About the position
The Department of Animal and Aquacultural Sciences, Faculty of Biosciences at the Norwegian University of Life Sciences (NMBU) has a vacant 3-year Ph.D.–position in evolutionary genomics. The candidate will work in the project SalmoSV that is funded by The Research Council of Norway (RCN). The project is seeking to understand the genome evolution and phenotype-affecting variants following a recent whole-genome duplication of Atlantic salmon. The candidate will work closely with another recently hired PhD student. The principal investigator of the SalmoSV project will be the main supervisor of PhD position.
Genomic structural variants including deletions, duplications, inversions, and translocations of genetic sequences, are rich resources for genetic diversity. However, due to their complex nature, which and how structural variants have driven adaptive evolution with functional advantage are yet to be clarified. The goal of this project is to reveal the adaptive evolution and functional effect of structural variants in Atlantic salmon by integrating long-read sequencing and other state-of-the-art omics data sets.
The PhD project will focus on the estimation of the effects of structural variants on various phenotypes bioinformatically and reveal the adaptive evolution of structural variants of farmed salmon under domestication compared to their wild counterparts. The successful candidate will join CIGENE (cigene.no/), a multidisciplinary genome biology research group. CIGENE has established excellent wet lab facilities for automated high-throughput omics analyses and gene-editing technology, as well as the connected with IT specialists to support the transfer, storage, and analysis of omics data, currently administering a computer cluster.
 Lien, et al., doi.org/10.1038/nature17164
Bertolotti, et al., doi.org/10.1038/s41467-020-18972-x
 Saitou and Gokcumen, doi.org/10.1007/s00239-019-09911-6
 Saitou and Gokcumen, doi.org/10.1093/gbe/evz107
The main goal of this project is to reveal the adaptive evolution and functional effect of structural variants in Atlantic salmon. To achieve this goal, the recruited PhD. student will collaborate with the ongoing Atlantic salmon genomics project team (Transpose) and functional genomics project team (SynchroSmolt) at CIGENE.
The main tasks are bioinformatics analyses of nanopore long-read sequencing data and other various omics data sets, working closely together with another PhD student. Specifically, but not limited to:
Estimate the effect of structural variants on phenotypes and gene regulation by statistical genomics approach
Identify the adaptively evolved variants by comparative genomics approach
Publish solid peer-review papers
The successful candidate is expected to enter a plan for the progress of the work towards a PhD degree during the first months of the appointment, with a view to completing a doctorate within the PhD scholarship period. Presentation of findings at international conferences or/and attending international workshops/visiting relevant researchers are highly encouraged and financially supported.
The successful applicant must meet the conditions defined for admission to a PhD programme at NMBU. The applicant must have an academically relevant education corresponding to a five-year Norwegian degree programme, where 120 credits are at master's degree level. The applicant must have a documented strong academic background in genomics and be able to document proficiency in both written and oral English. For more detailed information on the admission criteria please see the PhD Regulations and the relevant PhD programme description. The applicant must document expertise and interest in the research subject.
Required Academic qualifications
Master’s degree in genomics, bioinformatics, evolutionary genetics, or a similar field (120 credits).
Experience with large genome data analysis
Experience with command-line-based operation of the High-Performance Computing (HPC) system
Experience/familiarity with R, Python, and other programming languages
Statistical/population genomics knowledge (For example, PLINK, VCFTools, GCTA)
The following experiences and skills will be emphasized:
Experience with RNA-sequencing, or eQTL, GWAS or similar functional genomics analysis (For example, DeSeq2, Kallisto, STAR)
You need to:
Have good collaborative skills and high motivation. You will closely work with another PhD student.
Work with initiative and creative views.
Have analytical and academic approach to research questions.
Be proficient in English, both written and spoken.
Fish genomics expertise and Norwegian language skill are NOT necessarily required at the time of application.
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