PhD position: Compilation of a bovine haplotype reference panel in Zürich

100%, Zurich, temporary

The group at the Institute of Agricultural Sciences at ETH Zurich is dedicated to investigating genomic variation within and between livestock populations. The group applies state of the art technologies to collect sequencing data from large cohorts of farm animals and applies bioinformatics and statistical approaches to characterize trait-associated sequence variation. The lab is offering a PhD position on the compilation of a bovine haplotypre reference panel. 

Thousands of cattle genomes have been sequenced using short-read sequencing technologies. The availability of massive sequencing data for animals from different breeds provides insight into genomic variation that segregates within and between populations. Moreover, sequenced key ancestors may serve as a reference panel to predict sequence variant genotypes for all animals of a population in silico using genotype imputation. However, existing breed-specific reference panels are too small for most populations and most of them are limited to single nucleotide polymorphisms and short insertions and deletions. This position is part of a project funded by the Swiss National Science Foundation (SNSF) to compile a highly informative haplotype reference panel for a Swiss cattle breed. 

We are looking for an enthusiastic and highly-motivated candidate to work on the compilation of a haplotype reference panel for a Swiss cattle breed. The candidate will analyse and combine short- and long-read sequencing data from hundreds of cattle to create a library of haplotypes that segregate in the population. Genome graph-based approaches will be developed and applied in order to improve the genotyping of sequence variants beyond SNPs and Indels. The availability of long-read sequencing data also offers the opportunity to contribute to ongoing endeavors with regard to the de novo assembly of breed-specific reference genomes. This is a fixed term position for 4 years with an anticipated start date of January 1st, 2020 (negotiable). The position is based at ETH Zurich, Switzerland. The successful candidate will join the  led by Hubert Pausch.

The successful candidate should have a strong research interest in statistical genomics, computational biology, animal genetics or animal breeding. Experience with a programming language (e.g., python, R) is required and basic working knowledge with high-performance computing clusters is desired. Applicants should hold 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 required. The writing of scientific papers and 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.