Statistical Methods in Systems Biology - Modules and Promoters
Eran Segal's Module Networks paper gave a big push to this sort of analysis.
A slightly different explanation is here.
1. What is Segal trying to do? Is this approach obvious or is it profound?
2. Are the statistical ideas good or merely adequate? How might you improve them?
Harmen Bussemaker's paper was the first to integrate chromatin IP data and gene expression data in order to get at the effectiveness of TF binding in reality.
1. What does it mean to say that the binding of a transcription factor might or might not be effective?
2. What is their statistical methodology?
Martha Bulyk's paper addresses the issue of the contingency of regulation head on.