Tissue-based spatial -omics technology development postdoc position

About the job/team
A collaboration between EMBL Rome, EMBL Hamburg and EMBL Heidelberg has been awarded funding from CZI to link the detailed cellular morphology of a tissue with its repertoire of macromolecules: High Throughput X-ray Tomography to Target Transcriptomics (HiTT2T).
The Light Imaging Facility at EMBL Rome is developing spatial-omics technologies that permit multiplex RNA detection in thin tissue sections. Separately, EMBL Hamburg has recently established HiTT (High Throughput Tomography) – an X-ray imaging workflow which offers a fast and high-throughput approach to 3D structural imaging and virtual histology characterisation of entire tissue samples within minutes. The ability to target the 2D-omics data production based on the 3D X-ray data has the potential to revolutionise our understanding of disease. With this proposal, we will move beyond the current state-of-the-art of the methodologies and go to high throughput volumetric tissue analysis and transcriptomics via the development of HiTT2T – High Throughput Tomography to Targeted Transcriptomics. Using the information obtained via HiTT2T and the power of computational analysis presents the possibility of predicting and/or preventing disease with a greater degree of accuracy in the future.
As part of this project there is an opportunity for a 3 year postdoctoral position at EMBL Rome to develop technology and methods in the area of spatial transcriptomics. The successful candidate will work closely with the EMBL Hamburg teams to optimize sample preparation for X-ray imaging as well as develop protocols for 3D imaging-based transcriptomics. In addition the successful candidate will work closely with the computational team at EMBL Heidelberg in order to ensure that maximum value is extracted from the 3D X-ray data.

Your role
The fellow is expected to develop tissue processing methods for imaging-based spatial -omics. The position has a strong focus on wet-lab work and experimental protocol development to improve tissue processing methods for -omics. The fellow will work within the Light Imaging Facility at EMBL Rome. The fellow will apply developed methodology towards biological questions in collaboration. As a technology development position the fellow could then transit towards developing research service infrastructure for other institutions, create a start-up with generated IP or have a leading role in industry.

You have:
– PhD in Biology, Engineering, Chemistry or related subjects.
– Solid knowledge in molecular biology, in particular oligo design for RNA or DNA detection
– Track record in tissue or whole-organ/organism sample preparation methods for fluorescence microscopy such as IF and RNA/DNA detection.
– Experience in protocol optimization
– General knowledge in microscopy and image analysis
– Excellent manual dexterity and organizational skills.
– Pro-active attitude and hands-on approach to problem solving.
– Excellent communication, teamwork and interpersonal skills with highest ethical standards.
– Fluency in written and spoken English.
You may have:
– Experience in method development
– Experience in whole organ/organism clearing techniques and/or expansion microscopy
– Exposure to fluidics and/or microscopy automation
– Previous experience performing multiplex immune-fluorescence or spatial transcriptomics.
– Knowledge in computer vision and/or programming language such as Python, R or Matlab

For more information, please contact Alvaro Crevenna alvaro.crevenna@embl.it
Please apply with a CV and a cover letter