Genome-wide pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves hundreds of previously unknown non-coding RNAs. These recently identified transcripts either exist stably in cells (stable unannotated transcripts, SUTs) or are rapidly degraded by the RNA surveillance… (More)
Recent transcription profiling studies have revealed an unanticipatedly large proportion of antisense transcription across eukaryotic and bacterial genomes. However, the extent and significance of antisense transcripts is controversial partly because experimental artifacts are suspected. Here, we present a method to generate clean genome-wide transcriptome… (More)
Genome-wide transcription profiling has revealed extensive expression of non-coding RNAs antisense to genes, yet their functions, if any, remain to be understood. In this study, we perform a systematic analysis of sense-antisense expression in response to genetic and environmental changes in yeast. We find that antisense expression is associated with genes… (More)
The MYST HAT Sas2 is part of the SAS-I complex that acetylates histone H4 lysine 16 (H4 K16Ac) and blocks the propagation of heterochromatin at the telomeres of Saccharomyces cerevisiae. In this study, we investigated Sas2-mediated H4 K16Ac on a genome-wide scale. Interestingly, H4 K16Ac loss in sas2Δ cells outside of the telomeric regions showed a… (More)
We provide self-stabilizing algorithms to obtain and maintain a maximal matching, maximal independent set or minimal dominating set in a given system graph. They converge in linear rounds under a distributed or synchronous daemon. They can be implemented in an ad hoc network by piggy-backing on the beacon messages that nodes already use.
The Set3 histone deacetylase complex (Set3C) binds histone H3 dimethylated at lysine 4 (H3K4me2) to mediate deacetylation of histones in 5'-transcribed regions. To discern how Set3C affects gene expression, genome-wide transcription was analyzed in yeast undergoing a series of carbon source shifts. Deleting SET3 primarily caused changes during transition… (More)
In this paper we propose a new self-stabilizing distributed algorithm for minimal domination protocol in an arbitrary network graph using the synchronous model; the proposed protocol is general in the sense that it can stabilize with every possible minimal dominating set of the graph.
Whole exome sequencing (WES) is increasingly used in research and diagnostics. WES users expect coverage of the entire coding region of known genes as well as sufficient read depth for the covered regions. It is, however, unknown which recent WES platform is most suitable to meet these expectations. We present insights into the performance of the most… (More)
In this paper, we develop a new self-stabilizing (fault tolerant) protocol for publish/subscribe scheme in a P2P network. We provide a complexity analysis of the recovery (stabilization) time of the protocol after arbitrary failures in the network. The protocol converges in at most n 2 (∆ + 1)m + n 3 − n time in the worst case where n, m, and ∆ denote… (More)