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 with 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 are an interesting «model organism» to study inherited genetic variation and the molecular-genetic underpinnings of complex traits and dieseases. Whole-genome sequencing and dense phenotyping data are availble for tens of thousands of individuals that are connected thrpugh relatives. These data enable studying the transmission of alleles and powerful association testing to study 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 4-years project builds upon previous research conducted by the Animal Genomics group that investigated the presence of structural variants in the bovine genome. We have collected large amounts of long read sequencing data (PacBio HiFi) to build genome assemblies and integrate them into pangenomes. This allowed us to investigate the distribution of structural variants in cattle and related species, construct different pangenome graphs, and identify trait-associated structural variants.

OPISCOW aims at investigating the de novo mutation rate of structural variants in a large cattle pedigree using highly accurate long reads and near complete assemblies.

We are looking for an enthusiastic and highly-motivated candidate to investigate long read sequencing data collected from large a large cattle pedigree. We will sequence 50 trios (mother, father, offspring) with PacBio HiFi reads, and (a) map these reads against a recently built T2T assembly, and (b) create haplotype resolved assemblies for the offpspring animals. Both the read alignments and assemblies will be investigated to identify variants that are not present in both parental genomes. This will allow us to investigate the rate at which different types of variants occur de novo. There is also a possibility to contribute to our ongoing effort to establish a comprehensive bovine pangenome.

Prior experience with genomic data analysis on a high-performance computing cluster, along with strong communication skills, is desirable.

• 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 with high-performance computing clusters is required.
• A MSc degree in genetics, genomics, computational biology, bioinformatics, animal sciences or disciplines related to the PhD position.
• Affinity to computational genomics, bioinformatics or statistics is a pre-requisite.
• The writing of scientific papers and active participation in international conferences requires good knowledge of English.

An inspiring, supportive, and team-based research environment to facilitate seamless integration into an ambitious research project. Our team consists of a young and international group of researchers who share a common vision of contributing significantly to the highest-level academic research in the broad field of animal genomics. The team has an excellent track record of publishing in the field’s leading and key multidisciplinary journals. For a list of recent publications, see here.

Specifically, we offer

• integration into a young and dynamic research team with diverse backgrounds,
• own responsibility within a fully funded 4 year project,
• flexibility in designing and pursuing own research ideas within the scope of the overall project,
• collaboration with national and international partners,
• competitive salary conditions according ETH regulations.

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 find out how we ensure a fair and open environment that allows everyone to grow and flourish.

This is a fixed term position for 4 years with an anticipated start date of September 1st, 2025 (negotiable). Part of the data required to conduct the research have been collected, enabling also an earlier starting date of the project. You will join the Animal Genomics group led by Hubert Pausch.

We look forward to receiving your online application with the following documents:

• Cover/motivation letter that demonstrates your suitability for the offered position and addresses the research questions you would like to develop within the doctoral project at ETH,
• Curriculum vitae with complete academic record, copies of Bachelor and Master degrees,
• Name and contact information of two references.

Evaluation of applications will start May 20th, and continue until a suitable candidate has been identified. Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered.

Questions? Further information about the Animal Genomics group can be found on our website. For further information, please contact Prof. Hubert Pausch at e-mail [email protected] (no applications).

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