Postdoc in Subcellular-resolved Spatial Transcriptomics

University of Southern Denmark
February 15, 2023
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Postdoc in Subcellular-resolved Spatial Transcriptomics Postdoc in Subcellular-resolved Spatial Transcriptomics

At the Department of Biochemistry and Molecular Biology we are looking for a highly motivated researcher for a two-year position, who will work with state- of-the-art subcellular-resolved spatial 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 March 2023 or as soon as possible thereafter. Application deadline: 15 February 2023.

The selected candidate will be working in the group of Associate Professor Kim Ravnskjaer, 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 (KU) 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 (ATLAS) in close affiliation with the Danish Molecular Biomedical Imaging Center at the Department of Biochemistry and Molecular Biology.

The revolution in single-cell transcriptomics has 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 have implemented the MERFISH technology to elucidate tissue micro- environments in both human 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 the MERFISH technology with other state-of-the-art transcript- and protein-based technologies to characterize cell-cell and cell-extracellular matrix interactions in healthy and diseased human tissues including liver biopsies from patients with non- alcoholic fatty liver disease (NAFLD), skin biopsies, as well as bioprinted models of human skin cancer.

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 characterize the effect of mechanical stimuli on the tissue by performing 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.

Spatial analyses of liver biopsies will allow us to resolve hepatic tissue plasticity in the progression and regression of human liver disease. The analyses will leverage our current single cell-resolved insights of human liver function and allow us to infer shifting cell-cell and cell-ECM interactions at different disease stages. High resolution interaction trajectories will be linked to clinical data from our comprehensive patient characterization to give novel insights into the cellular and structural basis for NAFLD progression and regression.

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 Ravnskjaer, 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 with the following competencies and experience:

Essential experience and skills:

  • A PhD in biomedicine, molecular biology, biophysics, or similar field.
  • Experience with sample preparation for transcriptomics, single-cell transcriptomics, and/or spatial transcriptomics such as MERFISH.
  • Experience with advanced analysis of transcriptomics data in R or Python.
  • Experience with bioimaging and preparation of biological samples for microscopy.
  • 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:

  • Molecular biology skills such as qPCR and in vitro transcription for MERFISH probe design.
  • Experience with single molecule localization microscopy (STORM).
  • Insights into the biology of cell-cell interactions or cell-ECM interactions in mammalian tissues.
  • Insights into the pathologies of either NAFLD or skin cancer.
  • Questions For further information please contact Associate Professor Jonathan R. Brewer ; .

    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 salary and taxation.

    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. • Motivated letter of application (max. one page).

    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 How to apply before you apply.

    Further information for international applicants about entering and working in Denmark.

    Campus: Odense

    Application deadline: 15/02/2023

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