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

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).

• 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.

Essential

• 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

• 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.

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] ).