PhD position in Gene Regulation and Stem-Cell Research

Updated: 8 months ago
Deadline: 16 Oct 2019

We are recruiting a student for doctoral education. A doctoral education (PhD) consists of supervised research, combined with courses and other educational activities. An individual study plan is established for each doctoral student. For a doctoral degree, the equivalent of four years of full-time doctoral education is required. For more information regarding PhD education at Karolinska Institutet, see:

Research group
The research group of Björn Reinius ( is part of the Division of Biomaterials ( ) at the Department for Medical Biochemistry and Biophysics ( The Division of Biomaterials is located at the newly built Biomedicum research laboratory ( at the Solna campus of Karolinska Institutet, Stockholm, Sweden. The group uses a multi-disciplinary approach integrating methods development for RNA/DNA sequencing (particularly aimed at the single-cell resolution), bioinformatics, molecular cell biology, cell-culture and animal models, to characterize and understand the mechanisms of gene regulation in mammals. A special focus of the lab is X-chromosome inactivation, and more recently also X-chromosome hyperactivation (Nature Structural and Molecular Biology 2019, see lab homepage). During the last years, Reinius and colleagues pioneered the use of single-cell RNA-seq in the context of X-chromosome regulation (Science 2014, Nature Genetics 2016, Cell 2016 etc., see lab homepage). The lab is equipped with all components needed for executing state-of-the-art research in the topic, including cell and animal systems, molecular biology resources and equipment, access to high-throughput sequencing machines, and capacity for computation-intense analyses (a dedicated computational server is available within the lab). The facility, Biomedicum, wherein the lab is located, provides a vibrant international research environment and in-house access to core facilities, lectures by world-leading scientist, and excellent seminar series.

Applications are invited for a position in the Björn Reinius group, funded by the Swedish Research Council and the Ragnar Söderberg Foundation. The appointment will be on a temporary basis for a period of 4 years (PhD student), starting late 2019 / early 2020. If you have any questions, do not hesitate to contact us by email:

Research project
This research project will characterize fundamental features of gene regulation, using the human and mouse X chromosome as model system. The PhD student will investigate the gene-regulatory underpinnings of X-chromosome inactivation, the major epigenetic process by which an entire X-chromosome copy is transcriptionally silenced in female cells to maintain correct X-gene dosage balance. By studying this remarkable gene-silencing process we may elucidate key aspects of both development and gene regulation, particularly important for understanding active versus silenced gene states. We will utilize high-throughput methods (RNA/DNA-sequencing and single-cell RNA-seq) in these analyses. The research is closely related to stem-cell biology, cell reprogramming, and regenerative medicine, and will further provide a molecular understanding of incomplete penetrance and variable expressivity, of X-linked genetic disorders and medical syndromes resulting from sex-chromosome copy number variation. Importantly, the project will offer substantial training in modern biomedical research and will further provide complementary skills - promoting both professional and personal development.

Educational outcome and responsibilities
The successful applicant will acquire basic as well as specialized knowledge and understanding in gene regulation, chromatin states, RNA biology, embryonic development and stem-cell biology. The work implies to apply, master and develop research methodologies in genomics, transcriptomics, next generation sequencing and bioinformatics, in which the group is specialized. Examples of skills that will be cultivated include state-of-the-art molecular biology experimentation (emphasis on high-throughput sequencing and single-cell omics), cell culturing (stem cells in particular), research animal science, and bioinformatics (emphasis on high-throughput RNA/DNA sequencing data analysis).

The PhD student is expected to take a strong lead in project design, management, data generation, as well as analyses and interpretation. The duties also include to working in a team and to adhere to high scientific standards and responsibilities. The ability to work in an interdisciplinary and international environment and to engage in continuous professional development is a must.

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.

    Skills and personal qualities
    We are looking for an enthusiastic and highly motivated candidate who has a degree in Genomics, Bioinformatics, Molecular Biology, Biomedicine, or Biochemistry. Proven experiences in RNA biology, gene regulation, transcriptome-wide studies, mammalian cell or tissue culture techniques, animal science, bioinformatics and programming for statistical computing are particularly advantageous. A strong interest in interdisciplinary experimental method development and creative thinking abilities are essential. Applicants wishing to integrate computational and experimental biology approaches are especially encouraged to apply.

    The ideal candidate should be collaborative, scientifically adventurous, curiosity-driven, and should bring independent and original ideas into the project. Any previous records of independent research as well as productive interactions within a multi-disciplinary team environment (e.g. first- or co-author publications) are advantageous. Since the applicant will work in a multidisciplinary environment the ability to work with other scientist and good communication skills (proficiency in spoken and written English) are necessary. Since some of our experiments are performed on cells and tissues derived from mouse, the applicant must be willing to perform animal research.

    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 personal 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)

    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.

    KI 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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