PhD position in Computational Genomics / Animal Genomics
The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich investigates DNA variation in individual genomes and at the population scale. Our group applies state-of-the-art technologies to sequence the genomes and transcriptomes of farm animals with long and short reads, and applies bioinformatics and statistical genomics approaches to characterize trait-associated sequence variation. We offer a PhD position at the interface of computational and statistical genomics, and bioinformatics.
Project background
Cattle are an interesting «model organism» to study inherited genetic variation and the molecular-genetic underpinnings of complex traits and diseases. Whole-genome sequencing and dense phenotyping data are available for tens of thousands of individuals connected through relatives. These data enable studying the transmission of alleles and powerful association testing to study the genetic architecture of complex traits and diseases.
OPISCOW aims to investigate the de novo mutation rate of structural variants in a large cattle pedigree using highly accurate long reads and near-complete assemblies.
We are looking for an enthusiastic and highly motivated candidate to investigate long read sequencing data collected from a large cattle pedigree. We will sequence 50 trios (mother, father, offspring) with PacBio HiFi reads, and (a) map these reads against a recently built T2T assembly, and (b) create haplotype-resolved assemblies for the offspring animals. Both the read alignments and assemblies will be investigated to identify variants not present in both parental genomes. This will allow us to investigate the rate at which different types of variants occur de novo. There is also a possibility to contribute to our ongoing effort to establish a comprehensive bovine pangenome.
Prior experience with genomic data analysis on a high-performance computing cluster, along with strong communication skills, is desirable.
Profile
* Research interest in statistical genomics, computational biology, computational genomics, or animal genomics.
* Experience with a programming language (e.g., Python, R) and basic working knowledge of high-performance computing clusters is required.
* A MSc degree in genetics, genomics, computational biology, bioinformatics, animal sciences, or related disciplines.
* Affinity to computational genomics, bioinformatics, or statistics is a pre-requisite.
* Good knowledge of English for scientific writing and active participation in international conferences.
Workplace
We offer
An inspiring, supportive, and team-based research environment to facilitate seamless integration into an ambitious research project. Our team consists of a young and international group of researchers who share a common vision of contributing significantly to high-level academic research in animal genomics. The team has an excellent publication record in leading multidisciplinary journals. For recent publications, see here.
Specifically, we offer:
* Integration into a young and dynamic research team with diverse backgrounds,
* Own responsibility within a fully funded 4-year project,
* Flexibility in designing and pursuing your own research ideas within the scope of the project,
* Collaboration with national and international partners.
In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity, and nurture a respectful working and learning environment. Visit our Equal Opportunities and Diversity website for more information.
Curious? So are we.
This is a fixed-term position for 4 years with an anticipated start date of September 1st, 2025 (negotiable). Some data collection has already been completed, allowing for an earlier start. You will join the Animal Genomics group led by Prof. Hubert Pausch.
We look forward to your online application with:
* A cover/motivation letter demonstrating your suitability and research interests for the position,
* A curriculum vitae with complete academic records, copies of Bachelor and Master degrees,
* Contact information for two references.
Applications will be evaluated starting May 20th and until the position is filled. Please submit your application exclusively through our online portal; email or postal applications will not be considered.
Questions? Further information about the Animal Genomics group can be found on our website. For inquiries, contact Prof. Hubert Pausch at hubert.pausch@usys.ethz.ch (no applications).
ETH Zurich is a leading university in science and technology, renowned for excellent education, cutting-edge research, and societal impact. Located in Europe, with a global outlook, we are committed to developing solutions for today’s and tomorrow’s global challenges.
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