PhD Position in Microbiome and Exposome Research (Lifelines Cohort)

Job description

We are seeking a highly motivated PhD candidate with a focus on microbiome and multi-omics analysis in large population cohorts Lifelines. This project is part of ExposomeNL consortium, with the particular focus on studying the effect of environment and host factors on microbiome and health. For >8000 Lifelines participants the gut microbiome was profiled in 2017 (DOI: 10.1038/s41586-022-04567-7), and the data for the second timepoint 5 year later is currently being generated. The specific focus will be on effects of environmental stressors (e.g. pollutant chemicals, air pollution, socio-economic and demographic neighbourhood, etc) on human gut microbiome, metabolites, and other omics data. We combine the state-of-art exposome methodology, omics data expertise, and advanced statistical methodology to evaluate the individuals’ exposures to certain exposome parameters and further build a network of exposome-omics interactions.

The candidate will work in close collaboration with the members of the Groningen Microbiome Hub. Our team includes more than 25 researchers working on various aspects of microbiome development and function in adult population cohorts, longitudinal mother-baby cohorts, and patients with various diseases. Metagenomic data in more than 10 thousand adult subjects is already generated and cleaned. Dietary data and extensive environment information is also available. The project is covered by the NWO (Dutch scientific organization) grant.

PhD student working on this project will be expected to:

• Integrate and analyse the genomic-, metagenomic-, metabolomics- and environment datasets.
• Design, develop, implement and maintain new algorithms, applications and infrastructure components.
• Summarize and report key analytical findings in both oral and written form at work meetings, at international scientific conferences and in scientific publications.
• Work in a team.

Working environment

The position will be embedded at the department of Genetics at the University Medical Center Groningen, The Netherlands. The University of Groningen is a top 100 University that has built a reputation for world-class research. You will follow courses and do research in small groups where personal interaction with your supervisor is an important part of your education. As a result, our students design their research and their program to meet their own personal interests.

We have an enthusiastic team and a strong bioinformatics group. Our microbiome studies were recently published in leading journals such as Science, Nature Genetics, Cell, and Gut. The Department of Genetics at the University Medical Center Groningen is an energetic, dynamic and international environment with state-of-the-art laboratory and computing technology. The key metagenomic papers relevant for this application are:
https://www.nature.com/articles/s41586-022-04567-7
https://www.science.org/doi/10.1126/science.aad3369
https://www.cell.com/cell/fulltext/S0092-8674(21)00352-4
https://www.nature.com/articles/s41586-023-06893-w

What do we need

• An MSc in medical biology (or equivalent), mathematics, bioinformatics, computer science or environmental science
• The candidate must be highly motivated and have excellent mathematical, statistical and computer science skills
• Experience with advanced statistics, biology or biochemistry
• Excellent oral and written communication skills in English

Bonus experience would be:

• Experience handling large databases
• Knowledge of developing and debugging in Java/Python/R.
• Experience in biochemistry and metabolism

What do we offer

The PhD student position is for a duration of 4 years, with an initial contract of one year followed by an extension, based on performance. The candidate will be provided with a stimulating work environment and opportunities for professional development within the field of infectious disease diagnostics. Your salary will be a minimum of € 3.017,- gross per month in the first year and a maximum of € 3.824,- gross per month (scale PRO) in the final (4th) year, based on a full-time appointment. In addition, the UMCG will offer you 8% holiday pay, and 8.3% end-of-year bonus. The conditions of employment comply with the CAO-UMC.

To apply, kindly utilize the digital application form located at the bottom of this page. Only submissions made through this form will be considered, or until the position is filled. To ensure full consideration, please submit a complete application consisting of a cover letter, curriculum vitae, and the contact details of two professional references.
We are looking forward to your application and the possibility of you joining our team to contribute to this groundbreaking research endeavour.

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