animal genomics. We have an excellent track record of publishing in leading multidisciplinary journals.

We Offer

• Integration into a young and dynamic research team with diverse backgrounds.
• Responsibility for conducting research within a fully funded four-year project.
• A high level of support throughout the PhD journey.
• Flexibility in designing and pursuing your own research ideas within the project's scope.
• 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 alignment with our values, ETH Zurich promotes an inclusive culture. We advocate for equal opportunities, value diversity, and cultivate a working and learning environment where the rights and dignity of all staff and students are respected. Visit our Equal Opportunities and Diversity website to learn how we ensure a fair and supportive environment that enables everyone to thrive.

Curious? So Are We.

This is a fixed-term position for four years with an anticipated start date of October 1st, 2025 (negotiable). Much of the data necessary for the research has been collected, which could allow for an earlier project start date. You will join the Animal Genomics group led by Hubert Pausch.

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 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 fosters independent thinking and inspires excellence. Located in the heart of Europe, we forge connections worldwide to collaboratively develop solutions for today's and tomorrow's global challenges.