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PhD candidate at the intersection of Cell-Cell Communication models and Spatial Omics

Closing date
18 Jul 2024

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Life Science
Job Type
PhD Position
Employment - Hours
Full time
Professional certification

Job Details

Project Overview This PhD position is one of multiple positions within a larger project aimed at optimizing spatial omics analysis for a variety of biological applications. Your research will specifically focus on extending NicheNet, the Cell-Cell Communication Inference tool developed by the Saeys lab, for spatial omics data. You will collaborate closely with renowned groups, including the Martin Guilliams lab and the Chris Marine lab, leveraging extensive experience with spatial omics data generated at VIB (MERFish Vizgen, MACSima Miltenyi, 10X Visium-HD).

What you will do
  • Develop and enhance NicheNet for integration with spatial omics data.
  • Analyze and interpret spatial omics data to infer cell-cell communication pathways.
  • Contribute to the development of new computational methods and tools for spatial omics data analysis.


  • You obtained a Master's in Computer Science, Artificial Intelligence, Bioinformatics, Physics, Engineering, Bio-engineering, or equivalent.
  • Background in systems biology
  • Background in AI (deep learning, probabilistic modelling, generative AI) or machine learning
  • Proficient in Python or R programming
  • Strong communication skills in English

Desirable but not required 

Preference will be given to candidates with experience with

  • processing scRNA-seq or spatial transcriptomics data
  • high-performance computing and software containers

Key personal characteristics 

  • Strong interpersonal skills
  • Ability to work independently and as part of a team
We offer
  • Competitive stipend and benefits package
  • Fully funded PhD scholarship, but encouraged to apply for a national PhD fellowship (e.g., FWO)
  • A versatile and challenging academic position with very diverse contacts in a world-class research environment operating at an international level, and various opportunities to broaden your expertise.
  • Access to state-of-the-art compute & GPU infrastructure 
  • Collaborative and supportive research environment
  • Attendance of national and international conferences
  • Training courses in academic, technical, and career skills.
How to apply? Please complete the online application procedure and include a detailed CV, two reference letters, and a motivation letter.

For further information and questions, please send an email to Yvan Saeys  (


VIB’s core mission is to generate disruptive insights in the molecular underpinning of life and to translate these actively into impactful innovations for patients and society. VIB is an independent research institute where some 1,800 top scientists from Belgium and abroad conduct pioneering basic research. As such, they are pushing the boundaries of what we know about molecular mechanisms and how they rule living organisms such as human beings, animals, plants, and microorganisms. Based on a close partnership with five Flemish universities – Ghent University, KU Leuven, University of Antwerp, Vrije Universiteit Brussel, and Hasselt University – and supported by a solid funding program, VIB unites the expertise of all its collaborators and research groups in a single institute. VIB’s technology transfer activities translate research results into concrete benefits for society such as new diagnostics and therapies and agricultural innovations. These applications are often developed by young start-ups from VIB or through collaborations with other companies. This also leads to additional employment and bridges the gap between scientific research and entrepreneurship. VIB also engages actively in the public debate on biotechnology by developing and disseminating a wide range of science-based information. 

More info can be found on

Company info
Rijvisschestraat 120

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