Computational Microbial Ecology (CME) research group at the Research Programs Unit of the Faculty of Medicine is looking for a postdoctoral researcher.

About the position

You will develop a laboratory protocol for purifying high-molecular-weight viral DNA (and/or RNA) from human fecal samples, and sequence these using Oxford Nanopore long-read sequencing. Additionally, you may utilize Oxford Nanopore selective sequencing (real time selection of sequenced molecules) to deplete bacterial DNA. We will train you (if necessary) to bioinformatically analyze these data in collaboration with other researchers in the group. Bioinformatic analysis include, but are not limited to: 1) tracking phage-mediated horizontal gene transfer in bacteria, 2) investigating phage-bacteria interactions and their influence in microbiome population dynamics over time, 3) understanding mother-to-infant bacteriophage transfer and potential phage induction in the infant gut. There are possibilities to extend this work to understand phage roles in fecal microbiome transplants and (gut) microbial ecology in general. The balance between laboratory work, computational training and analysis and manuscript writing can be adjusted according to your preferences.

You will work in a project investigating the initial establishment of the gut phage populations and their functions at birth and in infancy. Specific goals include investigations of mother-to-infant phage transmission and phage roles in modulating the natural history of the gut microbial communities through predation, lateral gene transfer and other functions.

What we offer

• Competitive salary, local infrastructure and a top-level interdisciplinary and international collaboration network
• Training for state-of-the-art microbiome bioinformatics (if needed)
• Possibility to visit collaborators at the Broad Institute, Harvard University, or University of Auckland (according to training needs and candidate preferences)
• Supportive and non-discriminative working environment

University of Helsinki is an equal opportunity employer and offers an attractive and diverse workplace in an inspiring and interdisciplinary research environment with a variety of development opportunities and benefits. The monthly gross salary will start from between €3,300 to €3,700, depending on the level of experience of the applicant. In addition, the University of Helsinki offers comprehensive services to its employees, including occupational health care and opportunities for professional development. Further information at https://www.helsinki.fi/en/university/working-at-the-university

Beneficial skills and experience (we do not expect any individual applicants to have all the listed experience and skills):

• PhD in molecular biology, microbiology, or related field
• Strong publication record, excellent communication skills and demonstrated success in working on complex, novel research problems.
• Motivation to communicate research findings with the broader field through high-quality publications.
• Strong communication skills and willingness to engage with other members of the lab and contribute ideas through team meetings and discussions
• Experience in stool sample processing, viral DNA analysis and/or Oxford Nanopore sequencing
• Basic statistical analysis and bioinformatics skills

Research group

Our integrative microbial ecology (IME) research group investigates complex interactions between human microbial communities and their environment – gut metabolic microenvironment, human immune system, life events and life-style factors. Most of our work is conducted with biological samples from human cohorts and controlled trials. Our core competence is development of state-of-the-art bioinformatics and statistical analysis tools for integrating, interpreting and statistically analyzing complex data sets generated using modern multi’omics analysis techniques. For examples of recent work, see publications here.

Please submit your application as a single pdf file, which includes the following information in English:

• Cover letter (max. 1 page) briefly summarizing your recent work and motivation to obtain this role
• Curriculum vitae (max. 2 pages)
• List of publications
• Names and contact details of two referees

More information: Dr. Tommi Vatanen, tommi.vatanen@helsinki.fi