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

We are recruiting a student for doctoral education.

For more information regarding doctoral (PhD) education, see: http://www.ki.se/doctoral.

Research group
The research group of Professor Sten Linnarsson is focused on single-cell biology, in particular applying single-cell and single molecule technologies to characterize the cell types and lineages of the mouse nervous system.

The long-term goal of our research is to map the stable cellular states (‘cell types’) that human organs are made of, and to understand the regulatory networks that induce and maintain them. To achieve these goals, we develop novel technologies accurate detection of DNA and RNA in single cells and tissue samples. A combination of molecular biology, large-scale DNA sequencing, microfluidics, microscopy and advance analysis tools are used on a daily basis in the lab.

The doctoral education project and the duties of the student
The goal of the project is to develop an atlas of the cell types that constitute the human central nervous system and automatically define transcriptome-driven regions. The student will have access to single-cell RNA sequencing data that will use to select the cell-type markers that will map on tissue sections using single molecule fluorescence in situ hybridization (smFISH). The student will design the DNA oligo probes, optimize the smFISH conditions for human tissue and develop the transcripts encoding strategy (barcoded and/or additive). Due to the inherent large size of human samples the experiments will be imaging intensive and require the use of highly parallelized computer vision pipelines in order to be able to extract the expression data and the location of each RNA molecules. Modelling and advanced statistical analysis will be used to define multicellular regions and their interaction

Entry requirements for doctoral education at KI
To be eligible for doctoral education, the following requirements have to be met:

General entry requirements
A person meets the general entry requirements for doctoral/third-cycle/PhD education (according to Higher Education Ordinance Chapt 7, section 39) if he/she:

1. has been awarded advanced/second-cycle/master qualification (i.e. master degree) or
2. has satisfied the requirements for courses comprising at least 240 credits of which at least 60 credits were awarded in the second-cycle/master level, or

3. has acquired substantially equivalent knowledge in some other way in Sweden or abroad.

For more information regarding the general entry requirements, please see:
https://ki.se/en/phd/entry-requirements-eligibility-for-doctoral-education

Specific entry requirements
Proficiency in English equivalent to the course English B/English 6 at Swedish upper secondary school. Applicants who meet the general entry requirements (1 or 2 above) from a university in one of the Nordic countries fulfill the English language requirement.

For information on how other applicants can certify their English proficiency (such as through IELTS or TOEFL, previous upper secondary or university level studies), please see:
https://ki.se/en/phd/entry-requirements-eligibility-for-doctoral-education

State here any other formal entry requirements, beside the above, that an applicant must have to be considered for this project.

Skills and personal qualities
Besides the entry requirements stated above a successful applicant needs to have advanced computer skills preferentially in image processing and large data analysis. Python programming knowledge is strongly recommended together with previous experience in high throughput microscopy and oligo pools design.

The ideal candidate should be a positive and creative person with good communication skills, that thrives in a challenging and innovative environment. The student must have a strong ethics of collaboration because will be working tightly with the current group members.

Assessment criteria
A selection will be made among qualified applicants on the basis of the ability to benefit from doctoral education. 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.

The qualifications of the applicants will be evaluated on an overall basis.

Terms and conditions
All doctoral students at KI receive financial support during their doctoral education and employment on a doctoral studentship is the most common sort of support.

Application process
The application must contain the following documents in Swedish or English:

• A personal letter and a curriculum vitae
• Academic degree diplomas, transcripts of records in original language and, if applicable, authorised translations
• Copies of degree projects and any previous publications
• Proof of English proficiency as stated in the specific requirement above

All documents certifying the entry requirements must be scans of originals (scans of copies or certified copies will not be accepted). The scanned documents must be in color and both the front and the back of the documents must be scanned. Please note that there are specific documentation requirements for a number countries, please read the instructions at:

https://ki.se/en/phd/entry-requirements-eligibility-for-doctoral-education

The application and supporting documents are to be submitted through the Varbi recruitment system.