Thomas J. Hardcastle

About Me:

I am a post-doctoral researcher working in the Genetics and Epigenetics group of Prof. Sir David 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. At present, this work is motivated by the analysis of small RNA data, particularly with a view to identification of siRNA precursors and the analysis of patterns of differential expression between diverse sample groups.

Selected Publications:

• Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori.
  Walters, JR Hardcastle TJ
  Genome Biology and Evolution, 2011.
  
• baySeq: Empirical Bayesian Methods For Identifying Differential Expression in Sequence Count Data.
  Hardcastle TJ, Kelly, KA
  BMC Bioinformatics, 2010.
• Small Silencing RNAs in Plants Are Mobile and Direct Epigenetic Modification in Recipient Cells.
  Molnar A, Melnyk CW, Bassett A, Hardcastle TJ, Dunn R, Baulcombe DC.
  Science, 2010.
• The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci
  Havecker ER, Wallbridge LM, Hardcastle TJ, Bush MS, Kelly KA, Dunn RM, Schwach F, Doonan JH, Baulcombe DC.
  Plant Cell, 2010.
• Genomic analysis of genetic hetrogeneity and evolution in high-grade serous ovarian carcinoma
  Cooke SL, Ng CKY, Melnyk N, Garcia MJ, Hardcastle TJ, Temple J, Langdon S, Huntsman D, Brenton JD
  Oncogene, 2010.
• 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 TJ, 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.

Invited Speaker/Lecturer:

• Identifying small RNA loci from high-throughput sequencing data.
  MicroRNAs Europe 2011; Biology to Development and Disease.
• Differential expression in count data.
  Advanced RNA-Seq and ChiP-Seq Data Analysis with Bioconductor, European Bioinformatics Institute. 2011.
• Bioinformatics challenges in high-throughput sequencing of small RNAs.
  Applied Bioinformatics in Plant Sciences (COST) 2010.
• Analyses of small RNA sequencing data.
  Deep Sequencing Techniques: Bioscience Applications, Statistical and Computational Practice and Challenges, University of Gothenburg 2010.

Contact:

Department of Plant Sciences,
University of Cambridge,
Downing Street,
CB2 3EA, Cambridge, UK

telephone: +44 1223 748971 

e-mail: x[AT]cam.ac.uk (x = tjh48)