PhD position in Computational Genomics
100%, Zurich, fixed-term
The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich investigates DNA variation in individual genomes and at the population scale. We apply long read sequencing technologies to characterize animal genomes, and apply bioinformatics and statistical genomics approaches to identify trait-associated sequence variation. We offer a PhD position at the interface of computational and statistical genomics, and bioinformatics.
Cattle are an interesting «model organism» to study inherited genetic variation and the molecular-genetic underpinnings of complex traits and dieseases. Whole-genome sequencing and dense phenotyping data are availble for tens of thousands of individuals. These data enable studying the transmission of alleles and powerful association testing to study the genetic architecture of complex traits and diseases.
The project «OPISCOW - Origin, prevalence, and impact of complex structural variation in a large mammalian genome discovered through genome assembly at the population scale» is a 4-years project recently funded by the Swiss National Science Foundation (SNSF). OPISCOW aims at investigating the de novo mutation rate of structural variants in a large cattle pedigree using highly accurate long reads and near complete assemblies.
This project builds upon previous research conducted by the Animal Genomics group that investigated the presence of structural variants in the bovine genome. We have collected large amounts of long read sequencing data (PacBio HiFi) to build genome assemblies and integrate them into pangenomes. This allowed us to investigate the distribution of structural variants in cattle and related species, construct different pangenome graphs, and identify trait-associated structural variants.
Job description
We are looking for an enthusiastic and highly-motivated candidate that takes over responsiblity to investigate long read sequencing data collected from large a large cattle pedigree. HiFi data will be available for 50 trios (mother, father, offspring). The incoming PhD student will be responsible to (a) map these reads against a recently built T2T assembly, and (b) create haplotype resolved assemblies for the offpspring animals. Both the read alignments and assemblies will be investigated to identify variants in the offspring that are 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 workflow management software (e.g., snakemake or nextflow) and 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 with high-performance computing clusters is required
- A MSc degree in genomics, computational biology, bioinformatics, genetics, animal sciences or disciplines related to the PhD position
- Affinity to computational genomics, bioinformatics or statistics is a pre-requisite
- The writing of scientific papers and active participation in international conferences requires good knowledge of English
Workplace
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 the highest-level academic research in the broad field of animal genomics. The team has an excellent track record of publishing in the field’s leading and key multidisciplinary journals. For a list of recent publications, see here.
Specifically, we offer
- integration into a young and dynamic research team with diverse backgrounds
- responsibility to conduct research within a fully funded 4 year project
- high level of support throughout the PhD journey
- flexibility in designing and pursuing own research ideas within the scope of the overall project
- collaboration with national and international partners to develop a scientific network
- participation in international conferences and seminars
- competitive salary conditions according ETH regulations
We value diversity
Curious? So are we.
This is a fixed term position for 4 years with an anticipated start date of October 1st, 2025 (negotiable). Part of the data required to conduct the research have been collected, enabling also an earlier starting date of the project. You will join the Animal Genomics group led by Hubert Pausch.
We look forward to receiving your online application with the following documents:
- Cover/motivation letter that demonstrates your suitability for the offered position and addresses the research questions you would like to develop within the doctoral project at ETH
- Curriculum vitae with complete academic record, copies of Bachelor and Master degrees
- Name and contact information of two references
Evaluation of applications will start June 15th, and continue until a suitable candidate has been identified. Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered.
Questions? Further information about the Animal Genomics group can be found on our website. For further information, please contact Prof. Hubert Pausch at e-mail hubert.pausch@usys.ethz.ch (no applications).
About ETH Zürich
Curious? So are we.
This is a fixed term position for 4 years with an anticipated start date of October 1st, 2025 (negotiable). Part of the data required to conduct the research have been collected, enabling also an earlier starting date of the project. You will join the Animal Genomics group led by Hubert Pausch.
We look forward to receiving your online application with the following documents:
- Cover/motivation letter that demonstrates your suitability for the offered position and addresses the research questions you would like to develop within the doctoral project at ETH
- Curriculum vitae with complete academic record, copies of Bachelor and Master degrees
- Name and contact information of two references
Evaluation of applications will start June 15th, and continue until a suitable candidate has been identified. Please note that we exclusively accept applications submitted through our online application portal. Applications via email or postal services will not be considered.
Questions? Further information about the Animal Genomics group can be found on our website. For further information, please contact Prof. Hubert Pausch at e-mail hubert.pausch@usys.ethz.ch (no applications).