PhD scholarship on functional and evolutionary genomics
Deadline: 23.05.2021
Norwegian University of Life Sciences
NMBU has a particular responsibility for research and education that secures the basis for the life of future generations. Sustainability is rooted in everything we do and we deliver knowledge for life. NMBU has 1,800 employees of which about 250 phd scholarships and 6,000 students. The university is divided into seven faculties and has campuses in Ås and Oslo. We will be co-located in Ås from 2021.
NMBU believes that a good working environment is characterised by diversity.
We encourage qualified candidates to apply regardless of gender, functional ability, cultural background or whether you have been outside the labour market for a period. If necessary, workplace adaptations will be made for persons with disabilities.
More information about NMBU is available at www.nmbu.no.
About The Faculty of Biosciences
The Faculty of Life Sciences (BIOVIT) aims to help shape the future food- and bio-production of through teaching and research within biology and sustainable production and use of plants, livestock and fish. The faculty has an annual turnover of approx. 250 million kroner.
The faculty is organized into nine research sections: Genome biology, Breeding and Quantitative Genetics, Ruminant Nutrition and Physiology, Ethology and Animal Environment, Nutrition and Physiology, Agroecology, Genetics and Plant Breeding, Plant Protection and Food Crops, Pant Biology and Biotechnology. The faculty has seven large and small research centers and laboratories, including a center for outstanding innovation (CFI) - Foods of Norway.
The faculty is responsible for bachelor's and master's degrees in Aquaculture, Biology, Animal Science and Plant science as well as English-language master's degrees in Agroecology, Plant Sciences, Feed Manufacturing Technology and Genome Sciences. The faculty is responsible for PhD degrees in animal science and plant science. The faculty currently has about 550 bachelor and master students and 90 PhD students. The faculty has about 220 employees and its own faculty administration.
Are you interested in exploring through computational analysis how the genome shapes diverse traits?
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 position is financed with strategic funding from NMBU and will be linked to the RCN-funded project TRANSPOSE and FHF-funded project SynchroSmolt that seek to understand the genome evolution and phenotype-affecting variants following a recent whole-genome duplication of Atlantic salmon.
Genomic structural variants including deletions, duplications, inversions, and translocations of genetic sequences, are rich resources for genetic diversity. In particular, Atlantic salmon genomes show extreme levels of genomic structural variants, likely due to their unique history of recent whole-genome duplication. Structural variants in Atlantic salmon genomes are one of the most promising frontiers in both evolutionary genomics and aquacultural genomics. However, due to their complex nature, which and how structural variants have driven adaptive evolution with functional advantage are yet to be clarified. Long-read sequencing is a cutting-edge technique to identify previously undiscovered structural variants. In our ongoing project, the genomic map of Atlantic salmon with long-read sequences is getting ready for deep investigation.
The goal of this project is to reveal adaptive structural variants and their functional advantages by integrating omics data sets. The Ph.D. project will focus on the estimation of the effects of structural variants on various phenotypes bioinformatically.
The other focus of this Ph.D. project is to reveal the adaptive evolution of structural variants of farmed salmon under domestication compared to their wild counterparts. The candidate will work in close collaboration with other Ph.D. students, postdoctoral researchers, and senior researchers.
The successful candidate will join CIGENE, a multidisciplinary genome biology research group. CIGENE has established excellent wet lab facilities (CIGENE genomics lab) for automated high-throughput omics analyses and gene-editing technology, as well as the connected CIGENE Bioinformatics & Computational Unit with IT specialists to support the transfer, storage and analysis of omics data, currently administering a computer cluster. The unit will make use of both our local computer cluster with 580 CPUs, 4TB RAM and 600TB storage and national computational resources (NOTUR/Sigma2 and NORSTORE).
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 Ph.D. 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 genome data and other various omics data.
Specifically:
Literature review
Estimate the effect of structural variants on various phenotypes using data sets from genome-wide association studies
Estimate the effect of structural variants on gene expression
Compare population-scale genomes of wild and farmed Atlantic salmon and identify variants under artificial selection
Publish solid peer-review papers
The successful candidate is expected to enter a plan for the progress of the work towards a Ph.D. degree during the first months of the appointment, with a view to completing a doctorate within the Ph.D. 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 from previous studies 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
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
The following experiences and skills will be emphasized:
Statistical/population genomics knowledge
Familiarity with RNA-sequencing and eQTL analysis
You need to:
Have good collaborative skills and high motivation
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.
Remuneration and further information
The position is placed in government pay scale position code 1017 PhD. Fellow. PhD. Fellows are normally placed in pay grade 54 (NOK 482.200,-) on the Norwegian Government salary scale upon employment and follow ordinary meriting regulations.
Employment is conducted according to national guidelines for University and Technical College PhD scholars.
For further information, please contact:
Dr. Marie Saitou (Principal Investigator), E-mail: marie.saitou@nmbu.no; phone +47 6723 2646
To apply online for this vacancy, please click on the 'Apply for this job' button above. This will route you to the University's Web Recruitment System, where you will need to register an account (if you have not already) and log in before completing the online application form.
Application deadline: 23 May 2021
Applications should include (electronically) a letter of intent, curriculum vitae, full publication list, copies of degree certificates and transcripts of academic records (all certified), and a list of two persons who may act as references (with phone numbers and e-mail addresses).
Publications should be included electronically within the application deadline. The relevant NMBU Department may require further documentation, e.g. proof of English proficiency.
Printed material which cannot be sent electronically should be sent by surface mail to the Norwegian University of Life Sciences, Faculty of Biosciences, P.O. Box 5003, NO-1432 Ås, within 23 May 2021. Please quote reference number 21/02171.
If it is difficult to judge the applicant’s contribution for publications with multiple authors, a short description of the applicant’s contribution must be included.
