Postdoc position on ultra-long read sequencing for animal epigenomics, transcriptomics, and genomics

Postdoc position on ultra-long read sequencing for animal epigenomics, transcriptomics, and genomics

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 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 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 fixed term position with an anticipated start date of August 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 development and application of ultra long read sequencing for the analysis of (epi-)genomes and transcriptomes of individual cattle. The main aim of this project is to capitalize on long read sequencing to better understand the variability of animal (epi-)genomes, detect trait-associated structural variants, and predict their impact on (molecular) phenotypes. We already have collected plenty of data, these include

• more than 50 haplotype assemblies representing various breeds of taurine and indicine cattle
• long read sequencing data (HiFi & ONT) of >150 individuals. These data enable investigating structural variant diversity and methylation variation

Within the advertised project, we want to apply cutting edge technologies to collect and analyse additional long read sequencing data. Possible research directions include (but are not limited to)

• long read sequencing of bovine single cells
• long read-based transcript isoform quantification and analysis
• capitalizing on ultra long reads to resolve repetitive regions and assemble genomes

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 both short- and long-read sequencing technologies (Illumina, PacBio, ONT). We are committed to open and reproducible research.

Job description

We are looking for a researcher that is eager to

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

You are responsible to develop protocols and workflows to collect (ultra) long sequencing data from tissue and blood samples. You will be responsible to interact with our sequencing facility to ensure the protocols are robust and sequencing yields are stable. You'll be able to acces ONT and PacBio technologies to generate data. You will be responsible for the bioinformatic analysis of the generated data.

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.

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.

In general, postdoctoral researchers at ETH Zurich have a full-time employment. A part-time employment may only be considered in exceptional cases (e.g. child- or familycare, other projects or employment).

Your profile

Experience with either ONT or PacBio sequencing as well as proficiency with a programming/scripting language (e.g., python) and past experience to working in a high-performance computing environment are prerequisites. You should have a strong research interest in genomics, computational biology, and/or bioinformatics. This position is ideally suited for a researcher that is interested in developing and applying cutting-edge long read sequencing methods. Ideally, the successful candidate has both wet-lab and computational genomics experience.

Experience with workflow managers such as Snakemake, or the willingness to adopt these tools 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.

Your workplace

Your 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.

We value diversity

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 with (ultra) long read sequencing
• 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 June 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 hubert.pausch@usys.ethz.ch (no applications).

About ETH Zürich

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 with (ultra) long read sequencing
• 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 June 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 hubert.pausch@usys.ethz.ch (no applications).