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.

Researchers

Rowland Mosbergen, Stemformatics Business Manager 
Tyrone Chen, Research Assistant
Isha Nagpal, Full Stack Developer 
Isaac Virshup, Research Assistant
Chris Pacheco, Research Assistant

Collaborators

Stem Cells Australia
Othmar Korn, University of Queensland
Dr Kim-Anh Le Cao, University of Queensland
Professor Tessa Holyoake, University of Glasgow
Dr Jarny Choi, WEHI

Funding

NCRIS: Bioplatforms Australia

JEM Rseearch 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

Neuroscience

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 Neuroscience

Unit / Centre

Wells laboratory: Stem cell systems