Doctoral (PhD) student position in tumor systems biology

at Karolinska Institutet
Published April 10, 2023
Location Stockholm, Sweden
Category Machine Learning  
Job Type Scholarship  


Do you want to contribute to top quality medical research?

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

Jean Hausser lab is located at SciLifeLab and is a part of the Department of Cell and Molecular Biology (CMB) in the Biomedicum building, a new interdisciplinary research center designed to concentrate much of the experimental research conducted at Karolinska Institutet Campus Solna under one roof to promote collaboration. The Biomedicum houses approximately 1,200 researchers and other personnel and allows expensive equipment to be shared and utilised more effectively.

One of the job of the immune cell is to find and destroy pre-cancer cells. When pre-cancer cells manage to escape the vigilance of the immune system, cancer can take place. Cancer escape immunity is using a range of molecular tricks, some of them are targeted by immunotherapy in the clinic with promising results. But immunotherapy only works on some patients: when and why does immunotherapy fail? What can we do about it?

To adress this, we research how, in a given patient, cancer escape anti-tumor immunity by combining experiments, data science & bioinformatics and mathematical theory. We are inviting applications for  the  PhD student position to join us for an interdisciplinary project between our lab and Taku Okazaki’s lab at the Institute of Quantitative Biology at the University of Tokyo (Japan).

The doctoral student project and the duties of the doctoral student

You will investigate the interplay between the transcriptional heterogeneity of tumor cells, their fitness, and the spatial and immune architecture of tumors. To do so, you will analyze single-cell RNAseq and spatial transcriptomics data from patients. You will perform single-cell RNAseq and spatial transcriptomics on mouse tumors. You will use bioinformatics tools and multivariate statistics to interpret the data as well as develop machine-learning approaches. To explain the patterns found in the data, you will develop mathematical theories. Finally, you will use the insights won to design treatments and test them experimentally in vivo.

The project plan involves several short stays of 5-6 months in the lab of Taku Okazaki’s lab at the Institute of Quantitative Biology at the University of Tokyo (Japan) to learn and apply some of the techniques required for the proposed aim.

What do we offer?

Exciting science in a lab ideally positioned for you to learn how to do research at the interface between experimental and computational biology, in an area of direct medical relevance.
SciLifeLab is the Swedish national center for large-scale molecular bioscience, with stimulating
researchers and top facilities in-house.

Taku Okazaki’s lab at the University of Tokyo is at the fore-front in revealing the mechanisms of immune control in diseases ranging from cancer to auto-immunity. Both Tokyo and Stockholm are among the most inspiring and exciting cities in the world

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


- quantative background in multi-variate calculus, linear algebra, differential equations, dynamical systems theory, probability theory at the level of a Masters-level education in computational biology, physics or engineering.

- a good team spirit, self-motivation, an interest in discovering quantitative principles in cancer and immunology.

- R and Python programming, familiarity with the Linux environment.

- an interest in performing experiments in vitro and in vivo.

- good communication skills in English (written and verbal).

- willingness to spend a significant fraction of the PhD time in Tokyo, Japan


- prior experience with multivariate statistics, Bayesian statistics, mathematical modeling, single-cell or spatial gene expression data

- background in cancer biology and immunology, previous experience performing experiments on cells

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)


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.

Want to make a difference? Join us and contribute to better health for all

Type of employment PhD placement Contract type Full time First day of employment According to agreement Salary Monthly salary Number of positions 1 Full-time equivalent 100 City Stockholm County Stockholms län Country Sweden Reference number STÖD 2-1226/2023 Contact
  • Jean Hausser,
Union representative
  • Elisabeth Valenzuela, SEKO, 08-52486353
  • Taher Darreh-Shori, SACO,
  • Magnus Anå, OFR, 08-52486437,
Published 24.Mar.2023 Last application date 14.Apr.2023 11:59 PM CEST