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Best of 2006-2007

Best of 2007-2008

Past Reading


Next meeting

  • 11/19 at 10am in the Steele library.


  • Activity motifs
  • principles of timing
  • transcriptional control
  • yeast
  • metabolic networks


  1. Chechik G, Oh E, Rando O, Weissman J, Regev A, and Koller D. Activity motifs reveal principles of timing in transcriptional control of the yeast metabolic network. Nat Biotechnol. 2008 Nov;26(11):1251-9. DOI:10.1038/nbt.1499 | PubMed ID:18953355 | HubMed [stricker]


Promising, but ultimately disappointing. The curve fitting to the mRNA data was not convincing (the shape of the data did not match the fit). Measurements (mRNA and ChIP-chip in particular) should probably have large error bars, bringing fine distinctions in timing or affinity into question. Time resolution was also questionable - the first measurement was taken at 15 minutes, but differences in activation time of 3 minutes vs. 4 minutes were treated as significant. No data was presented to support the claim on correlation between binding affinity motifs and transcriptional activation motifs, and the conclusions were presented in a confusing fashion (why claim that 20/48 data sets showed correlation, rather than breaking things out by individual motifs?).