Doctoral (PhD) student position in deep learning modelling of cancer

Do you want to contribute to improving human health?

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

Our lab is advancing precision medicine through deep learning models of cancer cells. The models are trained on high-throughput datasets, including metabolomics, proteomics, and transcriptomics, and constrained to align with the cell’s molecular networks. This allows us to identify systems-level mechanisms in cancer that can be used to uncover new biomarkers, drug targets, and paths to drug resistance. The long-term goal of our lab is to enable computer-aided design of precision medicine. We are situated at the Science for Life Laboratory (SciLifeLab) and this position is part of the Data Driven Life Science program (DDLS). Assistant professor Avlant Nilsson will be the main supervisor for this position, he is a new DDLS-fellow with background from Massachusetts Institute of Technology and Chalmers University of Technology. Professor Rickard Sandberg at the Department of Cell and Molecular Biology will be co-supervisor.

The doctoral student project and the duties of the doctoral student

Precision medicine aims to tailor treatments to individual cancer cases, considering factors like the tissue of origin, mutation profile and the tumor micro-enviroment. However, the complexity of cellular processes hampers our ability to establish causal relations between molecular alterations and disease phenotypes. In this PhD you will address this by developing a deep learning model of cancer.

The PhD position focuses on predicting cell type-specific responses to genetic alterations, identifying transcriptional signatures indicative of treatment sensitivity, and predicting the effects of the cell type composition in the tumor microenvironment. In the dynamic research environment at SciLifeLab, you will have access to top-notch computational infrastructure and mentorship from experienced researchers. This project can have significant implications for precision medicine, and contribute to the advancement of personalized cancer therapies.

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

Necessary Skills:

• Strong programming skills in languages such as Python.
• The ability to work both independently and collaboratively within a team.
• Proficiency in written and spoken English.

Desirable Qualifications:

• Familiar with cancer-, and cell biology.
• Experience analyzing high-throughput biological data.
• Proven ability to conduct research and communicate findings effectively.
• Experience with deep learning models or automatic differentiation.
• Familiarity with version control systems like GitHub.

Our lab values diversity and inclusion, and we are committed to fostering an environment where all individuals feel empowered to contribute their unique perspectives and skills towards our shared goal of advancing precision cancer medicine.

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.

Description of the DDLS program: https://www.scilifelab.se/data-driven, and an interview with Avlant about DDLS:https://www.scilifelab.se/news/new-ddls-fellow-avlant-nilsson

Want to make a difference? Join us and contribute to better health for all