POSTDOCTORAL ENGINEER SPATIAL TRANSCRIPTOMICS

23 August 2018

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Interested?

For more information please contact Prof. dr. Thierry Voet, mail: thierry.voet@kuleuven.be.

You can apply for this job no later than September 23, 2018 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.

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Apply before 23 September 2018

You will play a key role in the establishment of highly multiplexed in situ RNA-profiling of single cells as well as fourth-generation sequencing technology that preserves the spatial coordinates of RNA and DNA sequences within tissue sections. Thus you will enable localized sequencing reads within single cells in their original histological tissue context, and the detection and visualization of transcripts from 100s to 1000s of genes at unprecedented accuracy and with spatial inter- and intracellular coordinates.

A human body comprises 10 to 100 billion cells. 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 individual cells in their native spatial location. This 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.
In this position, you will be responsible for developing, implementing and running complex molecular biology methods for (deoxy)ribonucleic acid profiling of single cells in a tissue context. Specifically, you will develop and automate new protocols for single-cell analyses in a spatial context and will take the experimental lead in setting up diverse methodologies, including sequential fluorescent in situ hybridization (seqFISH) and in situ sequencing approaches in particular. The position is placed in the context of a collaborative project using large-scale infrastructure for cancer and neuroscience applications. The collaborative project interacts with the KU Leuven and teams of Profs. Diether Lambrechts, Stein Aerts and Sebastian Munck as well.

You will play a key role in the establishment of highly multiplexed in situ RNA-profiling of single cells as well as fourth-generation sequencing technology that preserves the spatial coordinates of RNA and DNA sequences within tissue sections. Thus you will enable localized sequencing reads within single cells in their original histological tissue context, and the detection and visualization of transcripts from 100s to 1000s of genes at unprecedented accuracy and with spatial inter- and intracellular coordinates.
The team of Prof. Thierry Voet develops and uses cutting-edge molecular biology methods to study single cells, to investigate human development and disease biology. We use automated, and microfluidics assays that process hundreds to thousands of cells in parallel, innovative computational approaches, and are a pioneer in multi-omics measurements from the same cell.

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Responsibilities
  • Develop and establish complex molecular biology protocols for in situ single-cell(multi-omics) imaging and sequencing. Developing novel molecular biology methodologies for spatial single-cell omics
  • Handle primary human tissue, in particular, tumor tissue, for spatial single-cell omics. Develop, test and optimize innovative tissue handling protocols for spatial single-cell omics
  • To be responsible for developing automated and/or miniaturized versions of established spatial single-cell analysis 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 analyses of single cells, and coordinate with available core facilities and computational biologists
  • To be co-responsible for successful completion of the project(s),help in the data interpretation and play a key role in the publication of the results of these team-collaborative project(s)
  • To generate novel ideas and concepts for single-cell method development and biological application to the team, in particular in the context of spatial analyses of single cells
  • Manage existing and develop new collaborations and relationships internal and external to KU Leuven-VIB
  • Report and communicate on progress in meetings
  • Provide technical advice and guidance to less experienced team members where applicable
  • Be responsible for the delivery of project outcomes

Most challenging aspects of the role: Establishing robust protocols and workflows for spatial single-cell (multi)omics measurements will require a high degree of technical innovation, in-depth knowledge of 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 to meet the goals of key biological projects.

Profile

Essential knowledge, skills, and experience required:

  • MSc in Bioscience Engineering with a Ph.D. in Molecular Biology/Biotechnology/Genetics/Genomics
  • 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 liquid handling robots
  • Experience with high throughput assays (e.g.,microfluidics)
  • Experience with single-cell molecular biology work
Offer

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 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.

We initially offer a 1-year position, an extension of 1 year is already foreseen; we invite candidates to apply for (inter)national external funding.