Doctoral (PhD) student position in Cancer Genomics - Hiring in process/Finished, not possible to apply

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

Professor Henrik Grönberg is heading a translational prostate cancer research environment consisting of more than 30 people covering a range of disciplines. Several large studies are currently ongoing where genomic profiling is used to address tumor grading, prognostication at diagnosis and optimizing treatment in the metastatic setting. The research group is responsible for targeted sequencing in several clinical trials, where the tumor profile is used for prospective randomization of patients. To enable such trials, senior researcher Johan Lindberg and his team has established an infrastructure covering everything from sample handling, preparation for sequencing and subsequent bioinformatic data analysis.

The doctoral student project and the duties of the doctoral student

We are looking for a PhD student that will work with cancer genomics data from the ProBio trial (https://www.probiotrial.org). ProBio is a prospective clinical trial investigating if treatment choices based on a biomarker signature can improve outcomes in patients with metastatic castrate resistant prostate cancer. The biomarker signature is identified by performing targeted sequencing of DNA from dying cancer cells enriched from plasma (a liquid biopsy). ProBio is currently running in Sweden and Belgium and will expand to other European countries during 2020. In addition, the student will also explore in another project, if liquid biopsies may be applied to improve prostate cancer screening.

In these projects the PhD student will learn to:

1. Perform qualitative- and quantitative analysis of high-throughput sequencing data.
2. Perform multivariate logistic regression to predict binary outcomes
3. Apply machine learning of high-dimensional data for classification purposes.
4. Perform time-to-event analysis using classical statistical methods.

After these projects the PhD student will be able to perform state of the art analysis of NGS data and apply subsequent machine learning/statistical methods to address clinically relevant research questions.

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.

Skills and personal qualities

Requirements:

1. Experience from working in a Linux/Unix environment.
2. Programming experience in Python and R.

Other qualifying skills:

1. Hands on experience from analyzing high-throughput sequencing data.
2. Experience from coding and implementing high-throughput sequencing pipelines (DNA- and/or RNA-seq).
3. Experience from working with cloud based computing e.g. Amazon AWS Cloud.
4. Experience in development and management of databases.
5. Experience working with virtualization and container technologies e.g. docker.
6. Experience from working in cancer genomics projects.

To be successful in the environment, the candidate has to have the ability to work independently, to cooperate, to be ambitions and to take initiatives.

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)

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