PhD position in Computational genomics

PhD position in Computational genomics

The Animal Genomics group at the Institute of Agricultural Sciences at ETH Zurich investigates DNA variation in individual animal genomes and at the population scale. The group applies state of the art technologies to sequence the genomes 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. 

Cattle are an interesting «model organism» to study 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 powerful association testing to study the genetic architecture of complex traits and diseases. Moreover, the availability of a vast amount of omics data, an accurate functional annotation, and long read sequencing offer great opportunities to scrutinize trait-associated genomic regions. Integrating different types of data will eventually permit identifying causal trait nucleotides.

This project builds upon previous research conducted by the Animal Genomics group that aimed at investigating the genetic architecture of complex traits , and revealing trait-associated sequence variants . Moreover, access to variation-aware references , multi-assembly graphs , and the first bovine pangenome from multiple haplotype-resolved assemblies will also make structural variation amenable to association testing. The Animal Genomics group also has excellent collaborations with national and international academic and industry partners to establish large and informative datsets that permit exciting research at the forefront of animal genomics. 

We are looking for an enthusiastic and highly-motivated candidate to perform genome-wide association studies between sequence variant genotypes and complex traits and diseases in large cohorts of cattle. You will impute sequence variant genotypes for more than 100'000 individuals from various breeds using a sequenced reference panel of several thousand cattle. You will then implement novel statistical methods for association testing that take into account various modes of inheritance. Comprehensive omics and long read sequencing data will be investigated to fine-map trait-associated regions. Eventually, these analyses will identify candidate causal variants that will be subjected to in-depth functional characterization.

This is a fully funded fixed term position for 4 years with an anticipated start date of October 1st, 2022 (negotiable). Most of the data required to conduct the research have already been collected, enabling also an earlier starting date of the project. You will join the Animal Genomics group  led by Hubert Pausch.

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 https://ag.ethz.ch/publications/journal-articles.html

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 own research ideas within the scope of the overall project,
• collaboration with national and international partners,
• competitive salary conditions according ETH regulations .

• 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 genetics, genomics, computational biology, bioinformatics, 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.

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.

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 immediately, 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 www.ag.ethz.ch . For further information, please contact Prof. Hubert Pausch at e-mail [email protected] (no applications).