REANNOUNCEMENT - Postdoc in Spatial Transcriptomics hos University of Southern Denmark

We are looking for a highly motivated researcher for a two-year position, who will work with state-of-the-art spatial transcriptomics, transcriptomics, and bioimaging to comprehensively characterize cell-cell and cell-extracellular matrix interactions in healthy and diseased human tissues. The position is to commence 1 November 2022 or as soon as possible thereafter. Application deadline: 16 October 2022.
The selected candidate will be working in the group of Associate Professor Kim Ravnskjær, but will also be part of an interdisciplinary team involving four research groups at the University of Southern Denmark (SDU) and the University of Copenhagen (UCPH) under the common direction of Associate Professor Jonathan Brewer, SDU.
The selected candidate will be integrated into the Center for Functional Genomics and Tissue Plasticity () in affiliation with the at the .
The revolution in single-cell transcriptomics have shown the need for spatially resolved technologies to visualize cellular diversity and interactions in the context of intact tissues. This has led to the recent development of new technologies to acquire full transcriptome wide data at single cell level and with high spatial resolution. These new technologies are likely to transform our understanding of biological processes and human diseases and form the basis for development of new treatments.
We are focused on state-of-the-art imaging-based technologies for spatial transcriptomics. We have implemented MERFISH technology to elucidate tissue microenvironments in both patient and animal biopsies and in complex disease models using engineered tissues. Specifically, we are developing three MERFISH platforms for spatial transcriptomics at different scales to visualize the transcriptome from whole tissue slices, down to transcript distribution and co-localization at the sub-organellar scale.

Job description

The research focus for this position is to integrate these techniques with conventional transcriptomics and bioimaging, to characterize cell-cell and cell-extracellular matrix interactions in healthy and diseased human tissues including skin biopsies, 3D bioprinted human skin models, and liver biopsies.
A main goal of the work, regarding the study of human skin, will be to understand the molecular bases for its mechanical properties. We will therefore thoroughly characterize the effect of mechanical stimuli on the tissue by performing single-cell transcriptomics and MERFISH on unstimulated and mechanically challenged skin. We expect to identify hundreds of novel regulators of skin mechanical properties, which we will use to improve the properties of bioprinted human skin models.
Regarding the human liver, we wish to resolve hepatic tissue plasticity and infer cellular interactions from liver biopsies. Cell-cell and cell-ECM interactions are instrumental to disease progression. Comprehensive cell interaction trajectories will hence be inferred from single-cell transcriptomics and MERFISH data and linked to disease stage and detailed patient characterization to gain novel insight into the cellular and structural basis for disease.
You will be working in a dynamic international team focused on spatial transcriptomics and bioimaging. In your daily work, you will report to Associate Professor Kim Ravnskjær, but will also be associated with the group of Associate Professor Jonathan Brewer.

Your qualifications

We are looking for a highly motivated and enthusiastic scientist.
Essential experience and skills:
  • A PhD in molecular biology, biophysics, nanotechnology, physics, biochemistry, or a similar field.
  • Experience with transcriptomics, single-cell transcriptomics, and/or spatial transcriptomics such as MERFISH.
  • Experience with analysis of transcriptomics data.
  • Proficient communication skills and the ability and desire to work as part of a team.
  • Excellent English skills, both written and spoken.

Desirable experience and skills:
  • Experience with bioimaging and preparation of biological samples for microscopy.
  • Molecular biology skills such as qPCR and in vitro transcription for MERFISH probe design.
  • Experience with single molecule localization microscopy (STORM).


For further information please contact Associate Professor Jonathan R. Brewer; e-mail: .

Application, salary etc.

The successful applicant will be employed in accordance with the agreement between the Ministry of Finance and AC (the Danish Confederation of Professional Associations). Please check links for more information on and .
The application must include the following:
  • A curriculum vitae including information on previous employment.
  • A full list of publications stating the scientific publications on which the applicant wishes to rely.

Shortlisting may be used in the assessment process.
Incomplete applications and applications received after the deadline will neither be considered nor evaluated.
To qualify you must have passed a PhD or equivalent. Applications will be assessed by an expert assessor/committee. Applicants will be informed of their assessment by the university.
The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.
Applications must be submitted electronically using the link "Apply online". Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read before you apply.
for international applicants about entering and working in Denmark.

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