Placing regulatory variants into tissue context
Project ideaProject Description
With the rapid development of spatial transcriptomics techniques, the bioinformatics possibilities in this research area are growing as well. A recent approach (gsMAP) integrates spatial transcriptomics data with genome-wide association study (GWAS) summary statistics, enabling spatially resolved linking of genetic associations to individual cells.
In our lab, we developed a statistical approach (SNEEP, see project site) that identifies regulatory single nucleotide variants that impact transcription factor binding in cis-regulatory elements, such as enhancer. This project aims to incorporate SNEEP into gsMAP in order to improve the inclusion of functionally important regulatory variants to the spatial mapping step.
Research Goals
- Combine SNEEP and gsMAP
- Test the new implementation
- Evaluate and compare the results to the original method
Prerequisites
- Python programming
- Basic knowlegde of genomics is helpful, but not required
How to Apply
Send an Email with a short motivation to the corresponding supervisor n.baumgarten|em.uni-frankfurt.de.