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 leverages state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals using both long and short reads, and employs 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 as well as the molecular-genetic underpinnings of complex traits and diseases. Whole-genome sequencing and dense phenotyping data are available for tens of thousands of individuals interconnected through familial relationships. These data facilitate the investigation 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 prior research conducted by the Animal Genomics group that 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 endeavor has allowed us to assess the distribution of structural variants in cattle and related species, create various pangenome graphs, and identify trait-associated structural variants.
OPISCOW aims to investigate the *de novo* mutation rate of structural variants within 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 collected 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 built T2T assembly, and (b) create haplotype-resolved assemblies for the offspring. Both the read alignments and assemblies will be examined to identify variants absent in both parental genomes, enabling us to investigate the rate of occurrence of various types of *de novo* variants. Additionally, there may be opportunities to contribute to our ongoing efforts to establish a comprehensive bovine pangenome.
Prior experience with genomic data analysis on high-performance computing clusters, as well as strong communication skills, is desirable.
ETH Zurich provides an inspiring, supportive, and collaborative research environment aimed at facilitating seamless integration into an ambitious research project. Our team comprises a dynamic and international group of researchers who share a common vision of making substantial contributions to high-level academic research in animal genomics. The team has an excellent track record of publications in leading multidisciplinary journals.
In alignment with our core values, ETH Zurich fosters an inclusive culture that promotes equality of opportunity, values diversity, and nurtures a working and learning environment where the rights and dignity of all staff and students are respected. Visit our Equal Opportunities and Diversity website for more information about how we maintain a fair and open 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 necessary for the 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 through the form below.
**Please note that only applications matching the job profile will be considered.**
ETH Zurich is one of the world’s leading universities specializing in science and technology. Renowned for its excellent education, cutting-edge fundamental research, and direct transfer of new knowledge into society, ETH Zurich is home to over 30,000 individuals from more than 120 countries. We promote independent thinking and provide an inspiring environment for excellence. Located in the heart of Europe and connected globally, we work collectively to devise solutions for today's and tomorrow's global challenges.
Location : Zürich
Country : Switzerland