PhD position in genomics and bioinformatics

Institution/Company:
University of Oslo
Location:
Oslo, Oslo, Norway
Job Type:
  • PhD (The fellowship will be for a period of 3 years, or for a period of 4 years, with 25 % compulsory work (e.g. teaching responsibilities at the department) contingent on the qualifications of the candidate and the teaching needs of the department.)
Degree Level Required:
Masters
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PhD position in genomics and bioinformatics

  • The fellowship will be for a period of 3 years, or for a period of 4 years, with 25 % compulsory work (e.g. teaching responsibilities at the department) contingent on the qualifications of the candidate and the teaching needs of the department.
  • Application deadline: February 28, 2021
  • Starting date no later than October 1, 2021.

During migration through confined spaces, the cell and its nucleus is deformed. These changes are “sensed” by the cell to administer a proper cell response, and are critical for e.g. tumour and immune cells to adapt, survive and move through mechanically heterogeneous environments. However, nuclear deformations also cause reorganization of 3D genome structure - with uncharacterized consequences. In this project, the candidate will generate and analyze new high-throughput sequencing/genomics data on 3D genome organization using Hi-C and RNA-seq to investigate changes in cancer cells undergoing nuclear deformations. This is hypothesized to unravel new mechanotransduction pathways linked to 3D genome reorganization in cancer.

The candidate will be supervised within the recently established research group of Associate Professor Jonas Paulsen. Building on bioinformatics software developed in his research group [Nature Protoc. 2018; Nature Genetics 2019], the data will be used to generate predictive computational models of 3D genome deformation and gene expression changes during different types of nuclear deformations. Imaging techniques, including super-resolution imaging, will be used to validate the models.

Responsibilities:

  • Research
  • Teaching (optional)

Qualifications:

We seek a highly motivated and competent candidate, with the following formal qualifications:

  • Master’s degree (or equivalent) in bioinformatics, bioscience, molecular or cell biology, genomics or a related field
  • Foreign completed degree (M.Sc.-level) corresponding to a minimum of four years in the Norwegian educational system
  • Experience with bioinformatics analyses
  • Experience with analysis of genomics data, including data from high-throughput sequencing techniques and/or imaging
  • Hands-on experience in general laboratory work
  • Excellent English written and verbal communication skills

The following qualifications will be considered desirable

  • Experience with high-throughput sequencing and/or imaging techniques
  • Experience with programming (Python, C++, or similar)
  • Experience with UNIX/Linux and Bash/Shell scripting
  • Knowledge of statistical data analysis and/or machine learning, including the use of R
  • Experience with the use of high-performance computing (HPC) systems
  • Experience with mammalian cell culture
  • Candidates without a Master’s degree have until 30 June, 2021 to complete the final exam.