PhD Position: Linking Gene Regulation to Neuronal Phenotype and Circuit Function

Organisation/Company VIB Research Field Biological sciences Neurosciences Chemistry Computer science Researcher Profile First Stage Researcher (R1) Positions PhD Positions Final date to receive applications 12 Apr 2026 - 23:59 (Europe/Brussels) Country Belgium Type of Contract Temporary Job Status Full-time Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure?

No

VIB.AI, the VIB Center for AI & Computational Biology, is a research center dedicated to integrating machine learning with deep biological insight to understand complexbiological systems. Our mission is to move beyond descriptive biology and develop predictive, mechanistic models that connect molecular regulation to cellular and systems-level phenotypes.

The Laboratory of Computational Biology in Leuven ((Use the "Apply for this Job" box below). ), led by VIB.AI Scientific Director Stein Aerts, is seeking a highly motivated PhD candidate to study how gene-regulatory programs give rise to neuronal phenotypes. In the context of the Methusalem BioMedAI ( ), this interdisciplinary project aims to bridge gene regulation, neuronal cell types, electrophysiology, morphology, and connectomics into a unified framework.

Neurons are traditionally classified based on transcriptional an chromatin accessibility profiles, yet how these molecularly defined cell types relate to electrophysiological behavior and circuit integration remains poorly understood. In this project, you will develop and apply spatial transcriptomics methods and combine these with measurements of brain activity and cellular morphology to directly link gene-regulatory cell states to functional neuronal phenotypes.

This ambitious project integrates wet-lab experimentation with advanced computational analysis, and is ideal for a candidate eager to operate at the interface of molecular biology, neuroscience, and AI.

• Set up and optimize imaging based spatial transcriptomics protocols.
• Set up and optimize methods to measure neuronal activity and morphology.
• Combine the two methods to detect the cell type and neuronal physiology in one experiment.

• Apply advanced image analysis to extract cellular morphology and spatial features.
• Analyze multi-modal datasets combining transcriptomics, chromatin accessibility, imaging, and electrophysiology.
• Develop and apply machine learning approaches to link gene-regulatory programs to neuronal phenotypes.
• Use explainable sequence-to-function models to interpret regulatory logic underlying neuronal identity and function.
• Integrate molecular cell types with electrophysiological and neuronal connections.

• Work in a highly interdisciplinary environment spanning AI, genomics, neuroscience, and imaging.
• Collaborate with experimental and computational scientists within VIB and partner institutions, such as the labs of Pedro Goncalves and Maarten De Vos.
• Present results at international conferences and contribute to high-impact publications.

• Master’s degree in molecular biology, biochemistry, neuroscience, bioengineering, chemistry computational biology, computer science, or a related field.
• Strong interest in both experimental biology and computational analysis.
• Background in molecular biology, biochemistry, and/or neuroscience.
• Proficiency in Python.
• Experience with data analysis, machine learning, and AI methods.
• Motivation to tackle a challenging multi-disciplinary project.

• Experience with spatial transcriptomics, genomics, or imaging-based methods.
• Experience with image analysis, single-cell or spatial omics data analysis.
• Familiarity with machine learning frameworks (e.g. PyTorch, Tensor Flow)

• Curious, self-motivated, and eager to learn across disciplines.
• Comfortable working at the interface of wet lab and computation.
• Collaborative team player with strong communication skills.

• Interdisciplinary Training
  : A unique opportunity to develop both wet-lab and computational expertise during your PhD.
• Cutting-Edge Science
  :
  Work on fundamental questions linking gene regulation to neuronal function and circuits.
• State-of-the-Art Infrastructure
  :
  Access to advanced sequencing, imaging platforms, and high-performance GPU computing.
• Research Environment
  :
  An international, collaborative, and stimulating research setting at a top-tier university.
• Supervision
  :
  Supervision by prof. Stein Aerts and Lars Borm (postdoc)
• Funding
  :
  Fully funded PhD position (typically 4 years), with opportunities to apply for competitive fellowships.
• Start Date
  :
  Flexible; as soon as possible
• A detailed CV, including a brief summary of project work (thesis, internships etc.)

Number of offers available 1 Company/Institute VIB Center for AI and Computational Biology Country Belgium City Leuven Postal Code 3000 Street Herestraat 49 Geofield