An Improved Map of Conserved Regulatory Sites
You might still remember this paper by Harbison et al. that reported some high-quality S.cerevisiae TF binding sites. Well, now there's a followup by Maclsaac et al.. This time the authors used phylogenetic conservation based algorithms (PhyloCon and Converge) to search for binding sites, and reportedly got even better results than before.
Moreover, the authors provide a nice Python package TAMO for performing basic PWM-matching tasks.