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 employs state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals using long and short reads, and applies bioinformatics and statistical genomics approaches to characterize 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 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. This data enables the exploration of allele transmission and robust association testing to investigate 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 was recently funded by the Swiss National Science Foundation (SNSF). This four-year project builds upon previous research conducted by the Animal Genomics group that investigated the presence of structural variants in the bovine genome. We have amassed substantial long-read sequencing data (PacBio HiFi) to create genome assemblies and incorporate them into pangenomes. This has enabled us to examine the distribution of structural variants in cattle and related species, construct various pangenome graphs, and identify trait-associated structural variants.
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.
We are seeking an enthusiastic and highly motivated candidate to analyze long-read sequencing data obtained 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 constructed T2T assembly, and (b) create haplotype-resolved assemblies for the offspring. Both the read alignments and assemblies will be explored to identify variants absent in both parental genomes, enabling us to study the rate of different types of variants occurring de novo. There are also opportunities to contribute to our ongoing efforts to establish a comprehensive bovine pangenome.
Prior experience in genomic data analysis on a high-performance computing cluster, along with strong communication skills, is desirable.
An inspiring, supportive, and team-oriented research environment that encourages 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 high-level academic research in the field of animal genomics. The team boasts an exceptional track record of publishing in leading multidisciplinary journals.
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 where the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to discover how we ensure a fair environment that allows everyone to thrive.
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 the research have already been collected, allowing for an earlier starting date for the project. You will join the Animal Genomics group, led by Hubert Pausch.
Interested candidates are encouraged to apply online using the form below. Only applications matching the job profile will be considered.
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Location : Zürich
Country : Switzerland