Blood Atlas: Understanding cell state and differentiation using genomics data from blood cells

Project Details

The human body makes over 200 billion blood cells in a day. And since the complete range of blood cells can originate from a single haematopoietic stem cell, blood is an amazing system for studying cell differentiation, identity and fate. Overlapping with the “Stemformatics” and “Cell state and cell fate” projects in the lab, this project focuses on collating a set of exemplar datasets in the field and analysing them to better understand the basic biology of blood cells, such as: What gives a leukaemic cell its identity? What role does the bone marrow niche play? We are also developing a suite of data analysis and visualisation tools using the latest bioinformatics techniques to facilitate the discoveries in these areas.

Focus areas:

  • Single cell RNA-seq data processing and visualisation
  • Analysis of blood datasets for biological insight
  • Multi-omics data visualisation and tool development


Dr Jarny Choi, Bioinformatician,  
Isaac Virshup, PhD Student


Stem Cells Australia
BioPlatforms Australia
Dr Karen Keeshan, University of Glasgow
Professor Susie Nilsson, CSIRO
Professor Andrew Elefanty, MCRI


JEM Research Foundation

Research Publications

  • Wells CA, Mosbergen R, Korn O, Choi J, Seidenman N, Matigian NA, Vitale AM, Shepherd J. Stemformatics: visualisation and sharing of stem cell gene expression. Stem Cell Research 2013; 10(3):  387-95.
  • de Graaf C, Choi J, et al. Haemopedia: An Expression Atlas of Murine Hematopoietic Cells. Stem Cell Reports 2016 Sep 13; 7(3): 571-82.
  • Choi J. Guide: a desktop application for analysing gene expression data. BMC Genomics 2013 Oct 7; 14: 688.

Research Group

Wells laboratory: Stem cell systems

Faculty Research Themes


School Research Themes

Biomedical Neuroscience, Stem Cells, Systems Biology

Key Contact

For further information about this research, please contact the research group leader.

Department / Centre

Anatomy and Physiology

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