Postdoctoral Researcher-Human Microbiome Research

Helsinki, (FI)
Monday, 9 December 2019
End of advertisement period
Monday, 30 December 2019
Contract Type
Fixed Term
Full Time

The Faculty of Medicine promotes scientific research of a high standard and is responsible for providing research-based undergraduate and postgraduate education in medicine, dentistry, psychology and logopedics, as well as for the English-language Master’s Programme in Translational Medicine. In addition to its teaching and research activities, the Faculty serves as a significant expert organisation in the healthcare sector and contributes to the discourse on ethics in the field. In terms of research, the Faculty aims for a place among the best medical faculties in the world, while consolidating and strengthening its status as a top-level institution of medical education. Together with the HUS Helsinki University Hospital and the Helsinki Institute of Life Sciences (HiLIFE), the Faculty of Medicine, University of Helsinki, constitutes the Academic Medical Center Helsinki (AMCH). This medical center has been very successful in international comparisons, ranking among the top 10 medical campuses in Europe and among the top 50 globally. Research Programs Unit (RPU) of the Faculty of Medicine, University of Helsinki consolidates demonstrated research excellence, with focused research programs addressing the greatest challenges in human health. Human Microbiome Research Program (HUMI) is focusing on causal links between microbiota alterations and the increased risk or development of disease, mechanisms of host-microbe interactions, and microbiota-targeted therapeutics and diagnostics.

The research group of Adj. Prof. Anne Salonen at HUMI is looking for two Postdoctoral researchers to work on human gut microbiome data processing, analysis and integration. The postdoctoral researchers will work in the following projects:

  1. Academy of Finland funded project Early gut microbiota development: Perinatal determinants and impact on growth and health at four years. This project builds on our recently established Health and Early Life Microbiota (HELMi) birth cohort that investigates the drivers and health consequences of the early microbiota development in thousand Finnish children. The appointment is for 3 years, starting February-March 2020 at the latest.
  2. H2020 funded project on Sustainable Innovation of Microbiome Applications in Food System ( The post-doctoral researcher will work on analysing and modelling the interactions between diet, gut microbiota and intestinal and plasma metabolites and health markers in relation to gut health, type 2 diabetes and colorectal cancer. The appointment is a joint project between the Human Microbiome Research Program and Department of Food and Nutrition in the group of Dr. Anne-Maria Pajari who is the leader of WP5 on Sustainable food and gut microbiomes in the SIMBA project. The appointment is for 1.5 to 2 years with flexible start during spring 2020.

Job description and requirements:

Post-doctoral researcher (1) main tasks:

  • application and development of bioinformatic and statistical tools to study the associations between intestinal bacteria and different early life exposures and health outcomes, taking advantage of extensive longitudinal NGS data (both 16S amplicon sequencing and strain resolved metagenomics) and extensive clinical and other metadata;
  • processing, quality control and analysis of shotgun metagenomics and bacterial whole genome sequencing data;
  • design and implementation of novel analyses and storage of microbial NGS data in the group
  • co-supervision of PhD students for integrative NGS data analysis
  • developing new research ideas and (co)-applying for grants

The ideal applicant will hold a PhD in Bioinformatics, Biostatistics, Computational biology, Ecology, Microbiology or related field. Verifiable experience in computational bioinformatics and/or biostatistics applying machine learning and other modelling techniques to complex biological data, preferably in NGS setting (data assemblage, analysis and annotation) is required. Proficiency in R and Unix/Linus and knowledge on perl, python or other programming language as well as use of cluster computing will be needed in this position.

We would particularly welcome candidates with prior expertise in modelling of microbial community dynamics, analysis of shotgun metagenomic data and associative statistics, and practical knowledge on the available resources for microbiological bioinformatics.

Post-doctoral researcher (2) main tasks:

  • application and development of bioinformatic and statistical tools to study the dependencies between diet, intestinal microbiota, various biomarkers and metabolites analysed from stool and plasma as well as phenotypic analyses. These samples and data collected on randomized dietary interventions and in vitro studies provide unique multi-omic datasets to model the impact of gut microbiota variation and specific bacteria in mediating the dietary effects on host physiology and specific markers of gut and metabolic health.

The candidate must have prior knowledge and experience in the processing and statistical analysis of biological high-throughput data and a PhD degree in Bioinformatics, Biomedicine, Nutrition, Microbiology or related field. Knowledge on human physiology and/or microbiomes is considered as a strength. Apart from the computational skills good communication skills and willingness to work in a multidisciplinary project at two campuses are required.

Both positions require fluent English and ability to work independently, including ability to prioritize and balance competing demands. The posts offer opportunities for personal development in an enthusiastic and international group that has long track record in human microbiota research and great opportunities to connect and network internationally with research groups working on same or related fields. Please see more information on our group and publications at

Salary (level 5) is based on the demands level chart for teaching and research personnel in the salary system of Finnish universities. In addition, a salary component based on personal work performance will be paid. The overall starting salary will be ca. 3300-3600 €/month, depending on the previous relevant research experience of the candidate. Both positions will be filled with a 6 months trial period.

The application should include a motivation letter (max 1 page) stating the position(s) you are applying for, and a complete CV with: - education/previous degrees obtained - prior work/research experience - list of publications - recommendation letters or names and contact information of two references

The above attachments must be submitted as a single pdf file through the University of Helsinki electronic recruitment system by clicking on Apply for job. Internal applicants (i.e., current employees of the University of Helsinki) must submit their applications through the SAP HR portal.

The deadline for applications is 30.12.2019

For further information, please contact: anne.salonen(at)

In case you need technical support with the recruitment system, please contact recruit-ment(at)