Doctoral (PhD) student position in spatial transcriptomics, bioinformatics, and mucosal 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 Villablanca lab, in the intersection of immunology, mucosal immunology and spatial transcriptomics, with the goal to understand the spatial organization of inflammation and healing in the intestine. The overall aim of the lab is to define the complex dynamics of host-environment interactions required to sustain intestinal homeostasis, how breakdown in these interactions may lead to intestinal inflammatory disorders, and how we can promote mucosal healing to reverse the intestinal damage caused by inflammation. To accomplish these goals, we have built an interdisciplinary research program that combines the generation of novel experimental models of IBD (zebrafish and mouse), traditional molecular and cellular approaches (e.g. ex vivo, immune cell- intestinal organoid co-culture), cutting-edge technologies (scRNA-seq, spatial metabolomics, spatial proteomics, spatial transcriptomics), systems biology, and the use of clinical samples. In addition to the lab’s focus area, our research group has national and international collaborative projects within host-microbe interactions and other spatial technologies such as proteomics and metabolomics in situ.

The doctoral student project and the duties of the doctoral student

The Villablanca lab is an international reference in mucosal and intestinal immunology, using single-cell and spatial technologies to increase the understanding of inflammation and tissue regeneration. The candidate will contribute to cutting-edge research by spatially resolving the mechanisms of mucosal healing in ulcerative colitis and models of inflammation.

The PhD project aims to build comprehensive functional atlases of intestinal healing in UC and experimental colitis by integrating spatial transcriptomics, spatial proteomics and spatial metabolomics in both mouse models and human tissues. Through multi-modal spatial systems immunology, the PhD student will seek to identify key regulators of mucosal regeneration, uncover conserved and divergent healing mechanisms across species, and lay the foundation for future regenerative therapies. The candidate 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 other PhD students, postdocs, and researchers. The applicant is expected to actively perform analysis of spatial transcriptomics and other spatially resolved and single-cell omics, and present results to general and specialized audiences. The doctoral student candidate must have a master in computational biology and be proficient in R.

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 intestinal immunology, spatial transcriptomics, single-cell RNA-seq and bioinformatics (critical knowledge in Python, R and bash). The candidate should have a completed master’s degree in bioinformatics or computational biology. The candidate should have previous experience analyzing single-cell and spatial transcriptomic datasets in the context of ulcerative colitis and inflammatory bowel diseases. The candidate is expected to work with pre-clinical and clinical data, as well as being familiar with murine models of colitis and colorectal cancer. Previous experience with mass spectrometry techniques is considered a merit. We would also like to see that the candidate has experience in conducting reproducible research, especially within establishing computational workflows.

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.

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.

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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.

https://ki.se/en/people/eduardo-villablanca

https://ki.se/en/research/research-areas-centres-and-networks/research-groups/inflammatory-bowel-disease-ibd-research-group-eduardo-villablanca

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