Postdoctoral Researcher in Animal Genomics

100%, Zurich, fixed-term

The Animal Genomics group within the Institute of Agricultural Sciences at ETH Zurich investigates (epi-)genomes and transcriptomes of farm animals to identify trait-associated genomic features and causal sequence variants. To do so, we develop and apply bioinformatics and statistical methods to characterize population-scale short and long-read sequencing data. We are looking for a motivated researcher who is eager to propose and address cutting-edge research questions within a young and international team. This is a 24-months full-time position with an anticipated start date of March 1st, 2025 (negotiable). The position is based at the main campus of ETH Zurich in the vibrant city of Zurich, Switzerland. You will join the Animal Genomics group led by Hubert Pausch.

Project background

The research of the incoming postdoctoral researcher will focus on identification of trait-associated variants in cattle using comprehensive genomic, epigenomic, and transriptomic data with a particular emphasis on quantifying the contribution of structural variants to complex traits. Through collaborations with breed associations, we have established powerful mapping cohorts consisting of more than 150,000 cattle for which microarray-derived genotypes and phenotypes for many complex traits are available. Sequenced reference panels are available to impute both small variants and structural variants into these cohorts to conduct genome-wide association studies at nucleotide resolution. We anticipate that these data will facilitate QTL and causal variant identification. The incoming postdoctoral researcher will have access to the following datasets to comprehensively characterize the contribution of structural variants to trait heritability:

• whole-genome genotyping and imputed sequencing data of >150'000 individuals with excellent phenotypic records for more than 50 complex traits. These data enable powerful genome-wide association studies, the fine-mapping of trait-associated regions, etc.
• long read sequencing data (HiFi) of >250 individuals. These data enable compiling a SV reference panel to impute SVs into the mapping cohort with the aim to conduct association tests between SVs and complex traits
• more than 50 haplotype assemblies representing various breeds of taurine and indicine cattle. These data can be used to build highly informative graph-based pangenomes to study SV diversity
• a cohort of 120 individuals for which both DNA and RNA sequencing data are available for several tissues. This dataset allows characterising variants and features underpinning molecular phenotypes such as expression and splicing variation

Our group also contributes to large international collaborative projects such as the Bovine Pangenome Consortium and the Cattle Long Read Sequencing Consortium, and the successful candidate is encouraged to actively contribute to these efforts as well. Our group has access to ETH's high-performance computing cluster and state-of-the-art molecular user labs equipped with short- and long-read sequencing technologies. We are committed to open and reproducible research.

Job description

We are looking for an enthusiastic and collaborative researcher who is eager to contribute to ongoing cutting-edge research projects, support the projects of doctoral students, and develop and implement own research ideas. You will lead a research project that

• aims at characterizing the contribution of structural variants to the heritability of complex traits in cattle
• will identify trait-associated structural variants

To achieve these goals, you will be responsible to curate a long read-sequenced reference panel which allows imputing structural variant genotypes into large mapping cohorts. You will impute SV genotypes, assess imputation accuracy, and conduct association tests to identify causal variants. Statistical fine-mapping will be applied to prioritize candidate causal variants. You will work at a high performance compute cluster and establish reproducible computational workflows with Snakemake.

You are encouraged to make use of the wealth of (epi-)genomic and transcriptomic data we have accumulated over the past years to develop and execute your research ideas. Close interaction with other group members, contributing to other ongoing research projects, and establishing novel collaborations with other scientists are encouraged. Ideally, you will pursue research interests that complement our ongoing efforts.

We are looking for a computational genomics-oriented researcher with strong affinity to statistical genetics. Active participation in international conferences and scientific writing are very much supported.

Our group contributes to the teaching in the study program Agricultural Sciences at ETH. Depending on the seniority of the candidate, a contribution to supervising the Bachelor/Master thesis the teaching of existing courses is expected.

Profile

You should have a strong research interest in statistical genomics, computational genomics, animal genomics, computational biology or bioinformatics. Experience with a programming/scripting language (e.g., python) and working in a high-performance computing environment are required. Experience with workflow managers such as Snakemake is desired. Applicants should hold a PhD (or should be close to the completion of their PhD thesis) in disciplines that are related to the advertised position. The writing of scientific papers and participation in international conferences requires good knowledge of English.

Workplace

Workplace

We offer

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.

• Your career with impact: Become part of ETH Zurich, which not only supports your professional development, but also actively contributes to positive change in society
• We are actively committed to a sustainable and climate-neutral university
• You can expect numerous benefits, such as public transport season tickets and car sharing, a wide range of sports offered by the ASVZ, childcare and attractive pension benefits

We value diversity

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.

Curious? So are we.

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

• A cover/motivation letter (not more than two pages) that demonstrates (i) your suitability for the offered position and (ii) provides information about the future research questions you would like to pursue
• A Curriculum vitae including a list of publications, complete academic record, and copies of Bachelor's, Master's and PhD degrees
• Names and contact information of two references

Please note that we only accept applications submitted through our online application portal. Applications via email or postal services will not be considered. The application review will begin on December 15th and continue until the position is filled (and this advertisement is online).

Additional information about the Animal Genomics group can be found on our website. For questions about the position, please contact Hubert Pausch via email hubert.pausch@usys.ethz.ch (no applications).