PhD student in analysing biosynthesis gene clusters in the human gut microbiome

Genetica

Working Environment

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 Depart-ment of Genetics at the University Medical Center Groningen is an energetic, dynamic and interna-tional environment with state-of-the-art laboratory and computing technology.

Job description

This project is focused on analysis of human microbiome data and is integrated into the Dutch con-sortium of understanding the role of Ribosomally synthesised and posttranslationally modified peptides (RiPPs), both in agriculture and in human health. The main focus of the project will include searching for RiPPs and other biosynthetic gene clusters in human microbiome data and linking their presence to the host factors like diet, medication, and other environmental factors. The project will be based in UMC Groningen (UMCG) and will include collaboration with the bioinformatic team of Prof. Marnix Medema (Wageningen University), who has developed methods for the analysis of biosyn-thetic gene clusters (i.e. PMID 34581602). The candidate will work in close collaboration with the members of the Groningen Microbiome Hub. Our team includes >20 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 >11,000 adult subjects and 4500 samples from longitudinal mother-baby cohort 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. The Lifelines cohort and metagenomics data is described in our recent publications:
DOI: 10.1038/s41586-022-04567-7 and DOI: 10.1126/science.aad3369.

PhD student working on this project will be expected to:
- Integrate and analyze the genomic-, metagenomic-, metabolomics- and proteomics datasets.
- Modify and apply the RiPP-search databases and other tools for the analysis of biosynthetic gene clusters. Work with environmental, microbiome, and other ‘omics 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.

Requirements

- An MSc in medical biology (or equivalent), mathematics, bioinformatics or computer 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.

The UMCG has a preventive Hepatitis B policy. The UMCG can provide you with the vaccination, should it be required for your position.
In case of specific professions a ‘Certificate of Good Conduct’ is required.

Conditions of employment

You will get a contract 32-36 hours a week for the duration of the project. Your salary will be a minimum of € 2.901,- gross per month in the first year and a maximum of € 3.677,- 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 Collective Labour Agreement for Medical Centres (CAO-UMC).

For further information and application please contact:
- dr. Alexandra Zhernakova, email: sasha.zhernakova@gmail.com or a.zhernakova@umcg.nl;
- dr. Jingyuan Fu, email: fjingyuan@gmail.com;
- dr. Cyrus Mallon, email: cyrusmallon@gmail.com.

Links: Groningen Microbiome en RUG.

Additional information

For more information about this vacancy you may contact:

dr. Alexandra Zhernakova
sasha.zhernakova@gmail.com dr. Cyrus Mallon
c.a.mallon@umcg.nl

Applying for a job

Solliciteren

Please use the the digital application form at the bottom of this page - only these will be processed. You can apply until 21 April 2024. Within half an hour after sending the digital application form you will receive an email- confirmation with further information.

Digital application form