VIB Center for AI & Computational Biology Centers At VIB
PhD Position: Linking Gene Regulation to Neuronal Phenotype and Circuit Function
VIB Center for AI & Computational Biology Leuven PhD
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 (www.aertslab.org), 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 (www.kuleuven.be/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.
Responsibilities
* 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.
Computational & Data Analysis
* 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.
Collaboration & Research Environment
* 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.
Your profile
Education & Background
* 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.
Bonus (but not required)
* 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, TensorFlow)
Mindset
* 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.
Our Offer
* 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.)
* University degree certificates
For informal inquiries about the project, please contact: stein.aerts@kuleuven.be and lars.borm@kuleuven.be
VIB-VUB Center for Structural Biology Brussels
VIB-UAntwerp Center for Molecular Neurology Antwerp
VIB.AI is a brand new research center. Its core mission? To study fundamental problems in biology by combining machine learning with in-depth knowledge of biological processes. We are looking for junior and senior group leaders to help shape our research agenda.
Examples of research topics include, but are not limited to: development of new AI architectures for biology and hybrid models that combine deep learning with mechanistic models; foundation models of genome regulation using single-cell and spatial multi-omics data; AI-based modeling of protein structure and protein interaction networks; AI-based modeling of cell morphology and tissue function using imaging and computer vision; AI models of disease and digital twin applications.
An innovative region at the heart of Europe
Leuven and Ghent are based in Flanders, one of the top research destinations in Europe. VIB.AI is part of the VIB Life Sciences Institute (with colleagues working in cancer, biotechnology, immunology, plants, microbiology amongst others) and an extensive set of core facilities. VIB.AI is embedded within the University of Leuven, the largest university in Belgium and Europe’s most innovative university. KU Leuven is also home to the Leuven AI Institute and the Leuven University Hospital, one of the largest in Europe. Leuven is also home to Imec, a world-renowned research center for nanoelectronics and digital technology.
Leuven is an attractive university city with a rich history and a lively atmosphere. It offers an affordable, high standard of living, has an international school, and ample daycare options. The public education system and public health care system in Flanders are world-class, easily accessible, and low-cost to end users. Public transport is also excellent and widely available.
Brussels, the capital of Europe, is only 20 mins away. Leuven is also only 14 minutes by train from Brussels Airport which has many daily direct flights to North America, Africa and Asia. There are also high-speed direct international rail connections to numerous cities including Paris, London, Frankfurt and Amsterdam.
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Life in Ghent
Ghent offers an exceptional quality of life and seamlessly blends historical charm with modern convenience. With its picturesque canals, centuries-old architecture, and vibrant cultural scene, Ghent provides a unique and inspiring backdrop for both work and leisure.
Its world-class educational institutions and research centers contribute to a dynamic professional landscape.
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