Two PhD positions in Statistical Genomics​/Computational Genomics

Two PhD positions in Statistical Genomics / Computational Genomics

This is a unique opportunity for two doctoral students to participate in an international collaboration between two research institutes in Switzerland and Belgium. The Animal Genomics group at the
Institute of Agricultural Sciences at ETH Zurich and the Quantitative Genetics & Genomics group of Dr. Tom Druet from the University of Liège, Belgium, investigate DNA variation in individual animal genomes and at the population scale. Our groups apply stateof the art technologies to sequence the genomes and transcriptomes of farm animals with long and short reads,and apply bioinformatics and statistical genomics approaches tocharacterizetrait-associated sequence variation.

We offer two PhDpositions at the interface of computational and statistical genomics, and bioinformatics.

Pangenomi

X aims to study how structural variants (SV) on the sex chromosomes contribute to genetic variation in complex traits, particularly those related to reproduction and meiosis. To this end, a new cattle pangenome that includes near complete assemblies of the sex chromosomes will be generated and statistical methods will be developed to transfer information from the pangenome variation panel to large mapping populations through imputation so that association testing between complex traits and SVs will eventually be possible.

Pangenomi

X will exploit large-scale long and short read sequencing data from two cattle populations to characterize structural variant diversity on the sex chromosomes, and investigate how these types of variants influence male fertility and recombiantion rates.

We are looking for two enthusiastic and highly-motivated candidates to work on the project.

• The first candidate will build pangenomes from
  long read sequencing data collected fromtwo cattle breeds.Existing Pac Bio HiFi sequencing data will be complemented with ultra-long sequencing using ONT to build near complete assemblies for the sex chromosomes. This sub-project will be closely supervised by Prof. Hubert Pausch at ETH Zurich.
• The second candidate will focus on imputation and association testing. Approaches to impute structural variants into large mapping cohorts that had array- or short read sequencing-derived genotypes will be developed. The resulting genotypes will be tested for association with complex traits using methods that allow to account for the multi-allelic nature of the SVs. This sub-project will be closely supervised by Dr.
  
  Tom Druet at the University of Liége.

Close collaboration of both doctoral students is expected. Research exchanges between both groups are anticipated.

Prior experience with genomic data analysis on a high-performance computing cluster, along with strong communication skills, is desirable.

• 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 withhigh-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.

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,
• 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…