PhD position: Pangenome-wide analysis of bovine genomes

 

The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich investigates genomic variation within and between livestock populations. The group applies different state of the art technologies to sequence the genomes 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 with a focus on the long read-based assembly and pangenome integration of multiple bovine genomes. 

Project background

Long-read sequencing facilitates the assembly of large mammalian genomes. Sophisticated approaches such as «trio-binning» enable the production of two haplotype-resolved assemblies of reference quality from a sequenced trio. International consortia such as the «Bovine Pan-Genome Consortium» aim at producing haplotype-resolved assemblies for multiple breeds. Pangenomes offer a valuable framework to compare multiple haplotype-resolved assemblies and reveal structural variation within and between breeds. This project builds upon previous projects conducted by the Animal Genomics group that led to variation-aware references, multi-assembly graphs, and most recently, the first bovine pangenome from multiple haplotype-resolved assemblies. Further research is envisaged to exploit the diversity of an increasing number of haplotype-resolved assemblies, and enable pangenome-wide association testing.

Job description

We are looking for an enthusiastic and highly-motivated candidate to work on the assembly of multiple bovine genomes using long-read sequencing. You will produce haplotype-resolved assemblies using trio-binning and integrate these new resources into multi-assembly graphs to identify structural differences between individual genomes. The structural variants will be extrapolated to a large mapping population with phenotypes for dozens of complex traits using comprehensive short-read sequencing data. Association testing will be conducted to detect trait-associated structural variation. A large amount of short- and log-read sequencing data have already been collected. Comprehensive transcriptome data are also available.

This is a fully funded fixed term position for 4 years with an anticipated start date of May 1st, 2022 (negotiable). You will join the Animal Genomics group led by Hubert Pausch.

Your profile

• Strong 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, agricultural sciences, animal sciences or disciplines related to the PhD position
• Affinity to computational genomics, bioinformatics and statistics is a pre-requisite.
• The writing of scientific papers and active participation in international conferences requires good knowledge of English.

ETH Zurich is one of the world’s leading universities specialising in science and technology. We are renowned for our excellent education, cutting-edge fundamental research and direct transfer of new knowledge into society. Over 30,000 people from more than 120 countries find our university to be a place that promotes independent thinking and an environment that inspires excellence. Located in the heart of Europe, yet forging connections all over the world, we work together to develop solutions for the global challenges of today and tomorrow.

Interested?

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 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 March 15th. 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 www.ag.ethz.ch. For further information, please contact Prof. Hubert Pausch at e-mail hubert.pausch@usys.ethz.ch (no applications).

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.

Apply online now