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.

A doctoral position funded through the Marie Sklodowska-Curie Integrative Training Network ‘Cell2Cell’ (ESR#7. Project: “What makes a successful pathogen: Understanding the impact of cell to cell heterogeneity in chromatin structure on infection and adaptation”) is available in the Bienko Laboratory for Quantitative Biology of the Nucleus (https://bienkocrosettolabs.org).

The overarching goal of this doctoral project is to develop new single-cell methods for studying the three-dimensional (3D) arrangement of chromatin in the cell nucleus and cell-to-cell variability of the 3D genome.

The primary task of the doctoral student will be developing and applying new methodologies for mapping 3D genome architecture, by building on the GPSeq (Girelli et al., Nature Biotechnology 2020) and iFISH (Gelali et al., Nature Communications 2019) methods recently established in the Bienko lab. Therefore, this is to be considered primarily as a wet-lab position.

In addition to carrying on the aforementioned project in the Bienko lab, the doctoral student will take part to various activities organized by the Cell2Cell network and perform one or two short secondments in other network labs.

The research group

The Bienko Laboratory is located at SciLifeLab Stockholm (www.scilifelab.se), an interdisciplinary center for life sciences featuring state-of-the-art facilities and a broad range of groups working at the interface between biology, medicine, and computational sciences.

Our main research interest is in understanding how the nucleus of eukaryotic cells is spatially organized, and how the three-dimensional (3D) architecture of the genome influences gene expression regulation and genome integrity. We are also interested in understanding the role of 3D genome architecture in the context of human disease, with a particular focus on cancer.

Towards these goals, we combine high-end microscopy methods, next-generation sequencing techniques, and advanced computational approaches, to assess chromosomal contacts, chromatin modifications, DNA breaks, chromosomal rearrangements and gene expression levels in cultured cells and patient-derived tissue samples.

The Bienko lab offers a highly dynamic and interdisciplinary environment where senior scientists, postdocs and students from multiple disciplines—ranging from biology, engineering, physics, and computer science—work closely together on a daily basis.

The successful candidate will be immersed in a thriving scientific atmosphere and have the opportunity to join the active SciLifeLab PhD community and interact with peers from four different universities (Karolinska Institutet, Royal Institute of Science and Technology–KTH, Stockholm University, Uppsala University).

The doctoral student project and the duties of the doctoral student

This doctoral project aims at expanding the existing toolkit for mapping genome architecture, with a particular focus on developing single-cell methods and innovative approaches for charting the spatial arrangement of chromatin-bound RNAs and proteins in the nucleus. These methods will then be shared with the other members of the ITN network through which the project is funded. Specifically, the student will pursue three major aims:

Aim 1: Develop new methods for mapping the 3D genome at the single-cell level

Aim 2: Develop new methods for charting the arrangement of RNAs and proteins in the nucleus

Aim 3: Map the 3D genome in various cell and tissue types

This is a method development focused project that will allow the doctoral student to learn a variety of state-of-the-art genomic techniques while fostering her/his own creativity. The Bienko lab has a strong track record of developing molecular tools (Nat Meth 2013a, b; Cell Rep 2014; Nat Commun 2017; Commun Biol 2018; Nat Commun 2019a, b; Nat Biotechnol 2020), thus providing an optimal environment for the student to succeed. By joining the Cell2Cell ITN network, the student will be embedded in a scientifically thriving environment and have access to high-end expertise and knowledge relevant for the project.

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.

Additionally:

  1. The applicants can be of any nationality.
  2. They should be within four years of the diploma granting them access to doctorate studies at the time of recruitment,
  3. The applicant must not have resided for more than 12 months prior to the singing her/his contract in the country of the host institute.

Specific entry requirements

A Master’s Degree in Biomedicine, Biotechnology or equivalent is required. Documented prior hands-on experience in basic molecular biology techniques and sequencing-based techniques is required. A strong interest and attitude towards developing new methods and troubleshooting is also required. We will prioritize candidates who have previously worked hands-on with methods such as RNA-seq/ATAC-seq/ChIP-seq/Hi-C or alike, and/or have contributed to the development of new genomic methods. The candidate should also have basic knowledge on fluorescent microscopy and prior experience with FISH-based methods is a plus. Basic knowledge of programming languages such as Bash, C++, Python, R, Matlab and/or standard bioinformatic tools for the analysis of NGS data is desired, although not indispensable. Candidates who are genuinely willing to pick up basic programming skills and pro-actively interact with computational scientists on a daily basis, while being primarily focused on experimental work, are strongly encouraged to apply.

Furthermore, the candidate should have prior experience from working with infectious agents and have a keen interest in infectious diseases, given that the focus on the network is on the role of genome architecture in regulating host-pathogen interactions.

Skills and personal qualities

We are seeking for enthusiastic candidates who are truly passionate and curious about nature, and have a keen fascination for how the genome is arranged and functions in the cell nucleus. We require candidates to have a strong motivation to work in a highly interdisciplinary and collaborative environment, and willingness to interact with scientists with computational background is mandatory.

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.

Your application should contain the following documents:

- A cover letter and a curriculum vitae (Swedish or English)
- Degree projects and previous publications, if any (Swedish or English)
- Any other documentation showing the desirable skills and personal qualities described above (Swedish or English)
- 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
Reference number 2-2872/2020
Contact
  • Magda Bienko, magda.bienko@scilifelab.se
Union representative
  • Hongyan Xia, SACO, hongyan.xia@ki.se
  • Venus Azhary, OFR, 0707-124 127
Published 24.Jun.2020
Last application date 09.Jul.2020 11:59 PM CET

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