User profiles for Thomas J Hardcastle

Thomas J Hardcastle

BIOS.health
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Cited by 4793

[HTML][HTML] baySeq: empirical Bayesian methods for identifying differential expression in sequence count data

TJ Hardcastle, KA Kelly - BMC bioinformatics, 2010 - Springer
Background High throughput sequencing has become an important technology for studying
expression levels in many types of genomic, and particularly transcriptomic, data. One key …

Small silencing RNAs in plants are mobile and direct epigenetic modification in recipient cells

A Molnar, CW Melnyk, A Bassett, TJ Hardcastle… - science, 2010 - science.org
A silencing signal in plants with an RNA specificity determinant moves through plasmodesmata
and the phloem. To identify the mobile RNA, we grafted Arabidopsis thaliana shoots to …

The Arabidopsis RNA-Directed DNA Methylation Argonautes Functionally Diverge Based on Their Expression and Interaction with Target Loci

ER Havecker, LM Wallbridge, TJ Hardcastle… - The Plant …, 2010 - academic.oup.com
Argonaute (AGO) effectors of RNA silencing bind small RNA (sRNA) molecules and
mediate mRNA cleavage, translational repression, or epigenetic DNA modification. In many …

Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters

…, O Venn, JD Higgins, NE Yelina, TJ Hardcastle… - Nature …, 2013 - nature.com
PRDM9 directs human meiotic crossover hot spots to intergenic sequence motifs, whereas
budding yeast hot spots overlap regions of low nucleosome density (LND) in gene promoters. …

Mobile small RNAs regulate genome-wide DNA methylation

MG Lewsey, TJ Hardcastle… - Proceedings of the …, 2016 - National Acad Sciences
RNA silencing at the transcriptional and posttranscriptional levels regulates endogenous
gene expression, controls invading transposable elements (TEs), and protects the cell against …

Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis thaliana transposons and gene regulatory regions

…, TJ Hardcastle, H Serra, J Kim, HS Cho, J Kim… - Genome …, 2018 - genome.cshlp.org
Meiotic recombination initiates from DNA double-strand breaks (DSBs) generated by SPO11
topoisomerase-like complexes. Meiotic DSB frequency varies extensively along eukaryotic …

DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination in Arabidopsis

NE Yelina, C Lambing, TJ Hardcastle… - Genes & …, 2015 - genesdev.cshlp.org
During meiosis, homologous chromosomes undergo crossover recombination, which is
typically concentrated in narrow hot spots that are controlled by genetic and epigenetic …

Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration

CW Melnyk, A Gabel, TJ Hardcastle… - Proceedings of the …, 2018 - National Acad Sciences
The ability for cut tissues to join and form a chimeric organism is a remarkable property of
many plants; however, grafting is poorly characterized at the molecular level. To better …

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… - Rna, 2015 - rnajournal.cshlp.org
Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation
and has found broad application in recent years. Here we describe a modified profiling …

[HTML][HTML] Recombination rate heterogeneity within Arabidopsis disease resistance genes

…, CJ Underwood, X Zhao, TJ Hardcastle… - PLoS …, 2016 - journals.plos.org
Meiotic crossover frequency varies extensively along chromosomes and is typically
concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to …