Doctoral (PhD) student position in 3D Genome Biology

Karolinska Institute Stockholm

Sweden

August 1, 2021

Description

Are you passionate about DNA biology and driven by fundamental

questions?

Do you want to pursue a PhD in the exciting field of 3D Genome Biology

?

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 PhD position is now available in the Bienko Lab (https: // bienkocrosettolabs.org/) at the Karolinska Institutet and Science for Life Laboratory in Stockholm.

As a PhD student, you will gain extensive knowledge on how the genome is spatially organized in the cell nucleus and learn to design, perform, and critically interpret the results of experiments aimed at addressing fundamental open questions in the field.

You will be part of an international, dynamic research environment (https: // www. scilifelab.se/) where you will work alongside scientists from many different fields and backgrounds, which will foster your creativity and help you shape your project in unconventional ways.

Our ultimate mission is to understand how the complex higher-order structure of chromatin in mammalian cells is established during the cell cycle, how it is dynamically reshaped during cell differentiation, and how it is rewired during carcinogenesis.

The doctoral student project and the duties of the doctoral student

Preliminary observations made in our laboratory suggest that the blueprint of the 3D genome of interphase nuclei might be hidden in the complex three- dimensional (3D) structure of mitotic chromosomes.

Your main task will be studying how the 3D genome configuration characteristic of interphase nuclei is re-established at the onset of every G1 cell cycle phase in human cells. Furthermore, you will investigate the dynamics and mechanisms of chromatin condensation during mitosis.

Specifically, throughout the four years of your PhD studies, you will be challenged and guided to pursue three major aims, using a combination of cutting-edge sequencing, microscopy, and advanced computational methods:

Aim 1: Map the radial structure of metaphase chromosomes. Initially, you will get familiar with our recently developed GPSeq method for mapping the radial arrangement of chromatin in interphase nuclei ( Nature Biotechnology 2020) and work to adapt GPSeq to study the spatial arrangement of chromatin in mitotic chromosomes (mGPSeq).

Aim 2: Visualize the structure and placement of metaphase chromosomes. Instructed by results obtained using the mGPSeq method, you will apply super- resolution microscopy techniques to visualize the spatial organization of relevant histone marks, individual genomic regions, and structural proteins on metaphase chromosomes, and trace them as cells enter/exit mitosis.

Aim 3: Model the dynamics of chromatin compaction/decompaction. In the last part of your PhD studies, you will be challenged to learn and apply advanced mathematical and computational approaches for 3D genome modeling (under the supervision of an expert senior scientist). Thanks to the extensive knowledge that you will have accumulated in Aims 1 and 2, you will be in a unique position to build a long-awaited model of how the interphase 3D genome is remodeled into the mitotic one, and vice versa.

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:

  • 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
  • You hold a master's degree in Biology or Biotechnology or equivalent with a strong focus on molecular biology
  • You have basic skills in bioinformatics
  • You are interested in fundamental/basic research, as well as in methods development
  • You are curiosity-driven and have a problem-solving mindset
  • You are driven by challenges and seemingly unsolvable problems
  • You can focus on a problem until you have solved it
  • You like working in the lab and are meticulous
  • You have a collegial spirit and work well with others
  • You don't need to have expertise in bioinformatics, but you are expected to learn to process and (at least partially) analyze the data that you will be generating, under the supervision of senior bioinformaticians in the group.

    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.

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

    all

    Type of employment PhD placement
    Contract type Full time
    First day of employment Upon agreement
    Salary Monthly salary
    Number of positions 1
    Working hours 100
    City Stockholm
    County Stockholms län
    Country Sweden
    Reference number STÖD 2-2957/2021
    Contact
    • Magda Bienko, magda.bienko@scilifelab.se
    Union representative
    • Hongyan Xia, SACO, hongyan.xia@ki.se
    Published 01.Jul.2021
    Last application date 01.Aug.2021 11:59 PM CEST

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