Single cell RNA-seq for biomarker discovery and immune status assessment

Single cell RNA-seq for biomarker discovery and immune status assessment

Project details

This project involves single cell RNA-sequencing of blood from healthy people, as well as those with autoimmune disease (e.g. lupus and rheumatoid arthritis), and leukaemia

The student will learn to use custom microfluidic devices that merge single cells with DNA-barcoded beads to generate hundreds of thousands of single cell transcriptomes in a matter of minutes! These transcriptomes are then assessed using novel bioinformatics and computational analyses

By holistically assessing the composition, nature and molecular programs underlying blood cell heterogeneity, this project aims to identify novel biomarkers in cancer and autoimmune disease, and potential routes for clinical intervention. 

This project suits highly driven biology students who are inspired by technology and engineering, and interested in immunology and/or cancer. Bioinformatics or coding experience (e.g. R or Python) are extremely beneficial but not necessary.

About our research group

Our laboratory takes a single cell systems biology approach to studying how haematopoietic stem cells ultimately generate all of the red and white blood cells of the immune system. 

We are a very technology-driven lab with the philosophy that studying single cells at different functional and molecular levels, and integrating this information, will reveal the mechanisms behind their fate specification in health and disease.

To this purpose, we perform single cell analysis in vivo using: 

  • Cellular barcoding
  • Cell division tracking in vitro using long-term imaging for family tree construction
  • Single cell RNA-sequencing for lineage priming program identification. 

Combined, we anticipate this suite of tools will allow us to gain a high-resolution understanding into the principles and molecular mechanism governing development and the establishment of lineage fate in normal and cancerous tissues, with view to therapeutic interventions.


Dr Shalin Naik

Dr Shalin Naik in the laboratory
Laboratory Head

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