BIOINFORMATICIAN SPATIAL SINGLE-CELL OMICS

Organisation: The KU Leuven Cancer Institute (LKI), the KU Leuven Brain Institute (LBI), and the KU Leuven Institute for Single Cell Omics (LISCO) have jointly established a state-of-the-art spatial multiomics platform, which is already revolutionizing our understanding of healthy (e.g. development) and diseased tissues (e.g. cancer and neurodegenerative diseases). The upscaling of integration and analysis of spatial multiomics data now requires a concerted effort, for which we are currently recruiting a dedicated team of data scientists consisting of closely collaborating bioinformaticians, software developers, a data manager and an AI specialist. The position described in this form will be embedded within the platform for multiplexed immunohistochemistry (https://lisco.kuleuven.be/).

Scientific context: Single-cell omics aim at charting the different types and properties of all cells in the human body in health and disease. Over the past years, myriads of cellular phenotypes have been defined by methods that mostly required cells to be dissociated and removed from their original microenvironment, thus destroying valuable information about their location and interactions. Growing insights, however, are showing that such information is crucial to understand complex disease states. For decades, pathologists have interpreted cells in the context of their tissue using low-plex antibody- and morphology-based methods. Novel technologies for multiplexed immunohistochemistry are now rendering it possible to perform extended single-cell expression profiling using dozens of protein markers in the spatial context of a single tissue section. The combination of these novel technologies with extended data analysis tools allows us now to study cell-cell interactions, define cellular sociology, and describe detailed aberrations in tissue architecture, as such gaining much deeper insights in disease states.

Multiplexed IHC: Within LISCO, we installed a platform for high-dimensional multiplexed immunohistochemistry (including the MILAN, COMET/Lunaphore, Phenocycler/Akoya platforms), but we are expanding to additional technologies which can be combined (eg various types of spatial transcriptomics). For more information see: https://lisco.kuleuven.be/. While our platform offers the ability to analyse tissues at unprecedented resolution, data analysis remains challenging. Indeed, because hundreds of parameters are measured simultaneously in millions of single cells across tens-of-thousands of images across numerous areas of a tissue derived from hundreds of patients, data analysis requires the development of specific bioinformatics pipelines. In our plaform, we installed a team of dedicated bioinformaticians to cope with this challenge: while developing new tools, data analysis is also offered as a service to industry and academic users.. Thanks to the Opening the Future Foundation, we are further expanding our team.

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Responsibilities

We are looking for a motivated bioinformatician that will be embedded in our bioinformatics team. The main goal will be to analyse cancer related projects (projects fueling into our platform through the Leuven Cancer Institute) related to multiplexed IHC and multiome analyses, starting from raw data coming of the instruments to the spatially localized single-cell level, as such making clinical data interpretation and integration possible. We will provide the required training, but any expertise in (spatial) single-cell analysis is a major asset. You will have the opportunity to work in a young, dynamic and interdisciplinary team that brings together bio-informaticians, clinicians, pathologists and molecular biologists. Therefore, we offer an initial full time 2-year position within our team, with view on evolving towards a permanent long-term position. During this time, you will also receive the chance to strategically shape the future of the platform.

Profile

-       A background in (bio)informatics or alike; having obtained a PhD is an asset, but also candidates with significant hands-on experience are also encouraged to apply

-       Proficient in linux, python and R (minimally)

-       Excellent communication skills to deal with the multiple users of the platform who are often not bio-informaticians; fluent English is a must.

-       Facilitate the processing of raw data to data interpretation, including the preparation of publication grade graphs and figures, in close cooperation with the biologists, pathologists, researchers, clinicians, etc

-       Be involved in the implementation, improvement and development of new algorithms that are required to improve the processing and analysis of data.

-       You are a team player, well organized, a problem solver, scientifically curious and able to work independently. Results and progress are regularly discussed within the team and with the various users of the platform.

-       Considering the view on a long-term position, we are looking for a candidate that can take responsibility and can contribute strategically to shape the future of this platform.

Offer

We offer an initial full time 2-year position within our team, with view on evolving towards a permanent long-term position.

More information

https://lisco.kuleuven.be/Jobs
https://www.kuleuven.be/kankerinstituut/en/

Interested?

For more information please contact Prof. dr. Frederik De Smet, tel.: +32 16 37 25 75, mail: frederik.desmet@kuleuven.be.

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