Research Engineer Position in Imaging-Based Spatial Omics (Karolinska Institute Department of Medical Biochemistry and Biophysics)

Research Engineer Position in Imaging-Based Spatial Omics Are you an expert in microscopy and microfluidics and want to contribute to new technologies in the booming field of Spatial Biology? A research engineer position in Imaging-based Spatial Omics is immediately available in the Bienko Lab (https://bienkocrosettolabs.org/) at Karolinska Institute in Stockholm. You will lead the design and implementation of integrated microscopy and microfluidic systems suitable for high-throughput fluorescence in situ hybridization (FISH) assays, such as MERFISH (PMID: 25858977) and seqFISH (PMID: 30911168), as well as for new methods that will be developed in house. These methods enable the visualization of hundreds of DNA loci or RNA transcripts directly in cells or tissue sections, preserving spatial information about the biological context in which they are detected. The research group The Bienko lab has a long-standing track record in DNA/RNA FISH methods (www.hdfish.eu; www.fusefish.eu; www.ifish4u.org) and has recently obtained funding to establish a pilot Facility for Advanced FISH Technologies (AFT) within the Single Cell and Spatial Biology National Platform at the Science for Life Laboratory ((https://www.scilifelab.se/). In our lab, we develop and apply high-resolution FISH methods to understand how chromatin is spatially organized in the nucleus of mammalian cells, how dynamic is this organization during the cell division cycle and cell differentiation, and how genomic structural variants associated with various diseases exert their pathogenic effects by disrupting the 3D chromatin architecture. As a technology developer, you will work both in the Bienko lab and within the AFT facility, being part of a dynamic and international research environment where you will have the opportunity to network with scientists from very diverse fields and backgrounds, fostering your creativity and shaping your project in non-conventional ways. Your mission You will leverage on the existing state-of-the-art microscopy infrastructure in the Bienko lab (two custom-made Nikon Ti-E microscopes specifically tailored for single-molecule DNA and RNA FISH) and integrate it with a suitable microfluidic system, aiming at performing MERFISH, seqFISH and alike. Once the system is up-and-running and MERFISH/seqFISH is working in our lab, you will be in charge of securing smooth operations within the AFT facility and in parallel work to develop new assays for spatially resolved genomics and transcriptomics. In all these efforts, you will work in synergy with experts in FISH technologies and image analyses, contributing, among other things, to develop and validate open-source software specifically tailored around FISH data. Our ultimate mission is to develop spatially resolved omic technologies that can help us understand how complex tissues function and how they get disrupted by disease. Your profile You hold a MSc in engineering or equivalent and have a strong expertise in microscopy and microfluidics. You are technology driven and like to set up new devices/instruments using your skills and knowledge. You are fluent in programming languages such as Matlab or Python and know how to make different types of hardware (a microscope and a fluidic device) and software communicate. You have a problem-solving attitude and like troubleshooting. You like to work in a team and are able to make the best out of interactions with people from very different backgrounds. 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: Solna, SciLifeLab Application An employment application must contain the following documents in English: A complete curriculum vitae, including previous academic positions, academic title, current position, academic distinctions A complete list of publications A summary of current work (no more than one page) Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances Welcome to apply at the latest 30th of April 2021. 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 Type of employment Temporary position longer than 6 months Contract type Full time First day of employment Immediately/upon agreement Salary Monthly salary Number of positions 1 Working hours 100 % City Stockholm County Stockholms län Country Sweden Reference number STÖD 2-1433/2021 Contact Magda Bienko, magda.bienko@ki.se Published 18.Mar.2021 Last application date 30.Apr.2021 11:59 PM CET If you apply for this position please say you saw it on Physicaloxy

Research Engineer Position in Imaging-Based Spatial Omics

Are you an expert in microscopy and microfluidics and want to contribute to new technologies in the booming field of Spatial Biology?

A research engineer position in Imaging-based Spatial Omics is immediately available in the Bienko Lab (https://bienkocrosettolabs.org/) at Karolinska Institute in Stockholm.

You will lead the design and implementation of integrated microscopy and microfluidic systems suitable for high-throughput fluorescence in situ hybridization (FISH) assays, such as MERFISH (PMID: 25858977) and seqFISH (PMID: 30911168), as well as for new methods that will be developed in house.

These methods enable the visualization of hundreds of DNA loci or RNA transcripts directly in cells or tissue sections, preserving spatial information about the biological context in which they are detected.

The research group

The Bienko lab has a long-standing track record in DNA/RNA FISH methods (www.hdfish.eu; www.fusefish.eu; www.ifish4u.org) and has recently obtained funding to establish a pilot Facility for Advanced FISH Technologies (AFT) within the Single Cell and Spatial Biology National Platform at the Science for Life Laboratory ((https://www.scilifelab.se/).

In our lab, we develop and apply high-resolution FISH methods to understand how chromatin is spatially organized in the nucleus of mammalian cells, how dynamic is this organization during the cell division cycle and cell differentiation, and how genomic structural variants associated with various diseases exert their pathogenic effects by disrupting the 3D chromatin architecture.

As a technology developer, you will work both in the Bienko lab and within the AFT facility, being part of a dynamic and international research environment where you will have the opportunity to network with scientists from very diverse fields and backgrounds, fostering your creativity and shaping your project in non-conventional ways.

Your mission

You will leverage on the existing state-of-the-art microscopy infrastructure in the Bienko lab (two custom-made Nikon Ti-E microscopes specifically tailored for single-molecule DNA and RNA FISH) and integrate it with a suitable microfluidic system, aiming at performing MERFISH, seqFISH and alike.

Once the system is up-and-running and MERFISH/seqFISH is working in our lab, you will be in charge of securing smooth operations within the AFT facility and in parallel work to develop new assays for spatially resolved genomics and transcriptomics.

In all these efforts, you will work in synergy with experts in FISH technologies and image analyses, contributing, among other things, to develop and validate open-source software specifically tailored around FISH data.

Our ultimate mission is to develop spatially resolved omic technologies that can help us understand how complex tissues function and how they get disrupted by disease.

Your profile

You hold a MSc in engineering or equivalent and have a strong expertise in microscopy and microfluidics.
You are technology driven and like to set up new devices/instruments using your skills and knowledge.
You are fluent in programming languages such as Matlab or Python and know how to make different types of hardware (a microscope and a fluidic device) and software communicate.
You have a problem-solving attitude and like troubleshooting.
You like to work in a team and are able to make the best out of interactions with people from very different backgrounds.

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: Solna, SciLifeLab

Application

An employment application must contain the following documents in English:

A complete curriculum vitae, including previous academic positions, academic title, current position, academic distinctions
A complete list of publications
A summary of current work (no more than one page)
Verifications for crediting of illness, military service, work for labour unions or student organisations, parental leave or similar circumstances

Welcome to apply at the latest 30th of April 2021.

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

Type of employment Temporary position longer than 6 months
Contract type Full time
First day of employment Immediately/upon agreement
Salary Monthly salary
Number of positions 1
Working hours 100 %
City Stockholm
County Stockholms län
Country Sweden
Reference number STÖD 2-1433/2021
Contact
Magda Bienko, magda.bienko@ki.se
Published 18.Mar.2021
Last application date 30.Apr.2021 11:59 PM CET