Bioinformatician; focus on single-cell immune transcriptomics & epigenomics

Do you want to contribute to top quality medical research?
We are looking for up to two ambitious bioinformaticians with solid genome-wide bioinformatics/computational biology skills to join our highly accomplished team of immunologists in two European Research Council (ERC)-funded projects (GUT-SEQ and RESIDE).

We offer a stimulating environment in a rapidly moving research frontier. The successful candidate will be part of a cluster of other bioinformaticians working on similar topics.

Your mission
https://ki.se/en/medh/jenny-mjosberg-group and https://ki.se/en/medh/niklas-bjorkstrom-group groups hosting these two positions (one in each group) study development, regulation and function of human innate lymphoid cells (ILCs), including natural killer cells, and how these cells contribute to pathology and normal homeostasis in organs such as lung, gut, liver and uterus. The studies are translational as they involve advanced basic molecular and cellular immunological investigations of precious human tissue samples to discover novel disease mechanisms and therapy targets. The Mjösberg group consists of 2 PhD students and 4 postdocs and is internationally recognized as a leader in the ILC-field through several high impact publications in recent years (Nat Immunol 2016, JACI 2019, Cell Res 2021). The Björkström group consists of 3 PhD students and 4 postdocs and has a strong track-record working on human NK cells in tissues (Sci Immunol 2021, 2020, Sci Trans Med 2021 x2). Both groups work closely together with clinical partners at several Swedish hospitals and laboratory facilities at Science for Life Laboratories (SciLifeLab), Karolinska Institutet and abroad. The bioinformaticians will work in close collaboration with all members of the respective teams to continue the successful line of investigations utilizing single-cell RNA sequencing (scRNA-seq) and ATAC-seq to dissect human ILC biology in health and disease.

The bioinformatician will be a part of the Center for Infectious Medicine (CIM), Karolinska Institutet, which is a nationally leading and internationally competitive center for human translational immunology and infectious diseases research. The center consists of approximately 25 graduate students and 20 postdocs organized around 17 independent research groups. Importantly, the bioinformatician will also be part of a newly formed https://ki.se/cbb at the Karolinska Flemingsberg Campus which aims at creating a cutting-edge world-leading bioinformatic hub. The CBB facilitates access to the bioinformatics community at the campus and offers mentoring and career-development support.

We are seeking up to two PhDs that will work as an integrated bioinformatician in our teams, being involved in several ongoing projects. We already have large sets of high-throughput sequencing data including scRNA-seq (SMARTseq2 and 10X Genomics) and ATAC-seq data as well as multicolor flow cytometry data of human ILCs, which will be analyzed in close collaboration with other team members and other bioinformaticians at SciLifeLab and CBB.

Your profile
The candidate must hold a PhD in the field of computer science/bioinformatics/computational biology. The candidate should have been trained in computer science/bioinformatics/computational biology during her/his bachelor-, master- or PhD degree. The candidate should master (requirement) R and Python (be proficient in Python Data Stack tools such as NymPY, SciPY, Pandas, scikit), and have solid Unix/Linux experience and statistical knowledge. Experience working in version-controlled systems is a merit as well as experience from Matlab/Octave and C. Experience with high-performance computing for analysis is another merit. The candidate should have experience in genome-wide NGS data and in particular in working with scRNAseq from FASTQ to analyzed data, both with 10X, SS2 and other formats. Ability to formalize biological questions into computational models in order to consult and advise on experimental design before data generation is another merit. The candidate should be self-motivated, have good communications skills and a proven ability to interact effectively and work productively in an interdisciplinary team. Fluency in English is a requirement.

What do we offer?
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 better health for all. At Karolinska Institutet, we conduct innovative medical research and provide the largest range of biomedical education in Sweden. Karolinska Institutet is a state university, which entitles employees to several benefits such as extended holiday and a generous occupational pension. Employees also have free access to our modern gym and receive reimbursements for medical care.

Location: Flemingsberg

https://ki.se/en/medh/center-for-infectious-medicine
Read more about the projects you will be working on: https://cordis.europa.eu/project/id/850963or https://cordis.europa.eu/project/id/948692



Application
An employment application must contain the following documents in English or Swedish:

- A complete resumé, including date of the thesis defence, title of the thesis, previous academic positions, academic title, current position, academic distinctions, and committee work
• A complete list of publications
• A summary of current work (no more than one page)
• A personal letter explaining the interest in the position
• Contact details for two referees

Welcome to apply at the latest 2021-06-06.

The application is to be submitted through the Varbi recruitment system.

Want to make a difference? Join us and contribute to better health for all