PhD position in Computational Cancer Biology

Do you want to contribute to improving human health?

To be a doctoral student means to devote oneself to a research project under supervision of experienced researchers and following an individual study plan. For a doctoral degree, the equivalent of four years of full-time doctoral education is required.

The research group

The doctoral student will join the research group of Associate Professor Susanne Schlisio at the Department of Oncology-Pathology, Karolinska Institutet, located in Bioclinicum, Solna. The Schlisio laboratory investigates the molecular and cellular mechanisms underlying tumor initiation, progression, and therapy resistance in sympatho-adrenal cancers, such as neuroblastoma and paraganglioma.

The group applies single-cell and spatial transcriptomics, lineage tracing, and genetically engineered mouse modelsto dissect tumor plasticity, lineage hierarchies, and the developmental origins of cancer. A major goal is to translate fundamental discoveries into new concepts for precision oncology and patient stratification.

The laboratory is supported by prestigious national and international grants, including an ERC Synergy Grant, and is embedded in an active network of collaborations with SciLifeLab and the Swedish Childhood Tumor Biobank. The Department of Oncology-Pathology provides an inspiring and collaborative environment with strong links to translational cancer research and clinical applications at Karolinska University Hospital.

The doctoral student project and the duties of the doctoral student

The doctoral student will work on the project “Targeting malignancy in neuroblastoma and paraganglioma driven by cell plasticity using spatial transcriptomics and machine learning.”

High-risk neuroblastoma (NB) and malignant paraganglioma (PPGL) are neural crest–derived tumors with pronounced heterogeneity and therapy resistance. The project aims to elucidate how tumor cell plasticity and microenvironmental signals drive malignancy, progression, and treatment failure. By combining spatial transcriptomics (Visium HD, Xenium), single-cell RNA sequencing, and computational modeling, the student will map tumor cell states, lineage hierarchies, and differentiation trajectories. Insights from these analyses will guide functional validation using in vitro assays and genetically engineered mouse models to identify signaling pathways that promote differentiation and reduce aggressiveness.

The doctoral student will:

• - Generate and analyze spatial and single-cell transcriptomic data from human NB and PPGL tumors.
• - Integrate developmental reference datasets to reconstruct differentiation trajectories.
• - Apply graph-based and machine-learning tools to model signaling networks driving plasticity.
• - Validate candidate pathways in cell culture and mouse models.
• - Present findings at seminars and conferences and contribute to scientific publications.

The student will receive comprehensive training in computational techniques, participate in doctoral courses at Karolinska Institutet, and engage in international collaborations through the ERC-Synergy funded research network and the Karolinska Neuroblastoma and Paraganglioma Network. The goal is to develop the student into an independent researcher at the forefront of cancer plasticity, single-cell biology, and precision oncology.

What do we offer?

A creative and inspiring environment full of expertise and curiosity. Karolinska Institutet is one of the world's leading medical universities. Our vision is to pursue the development of knowledge about life and to promote a better health for all. At Karolinska Institutet, we conduct successful medical research and hold the largest range of medical education in Sweden. As a doctoral student you are offered an individual research project, a well-educated supervisor, a vast range of elective courses and the opportunity to work in a leading research group. Karolinska Institutet collaborates with prominent universities from all around the world, which ensures opportunities for international exchanges. You will be employed on a doctoral studentship which means that you receive a contractual salary. Employees also have access to our modern gym for free and receive reimbursements for medical care.

Eligibility requirements for doctoral education

In order to participate in the selection for a doctoral position, you must meet the following general (A) and specific (B) eligibility requirements at latest by the application deadline.

It is your responsibility to certify eligibility by following the instructions on the web page Entry requirements (eligibility) for doctoral education.

A) General eligibility requirement

You meet the general eligibility requirement for doctoral/third-cycle/PhD education if you:

1. have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
2. have satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the advanced/second-cycle/master level, or
3. have acquired substantially equivalent knowledge in some other way in Sweden or abroad.*

Follow the instructions on the web page Entry requirements (eligibility) for doctoral education.

*If you claim equivalent knowledge, follow the instructions on the web page Assessing equivalent knowledge for general eligibility for doctoral education.

B) Specific eligibility requirement

You meet the specific eligibility requirement for doctoral/third-cycle/PhD education if you:

- Show proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school.

Follow the instructions on the web page English language requirements for doctoral education.

Verification of your documents Karolinska Institutet checks the authenticity of your documents. Karolinska Institutet reserves the right to revoke admission if supporting documents are discovered to be fraudulent. Submission of false documents is a violation of Swedish law and is considered grounds for legal action.

(A) and (B) can only be certified by the documentation requirement for doctoral education.

Skills and personal qualities

Qualifications: 

• The successful candidate should hold a Master’s degree in bioinformatics, computational biology, computer science, engineering, or a related quantitative field.
• Strong programming skills in R and/or Python are essential, as well as prior experience in data analysis, statistics, or machine learning.
• The project involves large-scale single-cell and spatial transcriptomics data, so familiarity with RNA-seq analysis, data visualization, and computational workflowsis required.
• The candidate should have a strong motivation to apply computational approaches to biological and medical questions and the ability to work independently while collaborating effectively within a multidisciplinary team.

Desirable qualification

• Experience with single-cell or spatial transcriptomics, graph-based modeling, or deep learning will be considered a strong advantage.
• Familiarity with Linux/Unix environments, version control systems (Git), and high-performance computing is desirable.
• Basic knowledge of molecular or cancer biology is beneficial but not mandatory.

Personal qualities

• We seek a curious, analytical, and creative individual who enjoys solving complex data-driven problems.
• The ideal candidate is organized, communicative, and eager to learn new methods, while contributing actively to a collaborative and international research environment focused on cancer plasticity and precision oncology.

Terms and conditions

The doctoral student will be employed on a doctoral studentship maximum 4 years full-time.

Application process

Submit your application and supporting documents through the Varbi recruitment system. Use the button in the top right corner and follow the instructions. We prefer that your application is written in English, but you can also apply in Swedish.

Your application must contain the following documents:

- A personal letter and a curriculum vitae
- Degree projects and previous publications, if any
- Any other documentation showing the desirable skills and personal qualities described above
- Documents certifying your general eligibility (see A above)
- Documents certifying your specific eligibility (see B above)

Selection

A selection will be made among eligible applicants on the basis of the ability to benefit from doctoral education. The qualifications of the applicants will be evaluated on an overall basis.

Karolinska Institutet uses the following bases of assessment:

- Documented subject knowledge of relevance to the area of research
- Analytical skill
- Other documented knowledge or experience that may be relevant to doctoral studies in the subject.

All applicants will be informed when the recruitment is completed.

Apply at the latest  10 December.

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