Our paper on a test for detecting differential effects between two networks involving two types of measurements each is now available online:

Chaturvedi N, Menezes RX, Goeman JJ and van Wieringen WN (2018). A test for detecting differential indirect trans effects between two groups of samples. Statistical Applications in Genetics and Molecular Biology (in press). DOI: 10.1515/sagmb-2017-0058.

It can for example be used to compare gene expression networks built for two subsets of samples, conditional on underlying copy number changes.