I'm interested in seeing papers that describe useful applications of gene/protein networks (for example, in the analysis of transcriptomics studies). The catch is that I'm only interested in networks other than those based on physical protein interactions and gene co-expression. What other kinds of networks are available (and useful)?
Ok, wasn't sure it if fit your goal. But I did a blog post and tip on GRAIL here too: http://blog.openhelix.eu/?p=3037
Interesting, thanks! For reference, the paper describing the GRAIL method is here: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000534, which as Mary mentions is based on literature coexpression (in 250k PubMed abstracts).