Scientific collaborator in spatially resolved trancriptomics, EPFL, Switzerland

The School of Life Sciences of the Ecole Polytechnique Fédérale de Lausanne (EPFL) invites applications for a position of a scientist working in the field of spatial transcriptomics jointly at the Histology Core Facility (HCF) and the BioImaging and Optics platform (BIOP). The HCF and BIOP platforms benefit from core funding to provide the local and external scientific community with a comprehensive support to realise their ambitious research goals and to push the boundaries of knowledge in development, neurosciences, immunology, cancer, infectious diseases and bioengineering.

Spatially resolved trancriptomics compromises a variety of approaches allowing to decipher mRNA levels in cells, tissue and organisms with the advantage of relating them to the biological context. Common to all of these methods is the fact that they are depending on accurate sample preparation image acquisition and image analysis in order to be able to extract reliable information from the sample.

The successful candidate will drive the implementation of this technology at the HCF and BIOP technology platforms and will also promote and facilitate access of the EPFL research community to spatially resolved transcriptomics. The position is ideally suited to start a career in a scientific core facility and to gain experience in how to render a state-of-the-art technology accessible to a broad user base.

Major tasks:

• Develop tissue preparation and hybridization protocols allowing for different spatial transcriptomics approaches (e.g. smFISH, BaristaSeq, etc.).
• Develop generic acquisition protocols for spatial transcriptomics approaches. Support users in acquiring and managing their data.
• Responsible for maintenance and quality control of the instruments (e.g. microfluidic device and microscope) related to spatial transcriptomics analysis.
• In charge of the development of the data analysis pipelines. Team up with Bioinformaticians when needed for downstream analysis. Support users in data interpretation.
• Interact with EPFL research groups already using spatial transcriptomics to provide them with appropriate support and to allow for efficient knowledge transfer to other users.
• Participate in teaching and training activities organized by HCF and BIOP platforms.

Skills:

• Experience in light microscopy, ideally with setups used to acquire spatial transcriptomics data-sets.
• Solid skills in histology, previous experience with spatial transcriptomics related pipelines is an asset.
• Proven experience in image analysis. Coding experience with Python, ideally familiar with starfish (Python library for generating gene expression matrices from image-based spatially-resolved transcriptomics assays).
• Excellent written and oral communication skills in English, knowledge of French would be a plus. Eager to interact with peers and to adsorb and transmit knowledge from experts to regular users.

We offer:

• A dynamic and international work environment in a multidisciplinary School.
• Internationally competitive salary and benefits.
• EPFL is an equal-opportunity employer with family-friendly work policies. It is committed to increasing the diversity of its employees. It strongly encourages women to apply.

Application:

Please include cover letter, curriculum vitae and names and addresses (including e-mail) of two references. Review of applications will start early May and will continue until the position has been filled. Link for submitting the application: https://recruiting.epfl.ch/Vacancies/1757/Description/2