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 using both long and short reads, utilizing bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We are offering a PhD position that operates at the intersection of computational and statistical genomics as well as bioinformatics.
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 that are interconnected through familial relations. These datasets enable the examination of allele transmission and robust association testing to explore 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 has recently received funding from the Swiss National Science Foundation (SNSF). This four-year project builds upon previous work conducted by the Animal Genomics group, which investigated the presence of structural variants in the bovine genome. We have amassed significant amounts of long-read sequencing data (PacBio HiFi) to construct genome assemblies and integrate them into pangenomes. This has enabled us to analyze the distribution of structural variants in cattle and related species, create varied pangenome graphs, and identify trait-associated structural variants.
OPISCOW aims to investigate the de novo mutation rate of structural variants within an extensive cattle pedigree using highly accurate long reads and nearly complete assemblies.
We are seeking an enthusiastic and highly motivated candidate to examine long read sequencing data collected from a large cattle pedigree. We will sequence 50 trios (mother, father, offspring) using PacBio HiFi reads, allowing us to (a) map these reads against a recently generated T2T assembly, and (b) create haplotype-resolved assemblies for the offspring. Both the read alignments and the assemblies will be explored to identify variants absent from both parental genomes, facilitating the investigation of de novo variant occurrence rates. There is also the potential to contribute to our ongoing effort to establish a comprehensive bovine pangenome.
Prior experience with genomic data analysis on high-performance computing clusters, along with strong communication skills, is highly desirable.
We offer an inspiring, supportive, and team-based research environment designed to facilitate smooth integration into an ambitious research project. Our team comprises a young and international group of researchers who share a unified vision of making significant contributions to high-level academic research in the broad field of animal genomics. Our team maintains an excellent track record of publishing in leading multidisciplinary journals. For a list of recent publications, see our website.
In line with our principles, ETH Zurich fosters an inclusive culture. We promote equal opportunities, value diversity, and nurture a working and learning environment where the rights and dignity of all staff and students are upheld. Visit our Equal Opportunities and Diversity website to learn how we ensure a fair and open environment that allows everyone to grow and prosper.
This fixed-term role spans four years, with an anticipated start date of September 1st, 2025 (negotiable). Some data required for this research has already been collected, allowing for the possibility of an earlier project 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.
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Location : Zürich
Country : Switzerland