PhD student position in bioinformatics/evolutionary microbiology

Uppsala University, Dept of Medical Biochemistry and Microbiology (IMBIM)

The Department of Medical Biochemistry and Microbiology (IMBIM) at Uppsala University provides a broad international environment for research and teaching. Research at IMBIM) broadly spans the areas of biochemistry, cell and molecular biology, tumour biology, comparative genetics, functional genomics, immunology, bacteriology, and virology. The research is essentially of fundamental nature, but with relevance and application in health and disease in both animals and humans. More info: https://www.imbim.uu.se/research-areas/.

We are looking for a highly motivated PhD student to be involved in the project “A two-billion-years history of infections: evolution of host-adaptation in early Gammaproteobacteria”, funded by the Swedish Research Board. The project is led by Lionel Guy, and the PhD student will be located at the Biomedical Centre, Uppsala, Sweden.

Project description
The ability to feed on other organisms through phagocytosis is a crucial step in the evolution of eukaryotes, a prerequisite for food webs, multicellularity and, arguably, the acquisition of mitochondria. It also paved the way for intracellular parasitism, as some bacteria avoided digestion by their hosts and multiplied in the nutrient-rich cytoplasm.

Here, we focus on the Deep-branching Intracellular Gammaproteobacteria (DIG), a large group of related bacteria (e.g. Legionella and Francisella) with a wide variety of host-adaptation strategies. We hypothesize that the last common ancestor of DIG, appeared during eukaryogenesis, 2 Ga ago, and was among the first bacteria to infect eukaryotes.

In this project, the PhD student will gather a solid set of DIG genomes, reconstruct their evolutionary history, assess their metabolic potential, and identify their host-adaptation genes. They will screen genomes for horizontal gene transfers from early eukaryotes or Asgard archaea.

Through a better understanding of the relationships between the first eukaryotes and their early invaders, the gained results will shed light on eukaryogenesis, particularly the role of phagocytosis.

Duties
The main duties of PhD students are to devote themselves to their research studies, which includes participating in research projects and third cycle courses. The work duties can also include teaching and other departmental duties (not more than 20 % of full time).

Requirements
To meet the entry requirements for doctoral studies, you must

• hold a Master’s (second-cycle) degree in bioinformatics, molecular biology, microbiology, microbial ecology or similar field, or
• have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.
• Documented coding skills in Python or R
• Experience in using and/or developing methods in metagenomics and molecular evolution
• Background understanding of, and interest in, microbial evolution
• Proficiency in spoken and written English
• Ability to conceive, execute, and complete research projects independently
• Creativity and good group-working skills 

Additional qualifications

• Experience in creating pipelines for use with high performance computing clusters
• Competence in large dataset handling 

The requirements listed above need to be met before the employment starts, but not necessarily by the application deadline.

The selection is based on the following criteria: Completion of the above qualifications, grades in relevant courses, suitability of the courses to the research program, previous experience in working, and performing research in the wider area that relates to the project described above. An integrated assessment of the applicant is generated in order to employ the best possible candidate that can succeed in the doctoral studies and contribute to a positive development of the research program. Emphasis will be given on personal qualities, including analytical capacity, accuracy, flexibility and collaborative skills.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University’s rules and guidelines.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %.Starting date as agreed. Placement: Uppsala

For further details, please contact: Lionel Guy, lionel.guy@imbim.uu.se