PhD scholarship on functional and evolutionary genomics
Deadline: 15.08.2021
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.
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 Biosciences is organized into two departments: Department of Animal and Aquacultural Sciences and Department of Plant Sciences.
The main objective of the Faculty of Biosciences is to contribute to the development of sustainable agriculture and food production systems through basic and applied research on plants and animals including fish (aquaculture). The faculty houses Centre for Integrative Genetics (CIGENE) and the research center for Research-based Innovation (SFI) - Foods of Norway.
The faculty is responsible for bachelor- and master programmes in Biology, Animal Science and Plant Science, and international master programmes in Genome Science, Agroecology, Plant Science, Aquaculture, Animal Breeding Genetics and Feed Manufacturing Technology. PhD programmes include Animal Science and Aquaculture, and Plant Sciences. There are currently 500 bachelor and master students, and 110 PhD students, enrolled in these programmes. The faculty has approximately 220 permanent and temporary scientific employees, including technicians, and 21 administrative positions.
Information about student life in Norway is available here. NMBU has a special responsibility for research and education that ensures the basis of life for future generations.
Are you interested to explore how the genome shapes diverse traits with the computational analysis?
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, a multidisciplinary genome biology research group. CIGENE has established excellent wet lab facilities for automated high-through put 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.
References:
[1] Lien, et al., https://doi.org/10.1038/nature17164
[2]Bertolotti, et al., https://doi.org/10.1038/s41467-020-18972-x
[3] Saitou and Gokcumen, https://doi.org/10.1007/s00239-019-09911-6
[4] Saitou and Gokcumen, https://doi.org/10.1093/gbe/evz107
Main tasks
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. Planned starting date is October 1st, 2021.
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:
Literature review
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.
Competence
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.
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 491.200,-) 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 about the research group, please visit the website of Dr. Marie Saitou (Principal Investigator).
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 and log in before completing the online application form. Please do NOT send application material by email.
Application deadline: August 15th 2021
Publications should be included electronically within the application deadline. The relevant NMBU Department may require further documentation, e.g. proof of English proficiency. Master’s thesis in English may work.
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.
Applications should include (electronically)
1. A letter of intent includes:
Why are you interested in this particular project?
How can you contribute to the project based on your specific skillsets?
2. Curriculum vitae + publication list
3. Your sample SLURM script which does any genomics-related analysis.
4. One-page A4 report which explains the mechanism/theory/analytical methods etc. of (A) “Polygenic adaptation” or (B) “splicing QTL”. You can include figures and formulas in the report.
5. Your Master’s thesis if it is written in English.
6. Copies of degree certificates and transcripts of academic records (all certified)
