PhD Position in Metagenomics

Uppsala University

Application deadline

October 31, 2022

PhD Position in Metagenomics

Uppsala University is a comprehensive research-intensive university with a strong international standing. Our ultimate goal is to conduct education and research of the highest quality and relevance to make a long-term difference in society. Our most important assets are all the individuals whose curiosity and dedication make Uppsala University one of Sweden’s most exciting workplaces. Uppsala University has over 54,000 students, more than 7,500 employees and a turnover of around SEK 8 billion.

The Department of Medical Biochemistry and Microbiology (IMBIM) at Uppsala University provides a broad international environment for research and teaching. The Department’s research covers three collaborative and partially integrated sections: Cancer, infections and immunity as well as genetics and genomics. More info:

We are looking for a highly motivated person, with an ability to work independently and a strong interest in pursuing a PhD degree in the field of metagenomics with a focus on children and women’s health.

Project description and duties: The research group in epidemiology and infection biology investigates the symbiotic relationship between bacteria and the human host – both how the microbiota is affected by the host and how the host in turn is affected. We focus on women at different stages of life, especially during and after pregnancy. In the project, fecal samples collected during and shortly after delivery will be used to predict somatic and psychological pregnancy complications.

The studies are based on a combination of DNA sequencing, bioinformatic analyses and machine learning. The PhD project will form a transdisciplinary collaboration between microbiome researchers, biostatistics/bioinformatics and clinical experts from different institutions. This position is funded by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS), a 12-year initiative funded by the Knut and Alice Wallenberg (KAW) Foundation. The goal of the program is to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities that will advance life science in Sweden.

Qualifications: The person we’re looking for should have a master’s degree or equivalent (240 ECTS) in bioinformatics, biomedicine, molecular biology or similar, providing basic theoretic knowledge in molecular biology, microbiology and biostatistics. Experience in programming and/or bioinformatic skills, should be demonstrable through previous research projects or open source software development, such as Github or Bitbucket, is required.

The applicant must be fluent in written and spoken English. The candidate is expected to take initiative driving the project, but also collaborate with the other members of the groups, as well as national and international collaborator. Emphasis will be given on personal qualities, including analytical capacity, accuracy, flexibility and collaborative skills.

Additional merits or desired skills: The ideal candidate would be able to master programming in R or python and have experience from Unix. Previous experience with multidimensional datasets, e.g. RNAseq, is desirable.

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/or performing research in the wider area that relates to the project described above, and previous experience of clinical work. 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.

To be employed as a PhD student, the applicant must be accepted in a doctoral programme. Information concerning doctoral education, requirements and rules of admission can be found at Medicine and Pharmacy – Uppsala University (

The length of the study period for full time employment is a maximum of four years. Terms for graduate studies can be found in Högskoleförordningen 5 kap 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 soon as possible or as agreed. Placement: Uppsala

For further details, please contact: Luisa Hugerth,

Last updated: 2022-10-19

Content Responsible: David Gotthold(