Student Projects

Astrocytes are increasingly recognised as a transcriptionally diverse cell population, yet a systematic cross-species characterisation of this diversity remains lacking. This project proposes a comprehensive meta-analysis of astrocyte transcriptional states by integrating publicly available single-cell and single-nucleus RNA-seq and multiomics datasets from mouse and human, covering both normal development and neurological disease.

The student will be expected to:

• Assemble and harmonise a large-scale, cross-species astrocyte transcriptomic atlas by curating and integrating publicly available datasets, applying batch correction and standardised re-annotation.
• Map developmental trajectories and cell state transition axes, including reactive and disease-associated programmes, using pseudotemporal ordering and RNA velocity-based approaches.
• Explore genetic axes of astrocyte variability by linking GWAS risk loci for neurological and psychiatric disorders to transcriptional states and state-specific regulatory elements.

The project is designed to be completed within one year and will yield both a curated reference resource and biological insights into the determinants of astrocyte identity in health and disease.
Keywords: astrocyte heterogeneity, single-cell transcriptomics, cross-species atlas integration.

Supervisor:  Gioele La Manno
Co-supervisor: Dr. Amanda Brosius Lutz ((University of Bern)   
Contact: [email protected]

Required: Prior experience with omics data analysis, familiarity with computational tools for data analysis (pandas, scikit-learn), having taken at least an exam in neuroscience/neurobiology is important

Exciting interdisciplinary project combining in vivo two-photon calcium imaging with spatial transcriptomics (Direct HybISS) to characterize the relationship between neuronal function and molecular identity in adult mouse barrel cortex. The selected student will contribute to an innovative experimental pipeline that registers the same neurons across functional imaging and post-mortem transcriptomic analysis, with the goal of characterizing the actvitiy of cortical neuron types during mouse behavior. The student will be trained to process mouse brain sections, perform spatial transcriptomics experiments, operate microfluidic devices for tissue processing, and perform confocal imaging. Depending on interest and project needs, the student may also contribute to computational pipelines for gene decoding and cross-modality image registration. This position offers hands-on experience at the intersection of systems neuroscience, molecular biology, and computational biology.

Application: Motivated M. Sc. candidates are strongly encouraged to reach out to discuss mutual interests. Please include in your application: an up-to-date CV, grade transcripts, desired start date, and duration of stay. Because of the time required to become proficient in the diversity of wet lab techniques this project entails, applications for a stay less than 5-6 month long (full time) will not be considered. Start date is flexible (anytime in 2026 or 2027); the project timeline allows for initial involvement in pipeline development and testing, with transition to data collection as the experimental workflow matures.

Keywords: spatial transcriptomics, microfluidics, image registration, mouse barrel cortex

Supervisor:  Gioele La Manno
Co-supervisor: Carl Petersen   
Contact: [email protected]

Required: Great attention to detail and ability to follow protocols precisely and rigorously; motivation and willingness to work; prior wet lab experience (histology and/or imaging preferred); background in neuroscience, biology, bioengineering, or related field; interest in molecular and systems neuroscience; (Ability to code in Python for candidates interested in the computational opportunities this project offers)