Analysing single cell technologies to understand breast cancer

Analysing single cell technologies to understand breast cancer

Project details

This project is a collaboration between Prof Smyth's Lab, which specialises in statistical bioinformatics, and the Institute's breast cancer stem cell Lab lead by Professors Jane Visvader and Geoff Lindeman. We are currently using scRNA-seq to profile breast cancer tumours from BRCA1/BRCA2 patients and to explore the development of normal mammary cells in mice through puberty and pregnancy cycles. New technologies to be adopted in the next three years include scATAC-seq, CITE-seq and MIBIscope. This student will be involved in the analysis of new data being generated and will develop new statistical bioinformatics methods as appropriate. One problem will be to identify common cell subsets across patients and to develop formal statistical tests to assess whether each cell subset is increasing or decreasing in abundance between conditions.

About our research group

Professor Smyth's research lab has a history of developing new statistical techniques for the analysis of genomic data that are widely used or have become accepted international standards. Members the group typically have backgrounds in mathematics, statistics, computer science, genetics, engineering or physics. The group has developed a number of well-known software packages including limma, edgeR, goseq, Rsubread, csaw and diffHic, goseq. Professor Smyth's Lab has a long-standing collaboration with Profs Visvader and Lindeman on the genesis and treatment of breast cancer, leading to 25 journal articles so far (for example (Shackleton Nature 2006 439: 84-88; Lim Nature Medicine 2009 15:907-913; Asselin-Labat Nature 2010 465:798–802; Pal Nature Communications 2017 8(1):1627).


Professor Gordon Smyth

Professor Gordon Smyth writing on a whiteboard
Joint Division Head
Dr Yunshun Chen
Bioinformatics division

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