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

Ghent VIB-UGent Center for Inflammation Research

18 Jul 2024


VIB-UGent Center for Inflammation Research

Yvan Saeys Lab



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  ([email protected]).

VIB values diversity - in backgrounds and in experiences. The institute needs people from all backgrounds and ways of life to help build a thriving scientific environment. VIB is therefore looking for candidates who are not only strong in their own aptitudes but care deeply about supporting each other's growth. VIB's collaborators are people with different strengths, experiences and backgrounds, who share a passion for science that generates impact in science and in society. Diversity not only includes race and gender identity, but also nationality, age, disability status, sexual orientation, religion and many other parts of one’s identity. All of VIB’s employees’ points of view are key to its success, and inclusion is everyone's responsibility.