Doctoral (PhD) student position in single-cell analyses of splicing in the brain

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 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. We have developed a unique automated robotic lab for high-capacity full-length scRNA-seq that can provide state-of-the-art splicing information across complex tissues. Using this scalable scRNA-seq technology, we are systematically mapping out how alternative splicing of neurons is established during development, differ across cell types and brain regions, and its association with connectivity.

The doctoral student project and the duties of the doctoral student

This doctoral research project is KID-funded and focuses on decoding how alternative splicing is used to functionally diversify neurons of the mouse and human brain, and how splicing of synaptic proteins influences synaptic connectivity and function. We have ongoing collaboration with Allen Brain Institute and Harvard University to generate a systematic dataset on mouse brain development that will reveal when and how cell-types establish cell-type specific splicing patterns, and to what extent those are maintained to the adult stage.

The successful applicant will be responsible for operating a highly automated molecular biology setup for single-cell genomics, including FACS sorting cells, supervising the robotic infrastructure, sequencing the libraries on in-house sequencing machines, processing of sequencing data, including running the computational tools in the lab for systematic de novo capturing of splicing patterns and mapping to cell types. We are also exploring how deep learning models can aid the deciphering of RNA-binding protein codes that control cell-type specific splicing.

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

You should have knowledge of basic lab techniques such as PCR, basic enzymatic methods for nucleic acid manipulation (e.g. ligation, restriction digestion). The ability to conduct lab work and document results in a precise and neat manner and to discuss and present results comprehensively is required.

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

• RNA related work
• Single-cell library preparation
• Next-generation sequencing
• Animal handling, FACS sorting
• Working with bioinformatics tools in Python, R or Rust or deep learning Pytorch and similar

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.

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