Fiona Hamey


I first moved into the world of biology in 2013 to undertake a Masters degree in Systems Biology after doing my undergraduate studies in Mathematics. The course gave me an insight into how useful computational approaches can be in helping us to understand biological systems, and so in 2014 I started on the ‘MRC Physical Biology of Stem Cells’ 4-year PhD programme at the Cambridge Stem Cell Institute. In my first year I did 3 rotation projects working with Dr Ana Cvejic (Wellcome Trust Sanger Institute), Professor Bertie Göttgens (Department of Haematology) and Professor Alfonso Martinez Arias (Department of Genetics).

I then started my PhD in October 2015 with Bertie as my main supervisor and Alfonso as my co-supervisor. The system I am working on is adult haematopoiesis – the process of blood stem cells differentiating and specialising towards different mature cells types. Blood is composed of many cell types, each with specific functions, and all of these can be generated by a single blood stem cell. To maintain a healthy blood system it is vital that haematopoietic cell fate decisions are properly regulated, as failure to do so is linked to serious blood disorders such as leukaemia. My project focuses on applying computational methods to single cell gene expression data with the aim of understanding how these cell fate decisions are made. High-dimensional gene expression data, such as single cell qPCR or single cell RNA-seq, provides thousands of snapshot measurements of cells at different positions in a ‘transcriptional landscape’ of differentiation, and importantly captures the heterogeneity present at the level of individual cells in a population. I want to use this information to reconstruct how cells explore this transcriptional landscape to help understand which are the important genes and signals controlling how cells transition between regions of the landscape associated with particular cell fates.


  • Nestorowa S*, Hamey FK*, Pijuan Sala B, Diamanti E, Shepherd M, Laurenti E, Wilson NK, Kent DG, Göttgens B (2016). A single cell resolution map of mouse haematopoietic stem and progenitor cell differentiation. Blood, 128(8):e20-31. * equal contribution
  • Hamey FK*, Nestorowa S*, Wilson NK, Göttgens B (2016). Advancing haematopoietic stem and progenitor cell biology through single cell profiling. FEBS letters, doi:10.1002/1873-3468.12231. * equal contribution 
  • Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey FK, Voet T, Teichmann SA, Cvejic A (2016). Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells. Cell Reports, 4(4):966-977.
  • Hamey FK, Shavit Y, Maciulyte V, Town C, Lio P & Tosi S (2015). Automated Detection of Fluorescent Probes in Molecular Imaging. In C. di Serio, P. Lio, A. Nonis & R. Tagliaferii (Eds.), Computational Intelligence Methods for Bioinformatics and Biostatistics (pp. 68-75). Springer.
  • Shavit Y, Hamey FK & Lio P. (2014). FisHiCal: an R package for iterative FISH-based calibration of Hi-C data. Bioinformatics, 30(21):3120-3122.


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