Discovering Regulatory Overlapping RNA Transcripts

  • Timothy Danford
  • Robin Dowell
  • Sudeep Agarwala
  • Paula Grisafi
  • Gerald Fink
  • David Gifford
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6044)


STEREO is a novel algorithm that discovers cis-regulatory RNA interactions by assembling complete and potentially overlapping same-strand RNA transcripts from tiling expression data. STEREO first identifies coherent segments of transcription and then discovers individual transcripts that are consistent with the observed segments given intensity and shape constraints. We used STEREO to identify 1446 regions of overlapping transcription in two strains of yeast, including transcripts that comprise a new form of molecular toggle switch that controls gene variegation.


Tiling Array SER3 Gene Genomic Interval Stereo Algorithm TATA Element 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Timothy Danford
    • 1
  • Robin Dowell
    • 1
  • Sudeep Agarwala
    • 2
  • Paula Grisafi
    • 2
  • Gerald Fink
    • 2
  • David Gifford
    • 1
  1. 1.Massachusetts Institute of Technology 
  2. 2.Whitehead Institute 

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