Postdoctoral Engineer Spatial Transcriptomics

Leuven, Louvain (BE)
Tuesday, 30 June 2020
End of advertisement period
Friday, 31 July 2020
Contract Type
Fixed Term
Full Time


(ref. BAP-2020-372)

A new postdoc position is available at the Center of Human Genetics, KU Leuven, in the laboratory of Prof. Thierry Voet. Our multidisciplinary team develops and applies cutting-edge single-cell molecular biology methods to investigate human development, ageing and disease biology. We aim to answer key biological questions with high impact and are pioneers in multi-omics measurements of the same cell, using robots and microfluidics for high-throughput assay automation and innovative computational approaches. The team also actively contributes to leading large-scale international communities such as the Human Cell Atlas and the LifeTime initiative. Position: A human body comprises 10-100 billion cells, and as most of our organs function through the concerted action of those individual cells in a spatially organized context, it is important that we are able to research these individual cells in their native spatial location. Current state-of-the art single-cell sequencing methods, can already provide us with much information on cellular heterogeneity compared to traditional bulk sequencing approaches, but as tissue dissociation is still required prior to analysis, the essential spatial context is lost. This information is not only important to understand normal organ development and function, but also to investigate how (subpopulations of) cells are perturbed in diseased conditions like cancer or neurological disorders. Hence, in the context of the “Opening The Future” initiative, we are now developping a spatial multi-omics platform, with a particular focus on spatial transcriptomics (Prof. Thierry Voet), proteomics (Prof. Frederik De Smet), metabolomics (Prof. Johan Swinnen) and bioinformatics (Prof. Stein Aerts, Dr. Alejandro Sifrim), in collaboration with the Leuven Cancer Institute (LKI) and the Leuven Brain Institute (LBI). This spatial multi-omics platform will allow to research single cells in their native tissue context at high throughput, preserving the spatial coordinates of the targeted molecules, with potential clinical translation. This platform will also be a central part to the Innovation Lab of the Leuven Single Cell Institute in establishment. You will play a key role in developing and innovating the spatial transcriptomics subplatform, as well as in running and managing this platform focused on high-throughput spatial profiling of gene expression in (single) cells in various human and animal model (diseased) tissue types, primarily brain and tumor tissues. Initially this will entail implementing and optimizing in situ capturing (e.g. 10x Genomics Visium) and in situ sequencing (e.g. CARTANA) technologies, and in a later stage also other innovative spatial transcriptomics methods (e.g. in situ hybridization technologies) developed in coordination with other talented engineers in our team. This will be done in close collaboration between the lab of Prof. Thierry Voet, the KU Leuven Genomics Core and the VIB BioImaging Core lead by Prof. Sebastian Munk, in addition to the other groups involved in the spatial multi-omics platform.


  • Establish complex molecular biology protocols for in situ single-cell imaging and sequencing
  • Handle primary human and animal model tissue, in particular brain and tumor tissue, and optimize innovative tissue handling protocols for spatial single-cell omics
  • Develop automated and/or miniaturized versions of established protocols using liquid handling robots and microfluidics platforms to improve throughput, robustness, and cost
  • Lead in the experimental design and execution of large-scale projects requiring spatial analysis and coordinate with available core facilities and computational biologists
  • Be co-responsible for the successful completion of projects and the delivery of project outcomes, help with the data interpretation and play a keyrole in the publication of the results of team-collaborative projects
  • Generate novel ideas/concepts for biological applications and scout for novel technology developments in the context of single-cell spatial omics
  • Manage existing and develop new collaborations and relationships internal and external to KU/UZ Leuven and VIB
  • Report and communicate on progress in meetings, publish scientific articles, and participate in international conference.

Most challenging aspects of the role: Establishing robust protocols and workflows for spatial single-cell transcriptomics will require a high degree of technical in-depth knowledge and creativity with molecular assays and fluorescent microscopy techniques, attention to detail and high-level troubleshooting skills. High accuracy in experimental work, close coordination and effective communication with other team members and teams will be critical.


Essential knowledge, skills, and experience required:

  • MSc in Bioscience Engineering with a Ph.D. in Molecular Biology/Biotechnology/Genetics/Genomics, or equivalent
  • Extensive experience and in-depth knowledge of classical molecular biology techniques, including DNA/RNA/protein work
  • Extensive experience with and a broad understanding of nucleic acid probe design, nucleic acid hybridization for in situ RNA- and/or DNA-molecule detection, and imaging via fluorescence and confocal microscopy
  • Experience with high-throughput next-generation sequencing methodology, including barcoding strategies, knowledge of a wide range of platforms and library construction methods
  • Experience with development and implementation of sophisticated molecular biology protocols, and designing (complex/high throughput) experimental workflows
  • Advanced problem-solving skills
  • Attention to detail and accurate working style
  • Ability to be inventive and to present novel ideas in molecular method development
  • Ability to work independently and within a group
  • Evidence for productivity in a research setting such as publications, patents, etc.
  • Excellent written and oral communication skills

Additional desirable skills and experience

  • Experience with high throughput assays (e.g. liquid handling robots, microfluidics)
  • Experience with single-cell molecular biology work


We are offering a postdoctoral position in an intellectually challenging environment with state-of-the art facilities. KU Leuven is a research intensive, internationally oriented university that carries out both fundamental and applied scientific research. It is highly inter- and multidisciplinary focused and strives for international excellence. In this regard, it actively works together with research partners worldwide. It provides its students with an academic education that is based on high-quality scientific research. You will work in Leuven, a historic, dynamic and lively city located in the heart of Belgium, within 20 minutes from Brussels, the capital of the European Union, and less than two hours from Paris, London and Amsterdam.

We initially offer a 2-year position, with potential extension; we invite candidates to apply for (inter)national external funding.


For more information please contact Prof. dr. Thierry Voet, mail: thierry.voet@kuleuven.be or dr. Katy Vandereyken, mail: katy.vandereyken@kuleuven.be.

You can apply for this job no later than July 31, 2020 via the online application tool

KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR@kuleuven.be.

Similar jobs

Similar jobs