Doctoral (PhD) student position in spatial transcriptomics, bioinformatics, and cancer immunolo[...]

Varbi Recruit; Solna kommun; On-site; SEK 313,784 - 378,705; Full time

Benefits offered by this job

Contractual salary

Elective courses

Access to modern gym

Job summary

A research institution in Solna is seeking a Doctoral student to work on spatial transcriptomics, bioinformatics, and cancer immunology. The candidate will develop analytical tools and study immune cell interactions in breast cancer. Required qualifications include a Master’s degree and proficiency in bioinformatics, Python, and R programming. The position offers a unique opportunity to contribute to innovative medical research while engaging in collaborative projects. Employment is for a maximum of 4 years on a doctoral student salary.

Qualifications

• Research experience in computational biology or spatial transcriptomics techniques.
• Fluency in oral and written English is necessary.
• Documented ability to analyze and present results.

Responsibilities

• Develop tools for multimodal data analysis.
• Collaborate closely with other PhD students and researchers.
• Perform experiments and analyze data.

Skills

Proficiency in bioinformatics

Programming in R

Programming in Python

Experience in spatial transcriptomics analysis

Ability to work with clinical data

Mentoring experience

Education

Master’s degree

Job description

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

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

The Engblom lab provides a research environment under the supervision of Dr. Camilla Engblom and co-supervisor Dr. Joakim Lundeberg in the intersection of spatial transcriptomics, bioinformatics, cancer immunology. The overall aim is to uncover mechanisms of B and T cell–related immune responses in cancer and identify new therapeutic avenues. We interrogate spatial relationships between B and T cell clones and their niches using Spatial VDJ, and map B cell evolution, including class switching and somatic hypermutation, to identify candidate tumor‑regulatory antibody sequences for functional testing.

The doctoral student project and duties

In this PhD project, the student will develop and apply new tools for multimodal data to study spatial immune cell niches in cancer. The objectives are to:

• Develop tools for the 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 and resolve candidate tumor‑associated antigens.

The student will access already collected datasets, receive collaborative supervision, and work in a dynamic spatial biology environment. The work focuses on integrating B and T cell lineages with their transcriptional and metabolic niches in breast cancer, the most common type of cancer. The student is expected to design research questions, perform experiments, analyze data, take courses, write scientific manuscripts, communicate science to peers and the public, and engage critically with the scientific community.

The student will collaborate closely with other PhD students, postdocs, and researchers in the Engblom and Lundeberg labs, actively perform analysis of spatial transcriptomics and immune clone data, and present results to general and specialized audiences.

What we offer

We provide a creative and inspiring environment with expertise and curiosity. You will receive an individual research project, a well‑educated supervisor, a wide range of elective courses, and opportunities for international exchange. You will be employed on a doctoral studentship with a contractual salary, access to a modern gym for free, and reimbursements for medical care.

Eligibility requirements for doctoral education

Applicants must meet the following general (A) and specific (B) eligibility requirements by the application deadline.

A. General eligibility requirement

• 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.

B. Specific eligibility requirement

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

Verification of 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.

Skills and qualifications

We seek a candidate with proficiency and documented research experience in bioinformatics and/or computational biology, spatial transcriptomics analysis, and biology, as well as Python and R programming (critical). Prior experience analyzing high‑resolution spatial VDJ/transcriptomics, long‑read sequencing, single‑cell transcriptomics, protein structure analysis, or sensitive data will be considered a strong merit. The candidate should be able to work with clinical data. A completed master’s degree is considered a merit.

The position requires independent work and extensive collaboration with other experimental groups. Fluency in oral and written English is necessary. Documented ability to analyze and present results orally and in writing is important. Experience in mentoring students (e.g., bachelor level) 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 for maximum 4 years full‑time.