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The Animal Genomics group within the Institute of Agricultural Sciences at ETH Zurich investigates animal (epi-)genomes and transcriptomes. We apply long read sequencing to detect and characterize trait-associated sequence variation in farm animals with an emphasis on cattle. We are looking for a motivated doctoral student to work on cutting-edge research projects within a young and international team.

We are looking for a doctoral student to join our team. This is a full-time fixed term (4 years) position with an anticipated start date of October 1st, 2024 (negotiable). The position is based at ETH Zurich, Switzerland. You will join the Animal Genomics group led by Hubert Pausch.

Our group has collected vast amounts of short and long read sequencing data in cattle and their related species. These data were assembled into reference-quality genomes and pangenomes to detect trait-associated structural variation. Efforts are ongoing to collect ultra long reads with Oxford Nanopore technologies to resolve low-complexity regions in the bovine genome and build T2T assemblies.

We are actively contributing data and analyses to international efforts such as the Bovine Pangenomics Consortium and the Cattle Long Read Sequencing Consortium with the aim to build community-accepted graph-based references and structural variation reference panels.

The incoming doctoral student will utilize these data to investigate (epi-)genome and transcriptome diversity across different breeds of cattle. The main task of the incumbent is to develop, apply, and implement statistical and bioinformatic approaches to analyse long-read data from Oxford Nanopore and PacBio sequencing technologies, the resulting genome assemblies and pangenome graphs to identify trait-associated genomic variation. A non-exhaustive list of potential topics include the imputation of SVs into large mapping cohorts, SV-based association testing, pangenome-wide association studies, pan-transcriptomics and -epigenomics.

We have access to ETH's state-of-the-art molecular user labs equipped with both short- and long-read sequencing technologies (Illumina, PacBio, ONT) and the Euler high-performance computing cluster. We are committed to open and reproducible research. 

We are looking for a doctoral student that is eager to work on cutting-edge research questions that involve the analysis of third generation sequencing data. You will develop computational workflows to analyse (ultra) long sequencing data in order to identify trait-associated sequence variants. You will contribute to the generation of reference-quality genome assemblies and bovine pangenomes, and develop new approaches to analyse these data.

Active participation in international conferences is very much supported.

This is a fully funded position for 4 years with an anticipated start date of October 1st, 2024 (negotiable).

Further project details will be discussed further in the interview.

You have a MSc degree or are about to finish your MSc studies in a discipline relevant for the position. You are interested in applying computational genomics and bioinformatics approaches and/or ultra-long read sequencing to address scientific questions in an academic environment. You are interested in genetics and genomics. Some previous experience with the analysis of sequencing data is a prerequisite. This position is ideally suited for a researcher that is interested in developing and applying cutting-edge methods to analyse long read sequencing data and/or T2T assemblies and/or pangenome graphs. You will closely work with other doctoral and postdoctoral researcher.

The writing of scientific papers and active participation in internal meetings and in international conferences will require a good knowledge of English

ETH Zurich is a family-friendly employer with excellent working conditions. You can look forward to an exciting working environment, cultural diversity and attractive offers and benefits.