Doctoral Researcher in AI-based modeling of cell-type specific splicing

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.

This Data-Driven Life Science (DDLS) funded doctoral research position is available in the lab of Rickard Sandberg at the institution for Cell and Molecular Biology (CMB). The lab is located in Biomedicum, a top-notch research building with a modern infrastructure and equipment. Rickard’s lab has focused on developing single-cell technologies to study transcriptional regulation and post-transcriptional regulation. The lab performs all aspects of the projects (experimental and computational) and has a strong network of national and international collaborators. Resting on large-scale full-length single-cell RNA-sequencing data generated by the lab (and internationally), the lab is at the forefront of comprehensively identifying cell-type specific splicing patterns. Avlant Nilsson (also CMB) is co-supervisor and brings with him a deep expertise in neuronal network based modelling.

This doctoral research project focuses on decoding the regulatory grammar in the RNA that control cell-type specific alternative splicing. Deep learning models are making great advances in society and science. They hold promise to decode regulatory grammars hidden in genomic DNA sequences, and convolutional and transformer deep neural networks have recently extracted regulatory grammar involved in genome organization, tissue-specific gene expression and general RNA splicing. This research project will be built upon systematic in-house generated cell type splicing patterns, that will be used to train deep learning models to predict cell-type splicing patterns from RNA sequence. The core of the project is to develop deep learning models that from RNA sequence and cell-type context information can predict the splicing patterns of a cell type. To extract meaningful biological insights from the model, in silico mutagenesis screens will be performed to identify RNA elements that are most predictive of cell-type specific splicing. The developed models will be subject to experimental validation through collaborations. Finally, the developed model will be used to interpret mutations and genetic variation that are linked to human genetic disease – to shed light on the splicing consequences at cell-type resolution.

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.

General description of the DDLS program

Data-driven life science (DDLS) uses data, computational methods and artificial intelligence to study biological systems and processes at all levels, from molecular structures and cellular processes to human health and global ecosystems. The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS) aims to recruit and train the next-generation of data-driven life scientists and to create globally leading computational and data science capabilities in Sweden. The program is funded with a total of 3.1 billion SEK (about 290 MUSD) over 12 years from the Knut and Alice Wallenberg (KAW) Foundation.

During 2024 the DDLS Research School will be launched with the recruitment of 20 academic and 7 industrial PhD students. During the course of the DDLS program more than 260 PhD students and 200 postdocs will be part of the Research School. The DDLS program has four strategic areas: cell and molecular biology, evolution and biodiversity, precision medicine and diagnostics, epidemiology and biology of infection. For more information, please see https://www.scilifelab.se/data-driven/ddls-research-school/

The future of life science is data-driven. Will you be part of that change? Then join us in this unique program!

At Karolinska Institutet, we are looking to fill the position as PhD student in Data driven cell and molecular biology.

Data driven cell and molecular biology covers research that fundamentally transforms our knowledge about how cells function by peering into their molecular components in time and space, from single molecules to native tissue environments.

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:

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 .

You should have knowledge of programming, computer science, machine learning and basic understanding of biology. Du should have good skills in planning and documenting your experiments and in discussing and presenting your results.

It is advantageous if the applicant has experience in one or some of the following: 

• Strong experience in programming using Python (or similar languages), and experience with jupyter notebooks
• Strong experience with machine learning, in particular deep neuronal networks and their implementation in Pytorch (or similar modules/packages)
• An documented interest in studying biology. 

The doctoral student will be employed on a doctoral studentship maximum 4 years full-time.

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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)

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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