Doctoral (PhD) student position in spatial transcriptomics, bioinformatics, and cancer immunology as part of the national DDLS PhD program Full-time NEW

Doctoral (PhD) Student Position in Spatial Transcriptomics, Bioinformatics, and Cancer Immunology

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 DDLS PhD position is available in the Engblom lab, with main supervisor Dr. Camilla Engblom and co-supervisor Dr. Joakim Lundeberg, in the intersection of spatial transcriptomics, bioinformatics, cancer immunology, with the ultimate goal to understand tumor-associated immune responses and harness these for therapy. The overall aim of the Engblom lab is to uncover fundamental mechanisms of B and T cell-related immune responses in cancer to identify new avenues for therapy. To do this, we interrogate the spatial relationships between B and T 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.

The Doctoral Student Project and the Duties of the Doctoral Student

In this PhD project, the student will use and develop new tools for multimodal data to study spatial immune cell niches in cancer. Advances in high-throughput spatial omics technologies measuring various analytes now capture this complexity in remarkable detail, providing groundbreaking insights into how molecular relations shape health and disease in tissues. Yet, analytical tools capable of integrating multi-dimensional spatial data remain limited.

The project objectives are to:

• Develop tools for and perform integration of modalities with varying dynamic range, sparseness and non-linear behavior,
• Establish discovery methods for multicellular immune niches,
• Follow B-cell clonal evolution across the molecular landscape to understand the 'interactome' niche to resolve candidate tumor-associated antigens.

Importantly, the student will access already collected datasets, a synergized and complementary supervision team, and a dynamic cutting-edge spatial biology environment, making them well suited to computationally integrate B and T cell lineages alongside their transcriptional and metabolic niches in breast cancer, the most common type of cancer. The clinical need is significant, and the approach presented here-in represents an avenue for data-driven disease detection and surveillance.

The student is expected to learn to design research questions and hypotheses, 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 the other PhD students, postdocs, and researchers in the Engblom and Lundeberg labs. The applicant is expected to actively perform analysis of spatial transcriptomics and immune clone data, and present results to general and specialized audiences.

The data-driven life science initiative 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 3.3 billion SEK over 12 years from the Knut and Alice Wallenberg (KAW) Foundation. In 2026 the DDLS Research School will be expanded with the recruitment of 25 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!

At the Karolinska Institutet, we are announcing the position as DDLS PhD student in Data-driven precision medicine and diagnostics.

Data-driven precision medicine and diagnostics covers data integration, analysis, visualization, and data interpretation for patient stratification, discovery of biomarkers for disease risks, diagnosis, drug response and monitoring of health. The precision medicine research is expected to make use of existing strong assets in Sweden and abroad, such as molecular data (e.g. omics), imaging, electronic health care records, longitudinal patient and population registries and biobanks.

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:

• have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
• 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
• 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 focused on data-driven life science. We seek a candidate with proficiency and documented research experience particularly in bioinformatics and/or computational biology, spatial transcriptomics analysis, and biology, as well as Python and R programming language (critical). Previous experience analyzing high-resolution spatial VDJ/transcriptomics, long-read sequencing, single-cell transcriptomics, protein structure analysis, and sensitive data will be considered a strong merit. The candidate is expected to work with 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.

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