PhD project: Resolving cellular heterogeneity in human health and disease using highly multiplexed spatial (multi-)omics technologies

22 June 2020

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For more information please contact Prof. dr. Thierry Voet, mail: or Dr. Katy Vandereyken, mail:

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

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Ref. BAP-2020-494

Apply before 31 July 2020

A new PhD position is available at the Center of Human Genetics, KU Leuven, in the laboratory of Prof. Thierry Voet. Join our growing multidisciplinary team that develops and applies cutting-edge single-cell molecular biology and computational methods to investigate human development, ageing and disease biology. We are pioneers in multi-omics measurements from the same cell and aim to answer key biological questions with potential high impact.

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A human body comprises 10 to 100 billion cells and as most of our organ functions are executed by the concerted action of those individual cells in a spatially organized context, it is paramount 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 (sub populations of) cells are perturbed in diseased conditions, like cancer or neurological disorders.
The current PhD position is placed in the context of a KU Leuven interdisciplinary network (ID-N) project, focused on the development and implementation of a spatial single-cell multi-omics platform to study cellular heterogeneity in human health and disease. The project will focus on developing, implementing and running complex molecular biology methods for spatial RNA (+DNA/protein) profiling of single cells. Specifically, you will develop, automate and use novel methods for single-cell analyses in a spatial context, including sequential fluorescence in situ hybridization (seqFISH) or in situ sequencing (ISS) -based approaches. You will play a key role in the establishment of these novel technologies and their implementation for cancer and neurobiology applications in particular, studying cellular heterogeneity, cell-cell communication and interactions, the biology of cellular niches, and the cellular architecture of both normal and diseased tissues, primarily brain and tumor tissues, with potential valuable clinical translation.
This interdisciplinary project and spatial single-cell multi-omics platform involves collaborations with several KU Leuven and VIB groups with a wide range of expertise,including the teams of Profs. Frederik De Smet (KU Leuven Translational Cell& Tissue Research), Peter De Decker (KU Leuven Biochemistry, Molecular and Structural Biology Section), Johan Hofkens (KU Leuven Molecular Imaging and Photonics), Diether Lambrechts (VIB-KU Leuven Laboratory of Translational Genetics), Stein Aerts (VIB-KU Leuven Laboratory of Computational Biology) and Sebastian Munck (VIB-KU Leuven Research Group Molecular Neurobiology). The platform will also be a central part to the Innovation Lab of the Leuven Single Cell Institute in establishment.


  • Co-establish complex molecular biology protocols for in situ single-cell imaging and sequencing
  • Apply spatial single-cell omics methods to study normal and diseased primary human and animal model tissue, in particular brain and tumor tissue, and optimize tissue handling protocols
  • Co-develop automated and/or miniaturized versions of established protocols using liquid handling robots and/or microfluidics to improve assay throughput, robustness, and cost
  • Follow up on the literature on single cell sequencing and spatial omics technology development
  • Collaborate in large-scale projects for the implementation of spatial single-cell omics protocols, the data acquisition, analysis and interpretation
  • Report and communicate on progress in meetings, publish scientific articles about your results and participate in a number of international conferences where you present your work
  • Prepare a doctoral dissertation to be obtained at the KU Leuven Faculty of Biomedical Sciences
  • Take on limited tasks in support of education and science communications

Selected publications

  • Macaulay IC, Teng MJ, Haerty W, Kumar P, Ponting CP,Voet T (2016). Separation and parallel sequencing of the genomes and transcriptomes of single cells using G&T-seq. Nature Protocols 11,2081-2103.
  • Liao J, Lu X, Shao X, Zhu L, Fan X (2020). Uncovering an organ’s molecular architecture at single-cell resolution by spatially resolved transcriptomics. Trends in Biotechnology, S0167-7799(20)30140-2


  • MSc in Bioscience Engineering, Biochemistry, Biomedical Sciences, Biology or equivalent
  • Good knowledge of molecular biology, cell biology and genetics
  • Experience with classical molecular biology techniques, including DNA/RNA/protein
  • Experience with fluorescence and confocal imaging is aplus
  • Excellent research skills and a strong interest in molecular and cell biological methods
  • Eager to learn and have a lively interest in scientific research and novel technologies
  • Basic bioinformatics and statistical analysis skills are a plus
  • Good problem-solving skills, attention to detail and accurate working style
  • Ability to work independently and within a group and show initiative
  • Efficient, stress resistant and able to respect deadlines
  • Proficient in English and have good written and oral communication skills
  • Willing to supervise Bachelor and Master students
  • Experience with international mobility is a plus, though not obligatory


We are offering funding for a full-time PhD position; we will also invite candidates to apply for (inter)national external funding.

You will work in an intellectually challenging and stimulating environment with state-of-the art facilities and contribute to the team spirit of our research group consisting of several PhD students, technicians and postdocs. 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 in Belgium and abroad. 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. The salary will be in accordance with the University salary scales for doctoral researchers.