PhD in single-cell cancer multiomics or computational biology

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

Join us at the department of Oncology-Pathology, Karolinska Institutet. The research group led by Martin Enge is specialized in methodology-driven analysis of patient data, especially in the field of single-cell multiomics. We are a multidisciplinary group with expertise in both dry- and wet-lab methods. We combine cutting-edge basic science with strong ties to the clinic and aim to directly influence future clinical practice.

The doctoral student project and the duties of the doctoral student

Cell types in healthy tissues only take on a finite number of states, since they are generated following a strict developmental program. Cancer cells, however, carry genetic alterations that may remove such constraints, leading to a fundamental challenge: the potential co-existence of genetically distinct clones, each supporting multiple stable cancer cell states.

To understand the effect of subclonal variation in cancer, we have developed a set of single-cell multiomics methods, such as DNTR-seq for joint WGS/mRNA-seq (see: Zachariadis et al. Mol. Cell 2020, Andrews et al. Nat. Methods 2021, Enge et al. Cell 2017). In this project, we are applying the methods to leukemias and solid tumors with a high level of subclonal genetic heterogeneity to understand the general rules of how gene dosage affects expression, as well as longitudinally during treatment to better understand genetic and epigenetic features of treatment persistence.

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

We are looking for a highly driven scientist, with an interest in pushing the boundaries of single-cell cancer genetics. Our projects are multidisciplinary in nature, and the ideal candidates are comfortable with moving outside their field to understand both molecular biology and computational methods. We rely heavily on collaborations with clinicians, which the successful candidate will be expected to manage. Proficiency in written and spoken English is necessary.

We are primarily looking for candidates with the following profiles:

1. A computational researcher with an interest in cancer genetics. The ideal candidate has a strong foundation in computer science/computational biology. Specific experience in analyzing sequence-level data on single cell level, R/Bioconductor and Python/Tensorflow will be useful but is not a requirement.
   
   
2. An experimental researcher with an interest in methodologically driven cancer research. Strong track record demonstrating proficiency in molecular biology methods is necessary. Specific experience in cancer genetics or single-cell genomics will be useful but is not a requirement.

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.

Apply at the latest 2^nd July.

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