Doctoral (PhD) student position in spatial transcriptomics and cancer immunology

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

A PhD position is available in the Engblom lab, in the intersection of immunology, cancer, and spatial transcriptomics, with the ultimate goal to understand tumor-associated immune responses and harness these for therapy. The overall aim of the lab is to understand fundamental mechanisms of B cell-related immune responses in cancer (and beyond) to identify new avenues for B-cell mediated therapy. To do this, we interrogate the spatial relationships between B cell clones and their immediate niches within tissues using our in-house developed spatial transcriptomics-based technology (Spatial VDJ). Using established and newly developed algorithms, we map B cell evolution within tissues, including class switching and somatic hypermutation, and identify putative candidate tumor-regulatory antibody sequences for functional testing. In addition to the lab’s focus area, our research group has national and international collaborative projects within host-microbe interactions, vaccine research, technological development, and mucosal immunology. 

The doctoral student project and the duties of the doctoral student

The Engblom lab recently developed a new method to study B cells and B cell receptors within their tissue microenvironment using spatial transcriptomics. The candidate will contribute to cutting-edge research in spatially resolving immune responses during tumor progression and anti-cancer therapy.

The PhD projects will be focused on adapting and using the spatial vdj method to pre-clinical studies, analyze B cell clonal dynamics using spatial transcriptomics, and develop new tools to study and analyze these interactions.  

The candidate is expected to learn to develop research questions and hypothesis, design experiments, analyze data, take courses, write scientific manuscripts, communicate science to their peers and the general public, and to critically engage with the scientific community.

The applicant will work in close collaboration with other PhD students, postdocs, and researchers. The applicant is expected to actively perform analysis of spatial transcriptomics and immune clone data, and present results to general and specialized audiences.

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

Our lab has an opening for a highly creative and motivated PhD student. We seek a candidate with proficiency and documented research experience particularly in immunology, spatial transcriptomics, single-cell RNA-seq and bioinformatics, as well as Python and R programming language (critical). Additionally, the candidate should have documented experience in doing “wet lab” experiments generating the data listed above. We would also like to see that the candidate has experience in neural networks. Previous experience analyzing spatial VDJ/transcriptomics, long-read sequencing, and single-cell transcriptomics data will be considered a strong merit.  The candidate is expected to work with pre-clinical and clinical data. A completed master’s degree is considered a merit.

The position will require independent work as well as extensive collaboration with other experimental groups. Fluency in both oral and written English is necessary. Documented ability to analyze and present results orally and written is important. Experience in mentoring students (e.g., on bachelor level or similar) is considered a merit.

The applicant is expected to be highly engaged, independent, curious, and a team player.

Terms and conditions

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

--[Video about Karolinska Institutet, how we all work towards "a better health for all"] -

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.

Location

The position is located within the Department of Medicine, Solna. The department consists of eleven divisions and each division consists of several research groups. The position is located within the research group led by Dr. Camilla Engblom (SciLifeLab Fellow), hosted by Dr. Eduardo Villablanca in the Allergy and Immunology division, and physically located at CMM and SciLifeLab. Our lab aims to foster a creative, diverse, and inclusive work environment with the goal for all lab members to answer ambitious and exciting scientific questions. The lab is located within a vibrant immunology community with expertise in inflammation, infection, allergy and autoimmune diseasesdescribe your research group.

https://www.scilifelab.se/researchers/camilla-engblom/

https://ki.se/personer/camilla-engblom#publications

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