PhD Candidate - Spatial multi-omics and single cell analysis of human diseases

Maastricht University; Maastricht; On-site; EUR 36,000 - 45,000; Full time

Job summary

Maastricht University invites applications for a PhD Candidate role in Spatial multi-omics and single-cell analysis of human diseases. Based at the M4i Institute, the project combines MALDI-MSI, spatial transcriptomics and advanced computational analyses to map disease biology.

You will join a multidisciplinary team and collaborate across national and international projects, with supervision by Dr. Eva Cuypers.

Qualifications

• Master’s degree in relevant biomedical field.
• Proficiency in English (C1 or higher).
• Hands-on lab experience in molecular analysis.
• Ability to carry out practical research activities including data collection and analysis.
• Clear scientific communication in English.

Responsibilities

• Develop and apply spatial multi-omics and single-cell approaches.
• Integrate datasets from MALDI-MSI, spatial transcriptomics and other modalities.
• Contribute to method development and translational biomedical research.
• Collaborate with a multidisciplinary team and international partners.

Skills

English proficiency

Lab experience

Data analysis

MALDI-MSI

Spatial omics

Education

Master’s degree in Biomedical Sciences, Medicine, (Bio)Chemistry, Analytical Science and Technology, or related

Tools

MALDI-MSI

Laser microdissection

Spatial transcriptomics

Single-cell omics

Job description

Welcome to Maastricht University!

Are you interested in developing and applying cutting-edge spatial multi-omics and single-cell technologies to study human diseases? At the Maastricht MultiModal Molecular Imaging (M4i) Institute, you will contribute to the development of next-generation technologies for biomedical research.

PhD Candidate - Spatial multi-omics and single cell analysis of human diseases

• Our goal: We seek to advance the understanding of human disease by integrating spatial multi-omics and single-cell approaches. Combining molecular information across tissues, cell populations and local microenvironments enables us to uncover disease-driving mechanisms, identify novel biomarkers and support the development of more precise diagnostic and therapeutic strategies.
• Your colleagues: You will join the multidisciplinary research environment of the Maastricht MultiModal Molecular Imaging (M4i) Institute, embedded within the Faculty of Health, Medicine and Life Sciences (FHML) at Maastricht University. You will collaborate with experts in molecular imaging, mass spectrometry, computational biology, pathology and clinical research. You will be supervised by Dr. Eva Cuypers and become part of M4i’s vibrant and internationally recognized research community. The position offers extensive opportunities for method development, translational biomedical research and participation in national and international collaborations.

What you do

You will develop and apply advanced spatial multi-omics and single-cell approaches to investigate the molecular architecture of human diseases. The project focuses on mapping biological processes within complex tissues by integrating complementary technologies that capture molecular information across different spatial and cellular scales.

Using state-of-the-art platforms such as MALDI mass spectrometry imaging (MALDI-MSI), laser microdissection, spatial transcriptomics, single-cell omics, digital pathology and AI-driven data analysis, you will generate and integrate multidimensional datasets from patient-derived samples. In addition, you will contribute to the development of innovative workflows that combine spatially resolved molecular profiling with cellular-level characterization.

By linking tissue-wide molecular patterns to individual cells and their local environments, you will help reveal how cellular interactions and molecular pathways contribute to disease development and progression. The resulting methodologies will be applied across a broad range of biomedical questions, including cancer, inflammatory diseases, metabolic disorders and environmental health research.

This position offers a unique opportunity to gain expertise in spatial biology, mass spectrometry, computational analysis and translational medicine while contributing to next-generation technologies for biomedical research.

Are you ready to set the course for the years ahead? Then we’d love to meet you.

What you bring

We’re not looking for checkboxes; we’re interested in who you are and what you bring. Do you recognize yourself in this?

• A master’s degree in Biomedical Sciences, Medicine, (Bio)Chemistry, Analytical Science and Technology, or a related subject
• Proficiency in English (C1 or higher according to CEFR)
• Hands‑on basic laboratory experience in the molecular analysis of biological systems
• Interest in and ability to carry out practical research activities, including experimental work, data collection and analysis.
• The ability to communicate scientific information clearly and effectively, both orally and in writing in English.

Other experience / skills that would be helpful for the project:

• Imaging technologies (example spatial mass spectrometry, spatial transcriptomics, clinical imaging techniques)
• Mass spectrometry (theoretical and/or practical experience in reading mass spectra and understanding the information they provide about the molecular composition of samples)
• Ion beams and ion optics (knowledge of the principles of ion beams and ion optics, including their role in the generation, manipulation or focusing of ions in analytical instruments)
• Laser based imaging systems (knowledge of or experience with laser-based imaging systems and their application in imaging or analysing biological samples)Data science and data analysis (experience with data processing, statistical analysis and interpretation of research data, as well as familiarity with programming languages such as R or Python)
• Biological sample preparation (experience with the preparation and handling of biological samples for analysis, including the safe handling of human biological materials in accordance with relevant laboratory procedures)

What we offer

At Maastricht University, you’ll work in an international, open, and engaged environment. We offer:

• A 12‑month contract (1.0 FTE) with the prospect of a 3 year extension.
• A gross monthly salary between €3.204 and €4.051 (based on full‑time employment of 38 hours per week).8% holiday allowance and an 8.3% year-end bonus.
• 29 vacation days (based on full‑time), four additional days off (Carnival Monday and Tuesday, Good Friday, and Liberation Day), and the possibility to accrue up to 12 extra days through compensation hours.
• Flexible working hours, a home office allowance, and the option to work from home.
• Freedom and space to shape your work independently and develop your ideas.
• A close‑knit community of colleagues to collaborate and grow with.
• A solid pension plan via ABP, company fitness schemes, and access to various university sports facilities.
• An inspiring work environment in the heart of Europe.

Find out more about the PhD journey at Maastricht University, from starting your research to completing your PhD and beyond.

As a PhD candidate, you will be automatically enrolled in one of our Graduate Schools. Find out more about our Graduate Schools.

About the Faculty of Health, Medicine and Life Sciences (FHML)

FHML is committed to health in the broadest sense: from molecule to human, and from healthcare to prevention. We train healthcare professionals and researchers through innovative educational programmes and conduct groundbreaking research in health and well‑being. As part of Maastricht UMC+ (MUMC+), our international and interdisciplinary community forms a unique collaboration between university and academic hospital, where education, research, and care come together.

About the Maastricht MultiModal Molecular Imaging institute, M4i

M4i is a state‑of‑the‑art international institute at Maastricht University (The Netherlands) that brings together a powerful palette of innovative molecular imaging technologies. Its mission is to develop instrumentation and perform both fundamental, methodological and applied research in molecular imaging as part of a translational, synergistic, interdisciplinary research program that attracts top researchers from across the world. The successful PhD candidate will work at the boundaries of mass spectrometry imaging and omics in the IMS dicision where we develop and apply state‑of‑the‑art molecular imaging approaches for nanomedicine and biomedical research, including diagnostic and prognostic tools for personalized medicine in oncology, neurology and cardiovascular medicine. The institute is part of the Dutch Large Scale scientific Infrastructure and offers a plethora of advanced imaging instrumentation that are made available to regional, national and international researchers.

Interested?

Want to know more about this position or what it’s like to work at our university? Reach out to Dr. Eva Cuypers at [e-mail]. The end date of the publication is 8 November 2026.

The anticipated start date is in January 2027.

About Maastricht University

At Maastricht University, we collaboratively seek solutions to help move the world forward. We do this with 23,300 students and 5,400 employees across 5 regional locations, 6 faculties, and more than 70 research institutes. We encourage you to push boundaries and discover new opportunities for yourself and the world around you. Together, we can find the answers for tomorrow.

The vacancy is open for internal and external candidates. In case of equal qualifications, internal candidates will be prioritized.

At Maastricht University, we prefer to contact potential candidates directly. We therefore kindly ask that no agencies or intermediaries submit offers or approaches.

Maastricht University is committed to promoting and nurturing a diverse and inclusive community. We believe that diversity in our staff and student population contributes to the quality of research and education at UM, and strive to enable this through inclusive policies and innovative projects led by teams of staff and students. We encourage you to apply for this position.