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 utilize long-read sequencing technologies to characterize animal genomes and employ bioinformatics and statistical genomics approaches to identify trait-associated sequence variation. We invite applications for a PhD position at the intersection of computational and statistical genomics, and bioinformatics.
Cattle serve as a fascinating model organism for studying inherited genetic variation and the molecular-genetic foundations of complex traits and diseases. Whole-genome sequencing and dense phenotyping data are available for tens of thousands of individuals, permitting the exploration of allele transmission and powerful association testing to uncover 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 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 examined the presence of structural variants in the bovine genome. We have gathered substantial long-read sequencing data (PacBio HiFi) for building genome assemblies and integrating them into pangenomes. This has allowed us to analyze the distribution of structural variants in cattle and related species, construct various pangenome graphs, and identify trait-associated structural variants.
We are seeking an enthusiastic and highly motivated candidate to take on the responsibility of 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 be tasked with (a) mapping these reads against a recently constructed T2T assembly and (b) creating 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, thereby allowing us to investigate the rate at which different types of variants occur de novo. There is also 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, along with strong communication skills, is desirable.
We provide an inspiring, supportive, and team-oriented research environment to facilitate seamless integration into an ambitious research project. Our team comprises a young and international group of researchers who share a common vision of making significant contributions to high-level academic research in the broad field of animal genomics. The team has an excellent track record of publishing in the field's leading multidisciplinary journals.
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.
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 the research has been collected, allowing for an earlier start date if possible. You will join the Animal Genomics group led by Hubert Pausch.
Please apply online using the form below. Only applications matching the job profile will be considered.
Note: For further inquiries about the Animal Genomics group, please refer to our website. Questions can be directed to Prof. Hubert Pausch via email at hubert.pausch@usys.ethz.ch (no applications).
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Location : Zürich
Country : Switzerland