My research:
I am currently a PhD student in Assoc. Prof Timothy Bailey's group at the Institute for Molecular Bioscience, at The University of Queensland, Australia. My current research focuses on developing tools and methods to better under transcription factor binding and gene expression. One key focus of my PhD has been on integrating epigenetic (and particularly, histone modification) data into in silico methods of predicting transcription factor binding. This both greatly improves accuracy (less false positives), and allows these methods to be tissue-specific. I am currently experiencing the joyful period of writing up my thesis.
Published papers:
- Cuellar Partida, G, Buske F. A., McLeay, R.C., Whitington, T, Noble, W.S., Bailey, T.L. (2011). Epigenetic priors for identifying active transcription factor binding sites. Bioinformatics, doi: 10.1093/bioinformatics/btr614
- McLeay, R. C., Leat, C. J., and Bailey, T. L. (2011). Tissue-specific prediction of directly regulated genes. Bioinformatics, 27 (17): 2354-2360, doi: 10.1093/bioinformatics/btr399
- McLeay, R. C. and Bailey, T. L. (2010). Motif enrichment analysis: A unified framework and an evaluation on ChIP data. BMC Bioinformatics, 11, 165, doi:10.1186/1471-2105-11-165
Software Tools:
- DR Gene - Identify promoters bound by a given transcription factor in a tissue-specific manner (i.e. find Directly Regulated Genes).
- AME & RAMEN - Motif enrichment analysis. Find transcription factor motifs over-represented in a set of genes. AME is now maintained in the MEME Suite, and porting RAMEN is in progress.
- WigShrink - Reduce the size of a "wiggle" file by removing unnecessary runs of zeros.
- Genome-wide gene expression modelling - Supplementary data and scripts for gene expression modelling (for a submitted paper).
