Postdoctoral researcher microbiome data analysis & infrastructure

About your role

Approximately half of your time will be dedicated to the Center for Microbiome Analyses & Therapeutics (CMAT) and the other half to Georg Zeller’s Microbiome Systems Biology research group. The focus is on performing high-quality microbiome data analyses, developing robust analytical infrastructure, and supporting multiple research projects simultaneously. In this role, you will make a significant contribution to research by providing reliable workflows, analyses, and tools for researchers and collaborators within and beyond the LUMC.

Your main responsibilities include:

• Performing microbiome data analyses for CMAT clients and research projects, including taxonomic and functional profiling, statistical analyses, data visualisation, and reporting.
• Developing, automating, and standardising analytical methods into reliable and well-documented workflows for routine use.
• Designing and maintaining shared analysis infrastructure, including pipelines, HPC environments, data and metadata management systems, and internal R and Python packages.
• Coordinating multiple analysis requests simultaneously, aligning with stakeholders, and monitoring project timelines, quality, and progress.

In addition, you will contribute to collaborative research and software development projects, perform custom bioinformatics analyses, and co-author scientific publications resulting from the projects you support.

About your workplace

Leiden University Medical Center (LUMC) brings together patient care, research, and education. Innovative research is at the heart of the organisation, with the goal of translating fundamental knowledge into applications that contribute to the healthcare of the future.

The Center for Microbiome Analyses & Therapeutics (CMAT) and the Microbiome Systems Biology group are part of the recently established LUCID department. Researchers in microbiology, parasitology, immunology, and infectious diseases work closely together within this department on both fundamental and translational research.

CMAT supports researchers and clinicians with microbiome sequencing and data analysis for projects within and beyond the LUMC. The Microbiome Systems Biology group, led by Georg Zeller, investigates interactions between the microbiome and the human host. The group combines advanced sequencing and imaging technologies with computational analysis, statistics, and machine learning. Research focuses on topics such as the effects of nutrition and medication on the microbiome, the role of microorganisms in disease processes, and opportunities to harness the microbiome for health and therapeutic applications.

About you

Careful analysis motivates you. Delivering reliable and reproducible results is seen as an important contribution to collaborative research. You are comfortable working with researchers, clinicians, industry partners, and bioinformaticians. You quickly understand analytical questions by asking the right questions, identify risks at an early stage, and propose practical solutions. Continuous improvement is a natural part of your approach, with a focus on making processes smarter, more efficient, and more reusable.

In addition, you have:

• A completed PhD in a biomedical or quantitative discipline, such as computational biology, bioinformatics, microbiology with a strong computational component, or a related field.
• Experience with microbiome data analysis (16S and/or shotgun metagenomics), including taxonomic and functional profiling, statistical analyses, and data visualisation.
• Excellent programming skills in R and preferably Python, combined with experience in Unix/Linux environments, HPC systems, Git, and reproducible analysis environments, preferably Nextflow.
• Experience managing multiple projects simultaneously and an interest in developing infrastructure and tools that support a broad research community.

Our offer

Driven by health; that is our mission. This applies not only to our patients but also to our employees. We strive for a safe, inclusive, and equitable working environment in which talent development and connecting leadership are central. To support continuous learning and development, we offer internal training and educational opportunities. In addition, you are entitled to an end-of-year bonus (8.3%), holiday allowance, bicycle scheme, sports budget, home-working allowance, and an excellent commuting reimbursement scheme. As an employee of LUMC, you will also participate in the ABP pension fund. This means that no less than 70% of your pension contribution is paid by LUMC, leaving you with a higher net salary. A pleasant benefit indeed.

See all employment conditions of the LUMC.

What do we represent?

As an academic medical centre, LUMC aims for a workforce that reflects society. We are committed to the highest standards in healthcare, education, and (international) research, recognising that diverse perspectives are essential. Sustainability is also a key priority: we are committed to a healthy future, not only for people but also for the planet. In line with these values, we strive to be a creative and inspiring workplace where everyone feels welcome, safe, and valued. What matters to us is who you are and what you contribute, regardless of your background. Together, we are building a sustainable and inclusive future, both for the people around us and for the world we live in. Together, we are LUMC.

More information

• As a postdoctoral researcher microbiome data analysis & infrastructure, your salary ranges from €3,598 to €5,669 gross per month (scale 10, CAO UMC). These amounts are based on a full-time appointment.
• A salary increase of 3.5% will take effect on 1 July, followed by an additional 3.5% increase on 1 May 2027.
• This position is offered for a period of two years.
• The selection procedure consists of multiple rounds, including an initial online interview followed by a more extensive interview round with members of the Microbiome Systems Biology group and CMAT.
• Acquisition in response to this vacancy is not appreciated.