[SocBiN] computational biologist - Karolinska Institute

[Jonathan Coquet]

Dear all,

we are currently recruiting a post-doc (or equivalent) computational biologist to our team to help us to analyse the immune system in more detail.

Please find a link below and a broad description of the lab, project and responsibilities. All application should proceed through the Karolinska Institute portal.

Kind regards, Jonathan



https://ki.mynetworkglobal.com/en/what:job/jobID:88719/where:4/


Research group

Jonathan’s team is interested in lineage commitment and in particular in subset specification of a population of immune cells called T helper cells. T helper cells are central mediators of a range of inflammatory disorders including asthma, multiple sclerosis and inflammatory bowel disease and are known to acquire specialized functions.

The team is interested in 2 aspects of their differentiation; 1) What functions do these cells acquire in different inflammatory diseases and can these functions be extrapolated using unbiased techniques? 2) Identifying novel factors and gene networks that may regulate the acquisition of functions over time, and to test their functions in physiological models of disease.

To tackle these questions, Jonathan’s team is using Single Cell RNA-Sequencing among other array and sequencing based approaches to analyse T helper cells in diseased tissues. The lab’s goal is to more accurately define T helper cell functions in disease states and find novel regulators that may be the target of future therapies.

The Karlsson Hedestam group studies B cell biology, with a focus on understanding the development of antigen-specific B cells in memory compartments. This is studied through the isolation of monoclonal antibodies and next generation sequencing (NGS) analysis of antibody repertoires for longitudinal lineage tracing. The candidate will provide computational support for a recently established pipeline for NGS antibody analysis techniques and other programs being developed by the group. These bioinformatics tools for antibody repertoire analysis can be used for a wide range of pre-clinical and clinical applications, related to infections, cancer and autoimmunity.


Area of responsibilities/work description

The successful applicant will work with a team of biologists to apply existing, or to develop novel, statistical and computational bioinformatics methods for analysis of various -omics data, with particular focus on NGS technologies, including RNA-Seq, and single-cell RNA-Seq. An interest in the application of machine learning approaches is also desirable.

The duties also include:

  *   Consulting researchers on the NGS experimental design
  *   Data QC, data management and archival storage
  *   Analysis of large datasets, preparation of codes, development of new methods/tools for advanced analysis of datasets
  *   Support the ongoing research in the group, help write papers, grants and scientific meeting presentations
  *   Shape, develop and maintain the current computing resources of the group

Qualifications

The successful candidate has a solid background in bioinformatics, statistics and computational biology, good expertise in statistical and bioinformatics software, and an ability to work in a multidisciplinary research environment. The individual should be highly driven and be able to work independently, while being able to communicate effectively with other members of the team.

Preferably, the candidate should hold a PhD degree (or complete one within the next months) or have a track record of performing independent research over the past 4 years. Proven track record of publishing research results in high-ranked journals is appreciated. Experience with Python, R, Matlab or other software/programming languages is required.




Jonathan Coquet
Dept. of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet
Nobels väg 16
Stockholm 171 77, SWEDEN
+46 8 524 86952
http://ki.se/en/mtc/jonathan-coquet-project

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