Cell state and cell fate: Systems biology approaches to understanding cell identity

Project Details

Stem Cells are defined by a variety of means – by their capacity to self-renew and differentiate to different mature cell types; by their role in embryonic development; or by virtue of the anatomical niche in which they may be found.

Given that cells can be defined by their molecular makeup, this project sets out to identify archetype stem cell phenotypes using the Stemformatics stem cell atlas.  By defining molecular signatures of different stem cell or related cell types, we can next evaluate the identity of new samples, benchmark changes to isolation or culture methods, and provide meaningful definitions of different cell states.

Our three main projects focus on:

  1. Molecular signatures of mesenchymal stromal cells
  2. Integrating multi-omics systems scale data to understand stem cell states and differentiation cues
  3. Cancer stem cells and leukemia: The Leukomics project



Prof Erica Fletcher
Prof Martin Pera
Prof Janet Keast
Stem Cells Australia
Prof Tessa Holyoake, University of Glasgow
Prof John Quackenbush, Harvard University
A/Prof Jessica Mar, University of Queensland
Prof Alice Pebay, Centre for Eye Research


ARC Future Fellowship (2015-19): "The Systems Biology of Stem Cells"  Professor C Wells

Research Publications

  • Arner et al. Enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science 2015;  347 (6225): 1010-1014.
  • Rohart et al. A Molecular Classification of Human Mesenchymal Stromal Cells. Peer J 4:e1845; DOI 10.7717/peerj.1845 (2016)
  • Tonge et al. Divergent reprogramming routes lead to alternative stem cell states. Nature 2014; 516 (7530), 192-197.
  • Mason et al. Gene expression variability as a unifying element of the pluripotency network. Stem Cell Reports 2014; 3(2): 365-377.
  • Hough et al. Single cell gene expression profiles define self-renewing, pluripotent, and lineage primed states of human pluripotent stem cells. Stem Cell Reports 2014; 2: 881-895.

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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