Postdoctoral researcher, Computational Microbial Ecology research Group

Updated: 2 months ago
Job Type: FullTime
Deadline: 04 Mar 2024

Computational Microbial Ecology (CME, helsinki.fi/en/researchgroups/computational-microbial-ecolog y) research group led by Associate Professor Tommi Vatanen at the Institute of Biotechnology (Helsinki Institute of Life Science, University of Helsinki) is looking for a postdoctoral researcher with background in neural network models . Our group  develops computational models, machine learning and bioinformatics to understand the dynamics of human microbial communities – predominantly the gut microbiomes – and their implications to human development, health and wellbeing. 

About the position: 

In this role, you will develop and apply deep neural networks and large language models for the analysis of metagenomic data sets (DNA sequencing of microbial communities). Potential applications include but are not limited to 1) gene functional annotation (large language models, graph convolutional networks), 2) modeling and prediction of molecular interactions (e.g. drug-like-molecule and receptor, and bacteriophage-host interactions), and 3) prediction of health outcomes based on medical history and multiomics (metagenomics, metabolomics) data of preterm infants. You will be provided with unique, human cohort data sets (gut metagenomes from healthy and vulnerable infants, participants of fecal microbiota transplant trials). The models will be applicable for understanding microbiome roles in human health and for improving health outcomes. Our laboratory collaborates with world-leading institutions (The Broad Institute of MIT and Harvard, USA; Harvard School of Public Health, USA; The Liggins Institute, Auckland, New Zealand) providing valuable networking and training opportunities within the microbiome research community. 

We are seeking a highly motivated, enthusiastic, and creative individual with good teamwork skills to join our team. The candidate should hold a PhD degree in computer/data science, computational biology, or related fields. Experience in working with biological applications are considered highly beneficial. Good written and verbal communication skills in English are necessary. 

The position is initially limited to 2 years, with a possibility for an extension. A trial period of 6 months will be applied, and the salaries will be based on the University salary scheme for teaching and research personnel composed of both task specific and personal performance components. The monthly gross salary will start from between €3,400 and €4,000 depending on the level of experience of the applicant. 

What we offer 

  • Competitive salary, local infrastructure and a top-level interdisciplinary and international collaboration network 
  • Exceptional computational resources from the Finnish IT Center for Science (CSC) 
  • 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 

Finland is a member of the EU, has high quality free schooling (also in English), generous family benefits and healthcare, and was recently ranked as the best country in the world for expat families and in the world’s top ten most livable cities. Finland and the Helsinki region possess top expertise in sciences in terms of a vibrant talent pool, leading research, strong support services and functioning collaboration networks. For more information about working at the University of Helsinki and living in Finland, please see helsinki.fi/en/university/working-at-the-university.  

The application should consist of a motivation letter stating your research interests (one page, including experience and motivation to work with biological problems and metagenomic data), CV and contact information of at least 2 references in a single pdf file and be submitted through the University of Helsinki electronic recruitment system. The deadline for the applications is 4th March 2024. For further information and questions, please email Tommi Vatanen (tommi.vatanen (a) Helsinki.fi ). The earliest start date is 1 April 2024. 

The Institute of Biotechnology (BI) is a research institute that operates at the highest international level. It includes 40 research groups and 250 researchers. The Institute is situated in the Viikki science park. For more information on the Institute, please visit helsinki.fi/en/hilife-institute-of-biotechnology . BI is part of Helsinki Institute of Life Science (HiLIFE, helsinki.fi/en/hilife-helsinki-institute-life-science ), a research institute established in 2017 supporting high quality life science research across the University campuses and faculties. HiLIFE builds on existing strengths and new recruits and partnerships to create an attractive international environment for researchers to solve grand challenges in health, food, and environment. HiLIFE coordinates research infrastructures in life sciences and provides research-based interdisciplinary training.   

The University of Helsinki, founded in 1640, is one of the world’s leading universities for multidisciplinary research. The university has an international academic community of 40,000 students and staff members. The University of Helsinki offers comprehensive services to its employees, including occupational health care and health insurance, sports facilities, and professional development opportunities. The International Staff Services office assists employees from abroad with their transition to work and life in Finland. Further information at helsinki.fi/en/university/working-at-the-university 



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