
About Me:
I am a post-doctoral researcher working in the Bioinformatics group of Prof. Baulcombe's group at the Department of Plant Sciences of the University of Cambridge. I completed my PhD thesis, 'Model-Driven Analysis of High-Throughput Genomic Data in Late Stage Ovarian Cancer', with Prof. Simon Tavare and Dr. James Brenton at the Department of Oncology at the University of Cambridge.
Research:
My research focuses on the development and application of computational tools in bioinformatics and especially tools for analysis of data from next-generation sequencing machines.
Software:
The baySeq R package for differential expression analysis of data from next-generation sequencing machines, can be downloaded from Bioconductor.
I have collaborated with Irene Papatheodorou on a bootstrapped inductive logic programming method (bILP) for hypothesis generation on large data sets. The software is available here.
I have a small collection of (perl) scripts, developed in collaboration with Frank Schwach for the analysis and visualisation of data from next-generation sequencing machines. These primarily use the PatMaN tool for alignment of reads to a reference genome and so you will also need this tool in order to use the scripts. Some of the scripts also make use of the R programming language. Frank Schwach's version of the scripts can be found here.
short_read_gbrowse_image.tar.gz: A perl script for producing 'gbrowse'-type images by aligning a set of short reads in FASTA format to a reference genome (also in FASTA format).
short_read_histogram.tar.gz: As above, but uses a short R script to produce a histogram-type image rather than a gbrowse-type image.
run_standard_patman.tar.gz: A wrapper for patman, that produces results in a much more 'R'-friendly manner (i.e., tab-delimited, with counts for each match to the genome).
Selected Publications:
Contact:
Department of Plant Sciences,