Doctoral student position in Spatial organization of human brain cancer - Hiring in process/Finished, not possible to apply

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 research group of Sten Linnarsson is located at Biomedicum in the Molecular Neurobiology unit, at the Department for Medical Biochemistry and Biophysics, MBB. The Mol Neuro unit is a highly creative and collaborative environment that shares expertise, equipment, and lab space between groups in the unit. The unit has regular seminars where students and post docs present their work and get feed-back from the unit members.

Linnarsson lab currently consists of 16 members and have a weekly group meeting where members present their work and discuss scientific publications. All students have weekly scheduled meetings with their supervisor and collaborators. All members of the group are encouraged to participate in workshops and conferences and interact with scientists within KI as well as internationally.

The doctoral student project and the duties of the doctoral student

The main project is to create a comprehensive atlas of human brain tumours. This includes mapping out the healthy human brain in addition to a large number of various subtypes of benign and malignant tumours across all patient ages, with a particular focus on the immune cells present within tumours. As part of the first aim, we will analyse spatial transcriptomics data of the healthy human basal ganglia, with a focus on the subventricular zone, to establish a baseline of the healthy adult neurogenesis in comparison to tumorous growth. As part of the second aim, we will assess a wide range of human brain tumours based on their spatial organization using spatial transcriptomic methods, and cellular composition using single-cell multiomics. As part of the third aim, we will characterize interactions of tumour cells with cytotoxic immune cells within the same tumour samples.

To achieve these aims, firstly, the student will use state-of-the-art deep learning algorithms to perform analysis of spatial transcriptomics data of the healthy human basal ganglia. For the second aim of the project, the student will collect and prepare (cryopreservation and cryosectioning) a broad range of human brain tumour samples (including e.g., paediatric midline glioma, paediatric hemispheric glioma, glioblastoma, astrocytoma, oligodendroglioma, and meningioma). The student will assess the basic histopathology of the tumour samples using conventional histological staining techniques. The student will assess the spatial organization of each tumour sample using spatial transcriptomic methods. The student will assess the cellular composition of each tumour using single-cell RNA-seq and ATAC-seq. Lastly, the student will use assays (protein-protein interaction in situ assay, functional assays of T cell activity and T cell receptor specificity) to understand tumour-immune interactions within each tumour sample.

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

Candidates must have extensive practical experience with handling, freezing, and cryosectioning of human tissue samples, ideally brain or tumour samples, due to the large number of precious human brain tumour samples to be acquired during this project. Experience with mammalian cell or tissue culturing is advantageous, but not strictly required.

Candidates are expected to have prior practical experience with basic tissue staining methods and immunohistochemistry as well as optimization of tissue staining protocols. Similarly previous experience with brightfield and fluorescence microscopy is required. Prior experience with functional assays of T cell activity, T cell-receptor specificity, or protein-protein interaction in situ assays is advantageous, but not required.

Applicants must have a firm grasp of the Python programming language and its utilisation for handling large datasets, image processing, image registration and machine learning. Prior experience with deep learning and artificial neural networks is highly sought after. Prior experience with analysis of spatial transcriptomics data and single cell multiomics data is advantageous.

The general knowledge of the brain histology, brain tumour biology and histopathology is required. Similarly, general knowledge of spatial transcriptomics, and single cell multiomics analysis methods is expected. Knowledge, understanding and documented practical experience of state-of-the-art deep learning algorithms are required.

As general competences, the student is expected to perform laboratory experiments with minimal supervision, therefore extensive laboratory work experience is required. As parts of the project will be carried out in collaboration with other research groups, it is essential that the student works with utmost diligence and organization regarding sample collection, experimental work, and data presentation. For the same reason, excellent communication skills are essential. Lastly, the student will be expected to show a high degree of engagement, critical and original thinking when planning, optimizing, and performing experiments, as well as when reviewing results with the supervisor and other group members.

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.

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