PhD Student in Data-Driven Oncology

PhD Student in Data-Driven Oncology:
Identifying the Weak Spots in Brain Tumor Invasion

The Department of Immunology, Genetics and Pathology at Uppsala University has a broad research profile with strong research groups focused on cancer, autoimmune and genetic diseases. A fundamental idea at the department is to stimulate translational research and thereby closer interactions between medical research and health care. Research is presently conducted in the following areas: medical and clinical genetics, clinical immunology, pathology, neuro biology, neuro-oncology, vascular biology, radiation science and molecular tools. Department activities are also integrated with the units for Oncology, Clinical Genetics, Clinical Immunology, Clinical Pathology, and Hospital Physics at Akademiska sjukhuset, Uppsala. The department has teaching assignments in several education programmes, including Master Programmes, at the Faculty of Medicine, and at the Disciplinary Domain of Science and Technology. The department has a yearly turnover of around SEK 500 million, out of which more than half is made up of external funding. The staff amounts to approximately 345 employees, out of which 100 are PhD-students, and there are in total more than 700 affiliated people. Feel free to read more about the department's activities here: https://www.uu.se/en/department/immunology-genetics-and-pathology

Read more about our benefits and what it is like to work at Uppsala University

The Data-driven Life Science (DDLS) program. Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.7 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

In 2025 the DDLS Research School will be expanded with the recruitment of 19 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic research areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see https://www.scilifelab.se/data-driven/ddls-research-school/

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

Duties

Are you passionate about contributing to breakthrough cancer research and the development of next-generation precision medicine? We are looking for a curious and motivated PhD student to join an interdisciplinary project that combines computational biology, spatial transcriptomics, and tumor modeling to understand how the aggressive brain tumor glioblastoma spreads—and how that process might be blocked through novel interventions.

Glioblastoma is one of the most lethal brain tumors, with few treatment options. This project aims to uncover the genes and molecular mechanisms that drive its invasive behavior, both general and patient-specific. Using cutting-edge spatial techniques and CRISPR-based methods, we build data-driven models that link gene regulation to how tumor cells move through the brain’s microenvironments.

The project focuses on computational modeling of spatial gene expression patterns and is ideally suited for someone with a strong interest in data analysis, programming, and biology. You will be part of a collaborative research team with deep experimental and analytical expertise, with access to advanced tumor models and state-of-the-art technologies.

We use innovative technologies that combine CRISPR perturbations with spatial transcriptomics—enabling precise tracking of how gene changes influence the tumor’s invasion routes through brain tissue. The research is highly data-driven and involves close collaboration between experimentalists and computational scientists.

You will play a central role in developing new analytical tools and models, and contribute to identifying tumor vulnerabilities that may become future therapeutic targets.

What we offer:

• A dynamic and interdisciplinary research team with expertise in cancer biology, statistics, and spatial genomics.
• Supervision by leading scientists:

• Prof. Sven Nelander, expert in systems biology and tumor modeling (Uppsala University; main supervisor)
• Prof. Rebecka Jörnsten, professor in mathematical statistics (University of Gothenburg / Chalmers University of Technology)
• Prof. Mats Nilsson, pioneer in spatial genomics (SciLifeLab & Stockholm University) Integration into the national

• DDLS program (Data-Driven Life Science) with focus on precision medicine.
• Access to top-level infrastructure, a new therapy development initiative for brain diseases (CNSx3), and a strong network spanning academia and industry.

Requirements

The following qualifications are required:

• Solid knowledge in mathematics and statistics, in areas such as linear algebra, probability theory, machine learning, high-dimensional statistics, and optimization.
• Documented experience in working with biological data, especially genomics, or other types of high-dimensional data such as imaging.
• Excellent programming skills in Python, R, Matlab, or another widely used language in data science.
• Strong communication skills, and proficiency in spoken and written English.

We are looking for a candidate with a Master’s degree in bioinformatics, engineering physics, molecular biology, computer science, or a related field. You should have strong programming skills (e.g., in Python or R) and a keen interest in applying data-driven methods and computational modeling to understand complex biological processes.

Experience in statistical modeling, machine learning, or analysis of spatial or high-dimensional biological data is considered an asset—but most importantly, we value curiosity, a willingness to learn, and the ability to work well in a collaborative team environment.

Additional qualifications

Particularly valuable qualifications for this position include:

• Direct experience with single-cell genomics, spatial transcriptomics, or similar fields.
• Documented ability to independently contribute to and complete complex research projects.
• A collaborative mindset and strong motivation to work across disciplines.

Personal suitability will be a key selection criterion.

You can find information about education at postgraduate level, eligibility requirements and admission regulations at https://www.uu.se/en/disciplinary-domain/medicine-and-pharmacy/study/doctoral-studies

Selection of applicants is made by the supervisor in consultation with the department's postgraduate education group. The doctoral education committee in the discipline of medicine-pharmacy accepts the doctoral student. Salary placement takes place according to local guidelines at Uppsala University.

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date as agreed. Placement: Uppsala

For further information about the position, please contact: Prof Sven Nelander, +46 76 1380123, sven.nelander@igp.uu.se

Please submit your application by May 25 2025, UFV-PA 2025/1192.

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