PhD Position in Computational Mass Spectrometry Imaging and Spatial Metabolomics

PhD Position in Computational Mass Spectrometry Imaging and Spatial Metabolomics
Applications are invited for a PhD fellowship/scholarship at the Graduate School of Technical Sciences, Aarhus University, Roskilde Campus, Denmark, within the Environmental Science and Toxicology department. The position is available from February 2027 or as soon as possible thereafter.

Title
PhD Position in Computational Mass Spectrometry Imaging and Spatial Metabolomics

Research area and project description
Spatial metabolomics enables the study of biochemical processes and human–environment interactions at micrometer to cellular resolution (single cell metabolomics). Mass spectrometry imaging (MSI) is increasingly used to investigate how environmental stressors and micropollutants affect biological systems across space and time. However, data processing, image segmentation, multimodal image registration, reproducible computational workflows and biological interpretation remain major challenges.

This project will develop computational methods and open-source tools for processing, analyzing and interpreting MSI and spatial metabolomics data. The methods will be applied to microbial communities, environmental samples and tissues to uncover spatially resolved biotransformation processes and metabolic responses to environmental stressors.

The successful candidate will work at the interface of computational science, biochemistry, microbiology and analytical chemistry. The project will combine computational method development with experimental spatial metabolomics including signal preprocessing, machine learning, spatial statistics, image registration and interactive software development. The PhD student will join an interdisciplinary team of chemists, microbiologists, biologists and computational scientists and contribute to both methodological development and biological applications.

The position includes:

• Developing batch-processing workflows for MSI and metabolomics data, including normalization, quantification and feature alignment.
• Developing spatial segmentation methods, including uncertainty-aware and spatially regularized clustering.
• Collaborating with experimental scientists, mass spectrometrists and biologists to validate methods against experimental and biological datasets. Ensure reliable implementation of automated quality control, testing, documentation and reproducibility reporting.
• Communicating computational results clearly to interdisciplinary and non-computational re-searchers. Processing and analyzing imaging datasets and presenting results at internal and international scientific meetings.
• Publishing methodological and application studies and releasing well-documented open-source software.
• Close supervision and collaboration with dedicated researchers and senior investigators.

Project description
For technical reasons, you must upload a project description. Please simply copy the project description above and upload it as a PDF in the application.

Qualifications and specific competences
We are seeking highly motivated candidates with a strong interest in interdisciplinary research. Applicants should hold a master’s degree (or equivalent) in computer science, bioinformatics/ cheminformatics, AI/ML, data science, chemistry, computational biology, chemometrics, analytical chemistry or a related discipline.

Essential qualifications:

• Solid background in computational chemistry, image processing, omics data analysis and/or mass spectrometry
• Strong interest in spatial metabolomics and its applications

Desirable qualifications:

• Experience with mass spectrometry, microscopy, microbial systems, or analytical chemistry
• Ability to work independently as well as in collaborative, interdisciplinary teams

Place of employment and place of work
The place of employment is Aarhus University, and the place of work is Department of Environmental Science, Roskilde Campus, Frederiksborgvej 399, 4000 Roskilde, Denmark.

Contacts
Applicants seeking further information regarding the PhD position are invited to contact:

• Prasad Phapale, prasad.phapale@envs.au.dk (main supervisor)

For information about application requirements and mandatory attachments, please see our application guide. If answers cannot be found there, please contact:

• admission.gradschool.tech@au.dk

How to apply:
Please follow this link to submit your application.

Application deadline is 30 November 2026 at 23:59 CET.

Preferred starting date is 01 February 2027.

Please note:

• Only documents received prior to the application deadline will be evaluated. Thus, documents sent after deadline will not be considered.
• The programme committee may request further information or invite the applicant to attend an interview.
• Shortlisting will be used, which means that the evaluation committee only will evaluate the most relevant applications.

Aarhus University’s ambition is to be an attractive and inspiring workplace for all and to foster a culture in which each individual has opportunities to thrive, achieve and develop. We view equality and diversity as assets, and we welcome all applicants. All interested candidates are encouraged to apply, regardless of their personal background. Salary and terms of employment are in accordance with applicable collective agreement.