Research

My research can be divided into two complementary streams; tool and resource development and systems biology of plant and pathogen interactions.

I have developed a range of tools that were inspired by the needs of the research groups at The Sainsbury Laboratory, including the creation of tools for the delivery and visualisation of next-generation sequencing data, detection of phosphorylated sites in peptides, identification of sRNA loci in genomes. Allied to this I have created a 'toolkit' of modules and objects that can be used by all groups across the laboratory. All of these can be seen on my github page here. Currently in collaboration with Mario Caccamo's group at TGAC we are developing tools and methods for the detection of genetic polymorphisms from high-throughput sequencing data without a reference genome and visualisation of these within a draft assembly.

As part of The Sainsbury Laboratory I am in the enviable position of being able to take advantage of the large amount of data that the laboratory produces. I have worked on projects such as Boolean modelling of expression of bacterial Type III secretion systems, study of large complex networks of sRNA in plants and genomics of plant pathogens.