PhD researcher fungal genomics

We are looking for an enthusiastic PhD researcher within the challenging multi-disciplinary field of fungal multi-omics and metagenomics.

Dit ga je doen

Fungal pathogens within the Candida genus, including C. albicans, C. parapsilosis and C. auris, represent a growing public health concern on a global scale. Resistance to key antifungal drugs, particularly azoles and echinocandins, is on the rise. Increased virulence or resistance is driven by multiple factors including the dual use of antifungals, but our understanding of these drivers is incomplete. The implementation and utility of genomics in Candida epidemiology significantly lags behind its use for bacterial pathogens, and there is little data on the transmission dynamics of these species between clinical and non-clinical (One Health) environments. This PhD project will combine existing genomic data with novel omics and metagenome data from clinical and non-clinical settings. It will also characterise extensive wastewater and environmental samples from the UK and the Netherlands. 

The position is based at the UMC Utrecht where the bioinformatics part of the project will be carried out, and at the Radboud UMC Nijmegen where the laboratory work will take place. The successful candidate will generate sequencing data from existing collections and prospective and environmental sampling. The candidate will apply bioinformatics techniques to establish and expand whole genome sequencing databases, contribute to transmission and co-occurrence analysis and validates and characterises new markers. Furthermore, the candidate will analyse environmental metagenomics data for occurrence of Candida strains. This PhD position is part of the JPI-AMR project Fugaci and a collaboration between the UMC Utrecht, the Radboud UMC Nijmegen and several renowned international partners.

The candidate will carry out sampling and sequencing, will analyze data, will present the research and write open access scientific publications and will collaborate with other researchers within Fugaci.

Hier ga je werken

The position is based in the research group of Dr. Anita Schürch at the Department of Medical Microbiology of the University Medical Center Utrecht (UMCU) and the research group of Dr. Jo Rhodes at Radboud at the UMC Nijmegen and the University of Birmingham. 

The departments of Medical Microbiology are responsible for infectious disease diagnostics (bacteriology, virology, serology, mycology and parasitology), clinical microbiological consultancy, and infection prevention. The departments have an important role in teaching and training of medical doctors, PhD and undergraduate students. The mycology laboratory of the Radboud UMC Medical Microbiology is part of the Center of Expertise in Mycology of Radboud UMC/CWZ hospital. The UMC Utrecht is part of the Taskforce Clinical Mycology Utrecht in collaboration with the Westerdijk Fungal Biodiversity Institute.

The research group of Dr. Anita Schürch develops novel genomic methods for reconstructing and tracking antimicrobial resistance genes by building bioinformatics tools to facilitate data analysis of massive sequence data sets of pathogens and microbiomes. The research group of Dr. Jo Rhodes develops laboratory methods, computational pipelines and surveillance tools for emerging fungal pathogens and researches genomic epidemiology of fungal outbreaks and population genomics of emerging fungal pathogen species.

Dit neem je mee

Required Qualifications:

• Master's degree in Bioinformatics, Epidemiology or a related field.
• Good English language skills (written and spoken).
• Experience in bioinformatics techniques such as large scale sequencing analysis, reproducibility and high performance computing.
• Good communication and presentation skills.
• Ability to work together in teams.

Preferred Qualifications:

• Basic laboratory skills.

Dit bieden we jou

• A salary between €3017 and €3824 gross per month (salary scale OIO), based on full-time employment.
• Salary increase of 3% from July 2025, according to the collective labor agreement (cao). 
• Year-end bonus of 8.3% and holiday allowance of 8%. 
• Pension insurance with ABP. We take care of approximately 70% of the monthly contribution. 
• 100% public transport reimbursement. Are you coming on foot, by bike or by car? You will then receive a reimbursement of € 0.18 per km (by car up to a max. of 40 km one way). 
• Possibilities to develop yourself personally and professionally. 
• The option to select additional employment benefits in exchange for gross salary, such as purchasing a bicycle and memberships.