PhD student position in computational developmental biology and stem cell research

Updated: 1 day ago

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

We are opening a PhD student position in computational developmental biology and stem cell research at Adameyko lab (Karolinska Institutet, Stockholm, Sweden). This position is a part of SciLifeLab & Wallenberg National Program for Data-Driven Life Science (DDLS) and will provide fantastic training opportunities in computational biology. The co-supervisors on this PhD position are Prof. Sten Linnarsson (Karolinska Institutet, Sweden) and Prof. Carolina Wählby (Uppsala University, Sweden). 


The doctoral student project and the duties of the doctoral student

The PhD project will aim at integrating single cell clonal, spatial and dissociated cell transcriptomics data for 3D neurodevelopmental reconstruction using a machine learning approach and beyond. Combo of single cell and spatial transcriptomics adds a critical layer of information by mapping gene expression patterns to specific locations within the nervous tissue, revealing how cells interact within their microenvironment. Single cell clonal data tracks the lineage relationships between cells, providing insight into the clonal evolution of neural cells during development and regeneration. This clonal data is crucial for identifying progenitor cells and understanding their role in generating the diverse cell types. The integration of these diverse types of datasets allows for a more comprehensive reconstruction of neurodevelopmental processes, combining insights into what is happening in individual cells (gene expression), where it is happening (spatial context), and how it happened (lineage and clonal history). Also, the combination of these dataset types (cell state, cell place and cell genealogy) is particularly powerful in modeling neurodevelopmental disorders and neurodegenerative diseases, because it enables clonal phenotyping and multiplexing of multiple CRISPR-based perturbation experiments in embryos and human brain organoids. At the level of entry, we expect a good command of Python and R, and also understanding of biology (genomics/transcriptomics). 


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.


DDLS

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!


Subject description

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.


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:

  • have been awarded a second-cycle/advanced/master qualification (i.e. master degree), or
  • 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
  • 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

    We expect the applicants to be fluent in R or Python (or preferably both), and to have some experience in solving computational biology tasks in genomics/transcriptomics or image analysis. A machine learning experience is a plus. At the same time, the applicant shall have a general command of basic university biology, understanding genomic regulation of gene expression during tissue and organ development. 


    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. For more information, please visit: 


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