The gut microbiome affects human health largely via its metabolic capacity. Metagenomics-based sequencing data has identified millions of genes in microbial genomes, however their functional annotation is still very poor. It remains unknown which genes have enzymatic activities, which types of substrates these enzymes would need, and which products they can make. At the UMCG, metagenomics sequence has been generated for over 15,000 individuals, for which detailed phenotypic data and omics data are also available. This project aims to apply computational genomics, chemoinformatic, and computational structural biology approaches to shed light on dark matters of microbial metabolic reactions.

Specifically, the project encompasses the following aspects:
- Mining metagenomics data for metabolic genes and pathways.
- Using and developing cheminformatics, computational biology and structural biology approaches to predict novel microbial metabolites.
- Integrating the gut microbiome and human genome to understand host-microbe co-metabolism of dietary compounds and drugs.

- An MSc degree in bioinformatics, computer science, biochemistry, computational biology, cheminformatics.
- Knowledge in pharmacology, chemistry, metabolism and toxins is advantageous.
- The candidate should be proficient in Python and Linux. Other programming languages (RJava) is advantageous.
- Experience in genomics, cutting-edge methods for protein modelling (e.g. AlphaFold, RoseTTAFold), and chemistry of metabolites is highly appreciated.
- Experience in development and application of machine learning and AI algorithms is highly appreciated.
- Experience in large-scale genomics and metabolism databases is highly appreciated
- The candidate must be highly motivated and can work independently.
- Excellent communication skills in English, orally and writing.
- A team player.

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.

A full-time PhD contract for 4 years and an excellent environment for further development. First, a temporary one-year position will be offered with the option of renewal for another 3 years. Your salary will be a minimum of € 2.901,- gross per month in the first year and a maximum of € 3.677,- (scale PhD) 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). English: CAO University Medical Centra (CAO-UMC).

Genetica

The UMCG is one of the five medical research centers in the Netherlands. The student will work in the Lab of Integrative OMICS in Systems Medicine, led by Prof. Jingyuan Fu. The research group's mission is to develop an innovative bioinformatic and experimental framework to understand host-microbe interactions in human health and disease. We offer an energetic, dynamic, and international working environment, equipped with state-of-the-art laboratory and computing technology. The research team has published several high-impact papers, and selected publications include:
https://www.nature.com/articles/s41586-023-06893-w