Thomas J. Hardcastle

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:

• Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA.
  Djupedal I, Kos-Braun IC, Mosher RA, Söderholm N, Simmer F, Hardcastle TJ, Fender A, Heidrich N, Kagansky A, Bayne E, Wagner EG, Baulcombe DC, Allshire RC, Ekwall K.
  The EMBO Journal, 2009.
• Chromosomal instability determines taxane response.
  Swanton C, Nicke B, Schuett M, Eklund AC, Ng C, Li Q, Hardcastle T, Lee A, Roy R, East P, Kschischo M, Endesfelder D, Wylie P, Kim SN, Chen JG, Howell M, Ried T, Habermann JK, Auer G, Brenton JD, Szallasi Z, Downward J.
  PNAS, 2009.
• Identifying Patterns of Differential Expression in Count Data.
  Hardcastle, T.J., Kelly, K.A.
  In submission, 2010.
• Empirical Bayesian methods for model testing on array CGH data.
  Hardcastle, T.J., Garcia, M., Brenton J.D., Tavare, S. In submission, 2010.