PhD position Bioinformatics

The impact of the gut microbiome on human health has been well-supported by large-scale human cohort studies. Based on the Lifelines cohort (n=167,000), we have generated microbiome data for specific sub-cohorts, such as LifeLines-DEEP (n=1,500) and the Dutch Microbiome Project (n=8,000). Additionally, various omics data have been collected from these individuals who have been followed for over 10 and 15 years. Ongoing metagenomics analysis of follow-up fecal samples further contributes to the comprehensive dataset.

The primary objective of this project is to thoroughly analyze diverse sequencing data, including metagenomics and other types of sequencing, along with omics data, to gain deeper insights into host-microbe interactions in human health. The project encompasses the following key aspects:
- Mining metagenomics data for genetic variant profiling and strain analysis.
- Exploring microbial interactions from an evolutionary and genetic standpoint.
- Investigating the stability or instability of the microbial genetic landscape and identifying underlying factors that shape not only microbial composition but also its genetic structure.
- Integrating the gut microbiome with genetic and environmental factors to enhance disease prediction and patient stratification.

- An MSc degree in bioinformatics, computer science, mathematics, biomedical science, artificial intelligence (or equivalent).
- The candidate should be familiar with programming language and environments (R/linux/Java/Python).
- Experience in sequencing-based data analysis (genomic sequencing, RNA-seq, single cell RNA-seq, metagenomics) and omics integration (such as metabolism) is highly appreciated.
- Experience in machine learning and AI is highly appreciated.
- The candidate must be highly motivated and able to work independently.
- Excellent communication skills in English,both orally and in writing.
- A team player.

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,- (PhD salary scale) 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 Universitair Medische Centra (CAO-UMC). English:

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

Jingyuan Fu, j.fu@umcg.nl