Few papers that have come out recently that are of interest (some to be reviewed later)

A yeast-one-hybrid approach for mapping p-dna binding in vitro in elegans ( specied where chip/chip doesnt work)
A gene-centered C. elegans protein-DNA interaction network. Cell 2006

This one talks about the stability of using arrays for classification
Reliable gene signatures for microarray classification: assessment of stability and performance. Bioinformatics

Talks about designing drugs specifically toward protein-protein interactions
Rational drug design via intrinsically disordered protein. Trends in Biotechnology 2006

Also
A direct comparison of protein interaction confidence assignment schemes. BMC Bioinformatics
Suthram S, Shlomi T, Ruppin E,Sharan R, Ideker T