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Sökning: WFRF:(Golumbeanu Monica)

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1.
  • Golumbeanu, Monica (författare)
  • Applying Hidden Markov Models to RNA-seq data
  • 2013
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • Enterococcus faecalis is one of the most controversial commensal bacteria of the human intestinal flora that is also responsible for lethal nosocomial infections. Determining the factors that influence its pathogenicity is at present a great challenge. Cutting-edge approaches analyze the E. faecalis bacterium trough the next generation RNA-sequencing technology. Since next generation sequencing is recent and yields a large amount of data, there is a continuous need for appropriate statistical methods to interpret its output. We propose an approach based on hidden Markov models to explore RNA-seq data and show an example of how we can apply this statistical tool to detect transcription start sites. We compare this application with a previously developed method based on signal processing.
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2.
  • Innocenti, Nicolas, 1986-, et al. (författare)
  • Whole-genome mapping of 5′ RNA ends in bacteria by tagged sequencing: a comprehensive view in Enterococcus faecalis
  • 2015
  • Ingår i: RNA. - : RNA Society. - 1355-8382 .- 1469-9001.
  • Tidskriftsartikel (refereegranskat)abstract
    • Enterococcus faecalis is the third cause of nosocomial infections. To obtain the first snapshot of transcriptional organizations in this bacterium, we used a modified RNA-seq approach enabling to discriminate primary from processed 5' RNA ends. We also validated our approach by confirming known features in Escherichia coli. We mapped 559 transcription start sites (TSSs) and 352 processing sites (PSSs) in E. faecalis. A blind motif search retrieved canonical features of SigA-and SigN-dependent promoters preceding transcription start sites mapped. We discovered 85 novel putative regulatory RNAs, small-and antisense RNAs, and 72 transcriptional antisense organizations. Presented data constitute a significant insight into bacterial RNA landscapes and a step toward the inference of regulatory processes at transcriptional and post-transcriptional levels in a comprehensive manner.
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