Thomas J Hardcastle
Thomas J Hardcastle
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baySeq: empirical Bayesian methods for identifying differential expression in sequence count data
TJ Hardcastle, KA Kelly
BMC Bioinformatics 11 (1), 422, 2010
Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells
A Molnar, CW Melnyk, A Bassett, TJ Hardcastle, R Dunn, DC Baulcombe
science 328 (5980), 872-875, 2010
The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci  
ER Havecker, LM Wallbridge, TJ Hardcastle, MS Bush, KA Kelly, ...
The Plant Cell 22 (2), 321-334, 2010
Arabidopsis meiotic crossover hot spots overlap with H2A. Z nucleosomes at gene promoters
K Choi, X Zhao, KA Kelly, O Venn, JD Higgins, NE Yelina, TJ Hardcastle, ...
Nature genetics 45 (11), 1327-1336, 2013
Chromosomal instability determines taxane response
C Swanton, B Nicke, M Schuett, AC Eklund, C Ng, Q Li, T Hardcastle, ...
Proceedings of the National Academy of Sciences 106 (21), 8671-8676, 2009
Mobile small RNAs regulate genome-wide DNA methylation
MG Lewsey, TJ Hardcastle, CW Melnyk, A Molnar, A Valli, MA Urich, ...
Proceedings of the National Academy of Sciences 113 (6), E801-E810, 2016
Genomic analysis of genetic heterogeneity and evolution in high-grade serous ovarian carcinoma
SL Cooke, CKY Ng, N Melnyk, MJ Garcia, T Hardcastle, J Temple, ...
Oncogene 29 (35), 4905-4913, 2010
DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis
NE Yelina, C Lambing, TJ Hardcastle, X Zhao, B Santos, IR Henderson
Genes & development 29 (20), 2183-2202, 2015
Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions
K Choi, X Zhao, AJ Tock, C Lambing, CJ Underwood, TJ Hardcastle, ...
Genome Research 28 (4), 532-546, 2018
The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis
BY Chung, TJ Hardcastle, JD Jones, N Irigoyen, AE Firth, DC Baulcombe, ...
Rna 21 (10), 1731-1745, 2015
Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA
I Djupedal, IC Kos‐Braun, RA Mosher, N Söderholm, F Simmer, ...
The EMBO journal 28 (24), 3832-3844, 2009
Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration
CW Melnyk, A Gabel, TJ Hardcastle, S Robinson, S Miyashima, I Grosse, ...
Proceedings of the National Academy of Sciences 115 (10), E2447-E2456, 2018
Recombination rate heterogeneity within Arabidopsis disease resistance genes
K Choi, C Reinhard, H Serra, PA Ziolkowski, CJ Underwood, X Zhao, ...
PLoS genetics 12 (7), e1006179, 2016
Getting a full dose? Reconsidering sex chromosome dosage compensation in the silkworm, Bombyx mori
JR Walters, TJ Hardcastle
Genome Biology and Evolution 3, 491-504, 2011
Generalised empirical Bayesian methods for discovery of differential data in high-throughput biology
TJ Hardcastle
Bioinformatics, 2015
Sex chromosome dosage compensation in Heliconius butterflies: global yet still incomplete?
JR Walters, TJ Hardcastle, CD Jiggins
Genome biology and evolution 7 (9), 2545-2559, 2015
Identifying small interfering RNA loci from high-throughput sequencing data
TJ Hardcastle, KA Kelly, DC Baulcombe
Bioinformatics 28 (4), 457-463, 2012
Regulation of genome‐wide DNA methylation by mobile small RNAs
M Tamiru, TJ Hardcastle, MG Lewsey
new phytologist 217 (2), 540-546, 2018
Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution
TJ Hardcastle, KA Kelly
BMC bioinformatics 14 (1), 1-11, 2013
A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses
Z Wang, TJ Hardcastle, AC Pastor, WH Yip, S Tang, DC Baulcombe
Genes & development 32 (17-18), 1155-1160, 2018
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