ERC-funded Postdoctoral Researcher in Bioinformatics

Job Details
Institution: Karolinska Institutet
Keyword Names: Academic/Research, Bioinformatics / Data Analysis
Line 1: Karolinska Institutet
City: Huddinge
Country: Sweden

Job Description

ERC-funded Postdoctoral Researcher in Bioinformatics – single-cell immune transcriptomics and epigenomics

Karolinska Institutet, the Department of Medicine, Huddinge

The Center for Infectious Medicine, the Department of Medicine, Huddinge

The Department of Medicine at Huddinge comprises of seven units, three research centers, and a total of around 70 independent research groups. Our ambition is to be a leading department within medical research and education. At the Center for Infectious Medicine (CIM) ( research focuses on studies of the human immune system. The vision is to be a world leading translational research center within immunology.

Description of research group and project

We are looking for an ambitious postdoc with solid genome-wide bioinformatics/computational biology skills to join our highly accomplished team of immunologists in a project (GUT-SEQ) funded by the European Research Council (ERC). We offer a stimulating environment in a rapidly moving research frontier. The postdoc will be part of a cluster of other bioinformaticians working on similar topics. 

The Mjösberg group studies the development, regulation and function of a particular immune cell, innate lymphoid cells (ILCs), in humans, and how these cells contribute to pathology in mucosal organs such as the lung and gut. 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 working closely together with clinical partners at several Swedish hospitals and laboratory facilities at Science for Life Laboratories (SciLifeLab), Karolinska Institutet and abroad. The group is internationally recognized as a leader in the field through several high impact publications in recent years (Nat Immunol 2016, JACI 2018, JACI 2018). In particular, the postdoc will 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 postdoc 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.


We are seeking a PhD that will work as an integrated bioinformatician in our team, 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 bioinformaticians at SciLifeLab. Hence, excellent communication skills and fluency in English is essential. It is encouraged that the postdoc also supervise students and other researchers if necessary.

Entry requirements

The candidate must hold a PhD equivalent to a Swedish doctoral degree in the field of genome-wide 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 fully master R, Phyton, Matlab/Octave, bash and C and have solid Unix/Linux experience and statistical knowledge. The candidate should have experience in working with scRNAseq from FASTQ to analyzed data, both with 10X, SS2 and other formats. The candidate should have a strong publication track-record. The candidate should be self-motivated, have good communications skills and a proven ability to interact effectively and work productively in an interdiciplinary team. Fluency in English is a requirement. Candidates should preferentially have some experience with single cell-based assessment of immunological responses such as flow cytometry. However, this is not a requirement.