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Transcriptional profiling is a useful strategy to study development and disease. Approaches to isolate RNA from specific cell types, or from specific cellular compartments, would extend the power of this strategy. Previous work has shown that isolation of genetically tagged ribosomes (translating ribosome affinity purification; TRAP) is an effective means(More)
BACKGROUND DNA methylation of promoter CpG islands is associated with gene suppression, and its unique genome-wide profiles have been linked to tumor progression. Coupled with high-throughput sequencing technologies, it can now efficiently determine genome-wide methylation profiles in cancer cells. Also, experimental and computational technologies make it(More)
BACKGROUND Global profiling of in vivo protein-DNA interactions using ChIP-based technologies has evolved rapidly in recent years. Although many genome-wide studies have identified thousands of ERα binding sites and have revealed the associated transcription factor (TF) partners, such as AP1, FOXA1 and CEBP, little is known about ERα associated hierarchical(More)
Hypnotic drugs induced sleep is usually different from physiological sleep in restoring body energy. The cause of the differences is not clear. To investigate the differences between these two types of sleep, in this study, hypnotic drug diazepam (DZP) induced sleep was compared with the recovery sleep following sleep deprivation. Power spectral analysis(More)
Deregulation of the transforming growth factor-β (TGFβ) signaling pathway in epithelial ovarian cancer has been reported, but the precise mechanism underlying disrupted TGFβ signaling in the disease remains unclear. We performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) to investigate genome-wide screening of TGFβ-induced SMAD4 binding(More)
How stage-specific enhancer dynamics modulate gene expression patterns essential for organ development, homeostasis and disease is not well understood. Here, we addressed this question by mapping chromatin occupancy of GATA4--a master cardiac transcription factor--in heart development and disease. We find that GATA4 binds and participates in establishing(More)
Trimethylation of histone 3 lysine 27 (H3K27me3) is a critical epigenetic mark for the maintenance of gene silencing. Additional accumulation of DNA methylation in target loci is thought to cooperatively support this epigenetic silencing during tumorigenesis. However, molecular mechanisms underlying the complex interplay between the two marks remain to be(More)
— Complex systems involve the interaction between many processes that may or may not have causal relations to each other. In such systems, discovering causal relations can provide significant insights into the internals of the system and facilitate fault discovery and recovery procedures. In this paper, we provide a novel causality detection algorithm based(More)
Women with advanced stage ovarian cancer (OC) have a five-year survival rate of less than 25%. OC progression is associated with accumulation of epigenetic alterations and aberrant DNA methylation in gene promoters acts as an inactivating "hit" during OC initiation and progression. Abnormal DNA methylation in OC has been used to predict disease outcome and(More)
The correct operation of time-triggered protocols highly depends on the well-synchronized clocks of the system. To maintain the global time, one strict constraint must be exerted on communication activities (e.g. temporal padding and sparse time base etc.), which not only increases complexity of the protocol design but also incurs a penalty in the network(More)