Developing computational methods for spatial transcriptomics data

Developing computational methods for spatial transcriptomics data

Project details

Spatial transcriptomics (ST), which has been considered as the 'next generation' of single-cell RNA sequencing, has gained its popularity over the last few years. With the extra layers of spatial and morphological information, ST data provides further insights on cell type composition and formation within tissue specimens. However, the technology is still relatively new to the field, so there is no gold standard on the data analysis.

Recently, we adopted the 10X Visium platform for studying mammary gland structure in human breast tissue. We also plan to explore the Vizgen MERSCOPE and the BGI STOmics platforms. The project will 1) compare existing software tools using both in-house and public datasets and 2) develop novel methodologies for processing and analysing ST data from various platforms. 

About our research group

The Chen lab's research focuses on gene or transcript expression, alternative splicing, DNA methylation, single-cell omics and spatial technologies. We develop statistical bioinformatics methodologies and software tools to make sense of different types of sequencing data and to answer biological questions of interest.

We are a small but enthusiastic and motivated bioinformatics team, embedded in a top-class research division in cancer biology and stem cells. Through daily collaboration, you will be working at the forefront of cancer research with world-leading experts in the fields. You will have access to very exciting biological data generated by the latest cutting-edge sequencing technologies and develop novel methods to make groundbreaking discoveries in cancer research.


Email supervisors



Dr Yunshun Chen

Dr Yunshun Chen
Laboratory Head

Project Type: