Research assistant in computational biology

The research group led by Michael Ratz at the Department of Cell and Molecular Biology is looking for a research assistant. The lab is located on KI’s Solna campus in Biomedicum,  interdisciplinary research center with advanced laboratories and modern facilities designed to promote research and collaboration. The Ratz lab is developing and employing novel molecular tools (e.g., cellular barcoding) and genomic methods (single-cellspatial transcriptomics) to understand the development of neural circuits in the mammalian brain in health and disease.

The aim of the project is to contribute to the development and application of a novel approach termed “single-cell molecular connectomics”. The approach will allow high-throughput neural circuit tracing using (in situ) RNA-seq and we want to employ this method to decipher the molecular mechanisms of neural circuit development in the mammalian brain in health and disease.

You will get the opportunity to work with in situ RNA-seq data obtained from mouse brain slices. Your main role will be to establish a computational pipeline that enables to extract and analyze gene expression information from many fluorescence microscopy images. This will involve image processing (e.g. noise reduction, deconvolution, registration, cell segmentation), cell type identification and extraction of spatial gene expression patterns. You will work closely with experimental as well as computational scientists inside the lab.

We are looking for a curiosity-driven and ambitious research assistant with a background in bioinformatics or computer science and an interest in neural circuit (mis)development. 

Qualifications:

* Degree in bioinformatics, computational biology, computer science or a similar field.

* Experience in programming using Python (or a similar language) to address biological questions. * Experience in genomic and/or transcriptomic data analysis (e.g. sequence analysis, expression       analysis, gene regulatory networks, dimensionality reduction, clustering)
* Interest in brain development, neural circuits and mouse models of brain disorders
* Fluent written and spoken English 

Merits:

*Experience in single-cell and/or spatial transcriptomics.
* Experience in image processing with MATLAB. 

A creative and inspiring environment with wide-ranging expertise and interests. 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. Karolinska Institutet is also a state university, which entitles you to several good benefits through our collective agreement. And you get to practice freely in our modern wellness facilities, where trained staff are on site.

Location: Solna

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Welcome to apply!

The application is to be submitted through the Varbi recruitment system.In this recruitment, you will apply with your CV without a personal letter. Instead, you will answer some questions about why you are applying for the job in the application form. 

Permanent position is initiated by a six months trial period.