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Staff scientist in spatial transcriptomics for Danish infrastructure for omics technologies at the Department of Biochemistry and Molecular Biology

We are looking for a highly motivated and dynamic scientist for a 3-year staff scientist position, who will work with development and implementation of state-of-the-art spatial transcriptomics at the CellX node at University of Southern Denmark. CellX is a Danish national research infrastructure for omics technologies. The position is to commence September 1st, 2022 or as soon as possible thereafter and there will be a possibility for extension after the 3 years.

The revolution in single-cell transcriptomics have shown the need for spatially resolved technologies to visualize cellular diversity in the context of intact tissues.

This has led to the recent development of new technologies to acquire full transcriptome-/genome-/proteome-wide data at single cell level and with high spatial resolution. These technologies are likely to transform our understanding of biological processes and human diseases and form the basis for development of new treatments. To place Denmark at the international forefront of this technological development, CellX will be established as a platform for comprehensive analyses of the entire transcriptome, proteome and metabolome of single cells and/or with spatial resolution. The infrastructure will be fully open to users in academia, the healthcare sector, and the pharmaceutical sector. CellX is a collaboration between Aarhus University, the University of Southern Denmark and the University of Copenhagen and will be implemented to operate as an integrated unit.

The CellX node at the University of Southern Denmark is focused on imaging-based technologies for spatial transcriptomics. We will implement the MERFISH technology to elucidate tissue microenvironments in both patient and animal biopsies and in complex disease models using engineered tissues.

The applicant will be working at the Danish Molecular Biomedical Imaging Center (www.DaMBIC.dk) in close affiliation with Center for Functional Genomics and Tissue Plasticity (ATLAS) at the Department Biochemistry and Molecular Biology, Faculty of Natural Sciences, University of Southern Denmark

The Job

You will have the responsibility for developing the spatial transcriptomics platforms as well as the development of protocols for spatial transcriptomics measurements and analysis. You will be working to push the state of the art of spatial transcriptomics forward using advanced bioimaging techniques and will be responsible for training and supporting users in these applications.

Specifically, you will help develop and use three MERFISH platforms for spatial transcriptomics at different scales. For cellular interaction studies in whole tissue slices, we will use super resolution spinning disk microscopy for 3D scanning. For accurate transcript identification at the subcellular level, we will use STORM microscopy. Finally, you will work with the novel minFLUX microscope technique, which has a spatial resolution down to 2 nm and will be used to visualize transcript distribution and co-localization at the sub-organellar scale.

You will be working in a dynamic international team focused on spatial transcriptomics and bioimaging and will be in contact with a wide range of users and scientific projects. In your daily work, you will report to Associate Professor Jonathan Brewer and the CellX management group at the University of Southern Denmark.

Your qualifications

We are looking for a highly motivated and enthusiastic scientist with the following competencies and experience:

Essential experience and skills:

It would be an advantage for the applicant to have one or more of the following experiences and skills:

  • Molecular biology skills such as qPCR and in vitro transcription for merFISH probe design
  • Single molecule localization microscopy (STORM or MINFLUX)
  • Preparation of biological samples for microscopy
  • Analysis of transcriptomics data, potentially with some knowledge of programming in e.g. python or Java
  • Experience with image analysis

Questions
For further information please contact Associate Prof. Jonathan R. Brewer; [e-mail brewer@bmb.sdu.dk]

Application deadline: August 15th 2022

Employment shall take place in accordance with the framework agreement between the Ministry of Finance and AC (the Danish Confederation of Professional Associations).

Application must include Cover letter/Motivated letter of application (max. one page)., CV incl. education, work/research experience, language skills and other skills relevant for the position. a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do, list of publications. All documents in connection with the application should not contain CPR number (civil registration number) – in that case, the CPR number must be crossed out.

All attached files must be in Adobe PDF format. Cover letter and CV can contain max. 5 Mb.

We recommend that you read how to apply before you apply.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

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Staff scientist in spatial transcriptomics for Danish infrastructure for omics technologies at the Department of Biochemistry and Molecular Biology

We are looking for a highly motivated and dynamic scientist for a 3-year staff scientist position, who will work with development and implementation of state-of-the-art spatial transcriptomics at the CellX node at University of Southern Denmark. CellX is a Danish national research infrastructure for omics technologies. The position is to commence September 1st, 2022 or as soon as possible thereafter and there will be a possibility for extension after the 3 years.

The revolution in single-cell transcriptomics have shown the need for spatially resolved technologies to visualize cellular diversity in the context of intact tissues.

This has led to the recent development of new technologies to acquire full transcriptome-/genome-/proteome-wide data at single cell level and with high spatial resolution. These technologies are likely to transform our understanding of biological processes and human diseases and form the basis for development of new treatments. To place Denmark at the international forefront of this technological development, CellX will be established as a platform for comprehensive analyses of the entire transcriptome, proteome and metabolome of single cells and/or with spatial resolution. The infrastructure will be fully open to users in academia, the healthcare sector, and the pharmaceutical sector. CellX is a collaboration between Aarhus University, the University of Southern Denmark and the University of Copenhagen and will be implemented to operate as an integrated unit.

The CellX node at the University of Southern Denmark is focused on imaging-based technologies for spatial transcriptomics. We will implement the MERFISH technology to elucidate tissue microenvironments in both patient and animal biopsies and in complex disease models using engineered tissues.

The applicant will be working at the Danish Molecular Biomedical Imaging Center (www.DaMBIC.dk) in close affiliation with Center for Functional Genomics and Tissue Plasticity (ATLAS) at the Department Biochemistry and Molecular Biology, Faculty of Natural Sciences, University of Southern Denmark

The Job

You will have the responsibility for developing the spatial transcriptomics platforms as well as the development of protocols for spatial transcriptomics measurements and analysis. You will be working to push the state of the art of spatial transcriptomics forward using advanced bioimaging techniques and will be responsible for training and supporting users in these applications.

Specifically, you will help develop and use three MERFISH platforms for spatial transcriptomics at different scales. For cellular interaction studies in whole tissue slices, we will use super resolution spinning disk microscopy for 3D scanning. For accurate transcript identification at the subcellular level, we will use STORM microscopy. Finally, you will work with the novel minFLUX microscope technique, which has a spatial resolution down to 2 nm and will be used to visualize transcript distribution and co-localization at the sub-organellar scale.

You will be working in a dynamic international team focused on spatial transcriptomics and bioimaging and will be in contact with a wide range of users and scientific projects. In your daily work, you will report to Associate Professor Jonathan Brewer and the CellX management group at the University of Southern Denmark.

Your qualifications

We are looking for a highly motivated and enthusiastic scientist with the following competencies and experience:

Essential experience and skills:

It would be an advantage for the applicant to have one or more of the following experiences and skills:

  • Molecular biology skills such as qPCR and in vitro transcription for merFISH probe design
  • Single molecule localization microscopy (STORM or MINFLUX)
  • Preparation of biological samples for microscopy
  • Analysis of transcriptomics data, potentially with some knowledge of programming in e.g. python or Java
  • Experience with image analysis

Questions
For further information please contact Associate Prof. Jonathan R. Brewer; [e-mail brewer@bmb.sdu.dk]

Application deadline: August 15th 2022

Employment shall take place in accordance with the framework agreement between the Ministry of Finance and AC (the Danish Confederation of Professional Associations).

Application must include Cover letter/Motivated letter of application (max. one page)., CV incl. education, work/research experience, language skills and other skills relevant for the position. a) PhD certificate and b) Master of Science certificate. If the PhD is not completed, a written statement from the supervisor will do, list of publications. All documents in connection with the application should not contain CPR number (civil registration number) – in that case, the CPR number must be crossed out.

All attached files must be in Adobe PDF format. Cover letter and CV can contain max. 5 Mb.

We recommend that you read how to apply before you apply.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

Skriv i din ansøgning, at du fandt jobbet på ofir.dk


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Når du tilmelder dig accepterer du samtidig vores privatlivspolitik. Du kan altid trække dit samtykke tilbage.

Andre job der minder om dette

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At the Department of Physics, Chemistry and Pharmacy, University of Southern Denmark (SDU) we are looking for a postdoc in Biological Physics. Many cell types are elongated and they spontaneously align with their neighbours. In this respect, they are...
7. august 2022

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