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A User’s Guide to the Encyclopedia of DNA Elements (ENCODE)
The ENCODE Project Consortium (Shirley Pepke)
PLoS Biol 9(4): e1001046.doi:10.1371/journal.pbio.1001046
(link)
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High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
Genome Res. Published in Advance March 7, 2011,doi:10.1101/gr.104018.10
Anil Ozdemir, Katherine I. Fisher-Aylor, Shirley Pepke, Manoj Samanta, Leslie Dunipace, Kenneth McCue, Lucy Zeng, Nobuo Ogawa, Barbara J. Wold, and Angelike Stathopoulos
(Link)
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Computation for Chip-seq and RNA-seq studies
Nature Methods 6, S22-S32,15 October 2009.
Shirley Pepke, Barbara Wold, and Ali Mortazavi