Call for applications for a fully financed PhD fellowship

Project description

Neurodegeneration, such as Alzheimer’s disease (AD), is marked by selective neuronal vulnerability, yet the spatial and molecular mechanisms underlying this remain unclear. This project aims to develop and apply a 3D spatial transcriptomic and proteomic pipe-line to map vulnerable and resilient neurons in the mouse brain across disease stages.

Using whole-brain tissue clearing, multiplexed hybridization chain reaction for RNA/protein detection, and lightsheet microscopy, the candidate will generate high-resolution spatial maps of neuronal subtypes in AD mouse models (APP, Tau, and APP;Tau) and wild-type controls. These maps will be integrated with gene markers identified from single-nucleus RNA sequencing datasets to characterize cell type-specific vulnerability patterns. Morphological features (e.g., soma size, spatial clustering) will also be analyzed.

In parallel, the project will investigate whether early behavioral phenotypes in AD models, such as altered social interaction or motivation, correlate with spatially defined molecular pathology. Mice will undergo standardized behavioral assays prior to brain clearing and imaging, allowing behavior-pathology correlation.

The project provides training in spatial transcriptomics, neurodegeneration models, microscopy, and bioinformatics, and includes the opportunity for an international research stay. The candidate will join a multidisciplinary team with expertise in neuroscience, spatial biology, and neurodegeneration.

This work will contribute to understanding how neuronal identity and spatial context influence vulnerability to neurodegeneration and may uncover early biomarkers of disease progression.      

Qualifications

Required qualifications:

• A Master’s degree in Neuroscience, Molecular Biology, Biomedical Sciences, or a related discipline
• Demonstrated interest in brain development, neurodegeneration, or neurobiology
• Experience with laboratory-based research and basic molecular biology techniques
• Ability to work independently and collaboratively in a multidisciplinary environment
• Proficiency in written and spoken English
• Applicants must not already hold a PhD degree

Preferred qualifications:

• Experience with microscopy or image analysis
• Familiarity with in situ hybridization, immunostaining, or spatial transcriptomics
• Knowledge of mouse models or behavioral testing is an advantage
• Basic experience with transcriptomic data analysis (e.g., RNA-seq) or coding (e.g., R, Python)
• Strong motivation, attention to detail, and good organizational skills

How to apply

Please submit your application via this link. Application deadline is 24 June 2025 23:59 CET. Preferred starting date is 1 October 2025.

For information about application requirements and mandatory attachments, please see our application guide.  

Further information

Please contact Associate Professor Dong Won Thomas Kim, tkim@dandrite.au.dk, for more information.

All interested candidates are encouraged to apply, regardless of their personal background. Salary and terms of employment are in accordance with applicable collective agreement.