Stemformatics (Stem Cells Australia ); building bioinformatics pipelines and working with large data

​Stemformatics is a stem cell gene expression visualisation platform, providing well curated and quality controlled data for hundreds of exemplar human and mouse studies. Stemformatics bridges the gap between biologists and bioinformaticians, allowing the researcher to easily query and visualise their data and that of other experiments, all within the same web platform. The site is used extensively by national and international researchers and is a flagship project of Stem Cells Australia, under the direction of Prof. Christine Wells (formerly of AIBN) who now heads the newly opened Centre for Stem Cell Systems at the University of Melbourne.  

Othmar has a degree in Software Engineering (Griffith University, Brisbane) and worked in eResearch software development and support for a number of years. Bioinformatics became an area of specialisation under Prof. Christine Wells at the National Centre for Adult Stem Cell Research (Eskitis Institute, Griffith University) and subsequently at the Australian Institute for Bioengineering and Nanotechnology where Prof. Wells expanded her successful systems biology / bioinformatics lab. The Stemformatics project began in 2010 and Othmar has been a core developer on the resource since that time, building bioinformatics pipelines to process and ingest microarray, RNA-seq, ChIP-seq and other "multi-omics" assay types into Stemformatics. The success of the Stemformatics project has seen high profile collaborations such as "Project Grandiose", which published a set of five papers in Nature and Nature Communications with the comprehensive description of a novel stem cell reprogramming system which gives rise to a previously unknown stable stem cell state with exciting therapeutic potential.

Industry Engagement and Collaborations

Stemformatics hosts multi-omics datasets for "Project Grandiose", a high profile collaboration led by Prof Andras Nagy (Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital) whose team discovered a novel reprogrammed stem cell state. Stemformatics also worked with the Wellcome Trust Centre for Molecular Parasitology (University of Glasgow), Rheumatoid Arthritis Pathogenesis Centre of Excellence (Arthritis Research UK) and Centre for Immunobiology (University of Glasgow). In 2016 and beyond, Stemformatics will process and host multi-omics data for the Bioplatforms Australia Stem Cells project.


​Stemformatics development is primarily funded by an ARC Special Initiative in Stem Cell Science grant. The YuGene project was funded under an ARC Discovery grants.

Key Publications

  1. ​Wells CA et al, Stemformatics: Visualisation and sharing of stem cell gene expression. Stem Cell Research (2013), DOI 10.1016/j.scr.2012.12.003
  2. Lê Cao et al, YuGene: a simple approach to scale gene expression data derived from different platforms for integrated analyses. Genomics (2014), DOI 10.1016/j.ygeno.2014.03.001
  3. Rohart et al, A molecular classification of human mesenchymal stromal cells. PeerJ (2016), DOI 10.7717/peerj.1845
  4. Hussein et al, Genome-wide characterization of the routes to pluripotency. Nature (2014), DOI 10.1038/nature14046
  5. Tonge et al, Divergent reprogramming routes lead to alternative stem-cell states. Nature (2014), DOI 10.1038/nature14047