Postdoc Position on Genome Assembly at the Population Scale

100%, Zurich, fixed-term

The Animal Genomics group within the Institute of Agricultural Sciences at ETH Zurich investigates animal (epi-)genomes and transcriptomes. The group applies bioinformatics and statistical methods to detect and characterize trait-associated sequence variation from short and long-read sequencing data. We are looking for a motivated researcher who is eager to work on cutting-edge research projects within a young and international team.
We are looking for a researcher to join our team of doctoral, post-doctoral, and senior researchers as soon as possible. This is a full-time position with an anticipated start date of June 1st, 2024 (negotiable). The position is based at ETH Zurich, Switzerland. You will join the Animal Genomics group  led by Hubert Pausch.

Project background

This position focuses on the assembly-based characterization of structural variation in cattle. The main aim of this project is to use long read sequencing data (ONT, HiFi) from a large cohort of animals to build assemblies, detect structural variants, and predict their impact on (molecular) phenotypes. Plenty of data have been collected already, these include

• 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;
• long read sequencing data (HiFi & ONT) of >150 individuals. These data enable investigating structural variant diversity and methylation variation;
• more than 100 individuals for which both HiFi reads and RNA sequencing data for several tissues are available. This dataset is ideally suited to investigate the impact of structural variants on complex traits.

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. We have 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 a computational genomics-oriented researcher that is eager to

• contribute to cutting-edge research projects,
• support ongoing projects of doctoral students,
• develop and implement own research ideas

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 centered around the assembly-based detection of structural variation. 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. Potential topics that are most relevant for us include (but are not limited to) the de novo assembly of individual animal genomes, the development and analysis of pangenomes using (ultra) long-read sequencing data, and the development of novel association testing methods from graph-based pangenomes. Many other research directions are possible as the advertised position is not bound to a research project.

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, or the development of novel complementary offers is expected.

Your profile

You should have a strong research interest in computational genomics, computational biology, bioinformatics, or statistical genomics. Proficiency with a programming/scripting language (e.g., python) and working in a high-performance computing environment are prerequisites. Knowledge on genome assembly and pangenome tools is desired. Experience with workflow managers such as Snakemake, or the willingness to adopt these tools is a benefit. 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 advertised position is also available to more senior researcher (e.g., those who already finished a postdoctoral position) who want to take the next step in their career towards independence. The writing of scientific papers and participation in international conferences requires good knowledge of English.

Your workplace

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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.

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Curious? So are we.

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

• A motivation letter (not more than two pages) that demonstrates (i) your suitability for the offered position and (ii) future research questions you would like to address.
• 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 March 1st 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 [email protected] (no applications).

About ETH Zürich

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.