Dear all, Which are the well used protein protein interaction clustering methods that uses weights/scores given to nodes for module detection ? I know about jActiveModules in Cytoscape and BioNet R package. I don't prefer to use jActiveModules (because of random seed selection for each run, non-repeatable results), and right now I am playing around with BioNet package. I did not come across any other node weighted clusteing methods do you know about any of such algorithms used for ppi interaction clustering or graph clustering in general ?

Edit : I also found out about MINE cytoscape plugin, a perl implementaion of the same plugin takes node weights as input, but the algorithm just uses these scores as a threshold to remove which ever node that doesn't have minimum input score.

Thanks a lot.

Edit 2: I got a chance to talk with a Professor in algorithmic bioinformatics yesterday and what he told me was that what I want is actually called Prize-Collecting Steiner Tree Problem and he suggested using the R Bionet package