PhD Title: Analysis of the interaction between Botrytis cinerea and a host Arabidopsis thaliana using high throughput data

Supervisors: Dr Katherine Denby (Systems Biology and Life Sciences) and Prof. David Wild (Systems Biology)

Publications

• Cooke E.J., Savage. R.S., Kirk P.D.W., Darkins R., Wild D.L. Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. BMC Bioinformatics 2011, 12:399
• Stegle O., Denby K.J., Cooke E.J., Wild D.L., Ghahramani Z., Borgwardt K.M. A robust Bayesian two-sample test for detecting intervals of differential gene expression in microarray time series. Journal of Computational Biology 2010, 17:355-367
  
• Cooke E.J., Savage R.S., Wild D.L. Computational approaches to the integration of gene expression, ChIP-chip and sequence data in the inference of gene regulatory networks. Seminars in Cell and Developmental Biology 2009, 20:863–868

Conferences Attended

• The R User Conference, University of Warwick, August 2011 (Poster)
• School of Life Sciences postgraduate symposium, Univeristy of Warwick, May 2011 (Talk)
• Joint DTC conference, Imperial College London, May 2011
• 21^st Annual MASAMB (Mathematical and Statistical Aspects of Molecular Biology) workshop, Biocenter Vienna, April 2011 (Talk)
• HRI postgraduate symposium, Warwick HRI, May 2010 (Poster)
• CBC-MOAC-White Rose Joint DTC conference, Univeristy of Warwick, April 2010 (Talk)
• HRI postgraduate symposium, Warwick HRI, May 2009 (Abstract)
  
• UK Plant Systems Biology Meeting, Warwick HRI, March 2009
  
• Network Inference in Genetic Studies; the GeneSys Inaugural Meeting, e-Science Institute Edinburgh, October 2008
  

Software

• The time series clustering algorithm described in Cooke et al. 2011 has been implemented in the R/Bioconductor package, BHC.
  

Teaching

• Teaching assistant for BS364 Post Genomic Research practical (2009 - 2011)