User profiles for Thomas J Hardcastle
Thomas J HardcastleBIOS.health Verified email at cbas.global 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 …
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 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 …
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 …
mediate mRNA cleavage, translational repression, or epigenetic DNA modification. In many …
Arabidopsis meiotic crossover hot spots overlap with H2A.Z nucleosomes at gene promoters
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. …
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 …
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 …
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
During meiosis, homologous chromosomes undergo crossover recombination, which is
typically concentrated in narrow hot spots that are controlled by genetic and epigenetic …
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
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 …
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 …
and has found broad application in recent years. Here we describe a modified profiling …
[HTML][HTML] Recombination rate heterogeneity within Arabidopsis disease resistance genes
Meiotic crossover frequency varies extensively along chromosomes and is typically
concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to …
concentrated in hotspots. As recombination increases genetic diversity, hotspots are predicted to …