The Stemformatics Stem Cell Atlas

Project Details

Stemformatics is a web-based collaboration platform developed in 2010 to service the international stem cell community. Hosting hundreds of curated, publicly accessible datasets comprised of thousands of individual samples from stem cells and related differentiating progeny, it provides researchers with the means to visualize, share and benchmark data quickly and easily.

Work in the Stemformatics platform includes improving methods for visualizing complex genome-wide datasets, methods for integrating data from different sources, or generated across different platforms. This includes transcriptome data from microarrays, RNAseq, single-cell RNAseq, ChIP-seq, proteomics and metabolomics experiments. We are actively working to develop a stem cell ontology to assist in the meta-analysis of the data in the stem cell atlas. Our team includes software developers, systems architects, bioinformaticians, and stem cell annotators.


Dr Jarny Choi, Bioinformatician
Paul Angel, Research Fellow 
Jack Bransfield, Full Stack Developer


Stem Cells Australia
Othmar Korn, University of Queensland
Professor Tessa Holyoake, University of Glasgow
Dr Kim-Anh Le Cao, Senior Lecturer, Statistical Genomics, Mathematics and Statistics


NCRIS: Bioplatforms Australia

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.
  • Hussein SMI et al. Genome-wide characterization of the routes to pluripotency. Nature 2014; 516 (7530): 198-206.
  • Lee DS et al. An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator. Nature Communications 2014; 5: 5619.
  • Clancy JL et al.  Small RNA changes en route to distinct cellular states of induced pluripotency. Nature Communications 2014; 5: 5522.

Research Group

Wells laboratory: Stem cell systems

Faculty Research Themes


School Research Themes

Biomedical Neuroscience, Systems Biology, Stem Cells

Key Contact

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

Department / Centre

Anatomy and Physiology

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