Doctoral (PhD) student position in Systems Mucosal Immunology of Host–Microbiome Interactions in Intestinal Inflammation Full-time

Doctoral (PhD) Student Position in Systems Mucosal Immunology of Host–Microbiome Interactions in Intestinal Inflammation

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 Villablanca lab at Karolinska Institutet is based at the Department of Medicine, Solna, within the Division of Immunology and Allergy, and is housed at the Center for Molecular Medicine (CMM) in Stockholm. Our multidisciplinary research operates at the interface of immunology, systems biology, and human health, with a strong focus on understanding the cellular and molecular mechanisms that regulate intestinal homeostasis and inflammatory bowel disease (IBD). To address these questions, we have established a research program that integrates novel experimental models of IBD (zebrafish and mouse), human clinical cohorts, and advanced molecular and cellular approaches—including immune cell–organoid co-culture systems, single-cell RNA sequencing, and spatial transcriptomics. By combining experimental immunology with systems-level and data-driven analyses, we seek to uncover the mechanisms governing the initiation and resolution of intestinal inflammation, ultimately enabling the development of rational therapeutic strategies to prevent disease onset and promote intestinal repair.

The Doctoral Student Project and the Duties of the Doctoral Student

The PhD project aims to dissect host–microbe interactions in the intestinal mucosa using integrative spatial and single-cell multi-omics approaches. By combining spatial transcriptomics, single-cell RNA sequencing, and complementary omics technologies in human and experimental model systems, the project seeks to uncover how microbial communities shape mucosal immune responses and tissue homeostasis.

The doctoral student will primarily focus on computational and systems-level analyses, including integration of high-dimensional datasets, development of analysis pipelines, inference of cell–cell and host–microbial interaction networks, and identification of spatially resolved molecular programs associated with inflammation and tissue remodeling. The project also offers opportunities to contribute to experimental design and data generation in close collaboration with wet-lab researchers.

As part of the doctoral education, the student is expected to:

• Actively participate in research planning, data analysis, and interpretation
• Develop and implement reproducible bioinformatic workflows
• Present findings at national and international conferences
• Contribute to scientific publications
• Complete required doctoral coursework and engage in relevant advanced training in bioinformatics, systems immunology, and data science

The position offers a highly interdisciplinary training environment at the interface of mucosal immunology, microbiome research, and computational biology.

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

Essential

• Degree in biomedical sciences, microbiology, bioinformatics, or a related field.
• Proficiency in Python and R for analysis of large-scale biological datasets.
• Experienced in microbiome data analysis, including 16S amplicon sequencing and whole metagenome/shotgun profiling.
• Confident working in command-line environments and HPC clusters.
• Practical experience across multiple omics modalities, including bulk RNA-seq, single-cell, and spatial transcriptomics (both sequenced and image-based technologies such as Visium HD and Xenium/ISS).
• Solid understanding of statistical modeling and reproducible workflows.
• Ability to work both independently and collaboratively in an interdisciplinary team

Desirable / Advantageous:

• Background in mucosal immunology, with an understanding of host immune responses and their relevance to microbiome research.
• Proven experience in collaborative, interdisciplinary research, with published contributions reflecting the ability to work across computational and experimental domains.
• Basic experience with version control (Git) and reproducible data pipelines.

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.