Finding signatures of cell identity in Stemformatics

Supervisors: Jarny Choi and Christine Wells

Available for: Hons/MSc and undergraduate research projects.

Location: Centre for Stem Cell Systems, University of Melbourne

Project title: Finding signatures of cell identity in Stemformatics

Description: Stemformatics (stemformatics.org) is an established data portal containing over 350 gene expression datasets, and ~10,000 samples, with a major focus on stem cells and their stages of differentiation. A major question arising from this data, is whether we can identify robust signatures to identify stem cells, and differentiated progeny. This project involves extensive mining of the datasets within Stemformatics to find those signatures of cell identity. The project will give the student some basic skills in navigating and integrating large-scale datasets. The student will identify genes that can be used as controls in data normalisation and integration; evaluate patterns that distinguish different cell types and benchmark laboratory-derived cells against in vivo, developmental equivalents. The project has scope for exploring innovative visualisations that can summarise large amounts of data succinctly.

Suitable for: Students with a strong maths or computer science background, with either some knowledge of programming or able to learn data manipulation techniques quickly.