PhD student in Data Driven Research on Microbial Interactions


Application deadline

June 5, 2022

PhD student in Data Driven Research on Microbial Interactions

Interactions between microbes are fundamental to how ecosystems function and have direct implications for human health via the microbiomes hosted by our bodies. The Bengtsson-Palme lab is using data driven approaches to understand and modulate these interactions between microbes. We are looking for an aspiring student with a background in bioinformatics, computational biology or programming, with an interest in solving biological problems, to join us for a four-year PhD project.

Information about the  project

This project aims to uncover interactions between bacteria in microbiomes that are important for community stability and resilience to colonization by pathogens. In addition, the project seeks to unearth which environmental and genetic factors that are important determinants of bacterial invasiveness and community stability. The PhD project revolves around using large-scale data-driven approaches (including machine learning and metagenomic sequence analysis), combined with high-throughput molecular methods and established theories developed for macro-organism ecology to decipher the mechanisms behind interactions in microbial communities.

The project is financed by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS), and the student will participate in a national research school on data-driven life science. While working in the group, the student will interact with other lab members with expertise in microbiology, bioinformatics and large-scale data analysis. Close collaborations exist with partners in Gothenburg and nationally, as well as with international partners. You will join a productive interdisciplinary research environment at Chalmers SysBio. For more information about the Bengtsson-Palme lab and SysBio, please visit these websites: and The details of the departmental research activities may be found here.

Major responsibilities
As a PhD student, your major responsibility will be to pursue your own doctoral studies. You will be expected to analyze and interpret large-scale data from ongoing and future experiments and studies performed by the group and our collaborators. Furthermore, you will perform tasks related to predicting genes responsible for pathogenicity and other interactions from sequencing data, and perform large-scale screening for such genes in microbiomes. You will also increasingly be responsible for experimental planning, sample collection, data handling, writing of publications and communications of results from the project. You will also be expected to participate in the SciLifeLab national research school on data-driven life science. The position generally also includes teaching on Chalmers’ undergraduate level or performing other duties corresponding to 20 per cent of working hours.

To qualify as a PhD student, you must have a master’s level degree corresponding to at least 240 higher education credits in a relevant field, such as bioinformatics, molecular biology, biomedicine, statistics, computational sciences, or similar.

Mandatory qualifications and skills:
– Documented experience of bioinformatic, computational biology or programming work.
– An ability to work independently as well as in teams and take responsibility for progress in the project.
– Fluency in spoken and written English.
– Good scientific writing skills.

Meritorious qualifications and skills:
– Previous work with taxonomic and functional annotation of genome and metagenome data, as well as knowledge of biological databases.
– Experience of working with data analysis in R and programming (for example in a scripting language such as Perl or Python).
– Experience with building web sites and user interfaces.
– Previous experience with wetlab work, such as bacterial culturing, maintaining human cell lines, DNA extraction etc.
– Knowledge of cell biology, microbiology, machine learning, or microbial ecology.

If Swedish is not your native language, Chalmers offers Swedish courses.

Contract terms
Full-time temporary employment. The position is limited to a maximum of four years.

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Chalmers aims to actively improve our gender balance. We work broadly with equality projects, for example the GENIE Initiative on gender equality for excellence. Equality and diversity are substantial foundations in all activities at Chalmers.

Learn more and apply here:

Application deadline: June 5, 2022

For questions, please contact:
Assistant professor Johan Bengtsson-Palme, Systems and Synthetic Biology

Last updated: 2022-05-03

Content Responsible: David Gotthold(