PhD student position in Bioinformatics/Evolutionary Microbiology Full-time NEW

PhD Student Position in Bioinformatics/Evolutionary Microbiology

The Department of Medical Biochemistry and Microbiology at Uppsala University provides a broad international environment for research and teaching. Research at IMBIM spans biochemistry, molecular and cell biology, structural biology, tumour biology, comparative genetics, functional genomics, immunology, bacteriology and virology. The research has a basic-science orientation, with strong relevance to mechanisms of health and disease in both animals and humans.

We are looking for a highly motivated PhD student to join the project “A Two-Billion-Year History of Infections: Evolution of Host-Adaptation in Early Gammaproteobacteria”, funded by the Swedish Research Council and led by Lionel Guy. 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 probably 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 billion years ago, and was among the first bacteria to infect eukaryotes.

In this project, the PhD student will gather a solid set of DIG genomes, including isolates belonging to 30 novel species of Legionella, 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 and specifically analyse the evolution of the Legionella genus.

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

Required qualifications

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 a 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.

The degree should be completed, or expected to be completed, before March 2027.

• 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 plan, carry out and complete research projects independently
• Creativity and good teamwork skills

Desirable qualifications

• Experience of building pipelines for high-performance computing (HPC) clusters
• Competence in handling large datasets
• Experience with DNA extraction and sequencing library preparation

The selection is based on the following criteria: completion of the above qualifications, grades in relevant courses, the relevance of those courses to the research programme, and previous experience of work and research in the wider area of the project described above. An overall assessment of the applicant will be made in order to employ the best possible candidate, who can succeed in the doctoral studies and contribute to a positive development of the research programme. Emphasis will be placed on personal qualities, including analytical ability, accuracy, flexibility and collaborative skills.

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 soon as possible or as agreed. Placement: Uppsala.

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

Application: Please submit your application through the Uppsala University application portal, including a CV, a letter describing your research interests and skills, publications or a copy of your Master's thesis or equivalent, and contact details for two referees (telephone number and e-mail address).

Please submit your application by 29 October 2026, UFV-PA 2026/2912.