Graph-theoretic methods for overlapping complexes
Modular decomposition of protein-protein interaction networks
Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations
Identifying protein complexes based on an edge weight algorithm and core-attachment structure
A graph modification approach for finding core–periphery structures in protein interaction networks
benefits
extension
concepts used
modules
quotients
iterated quotients
iterated method directly produces results
method used for a specific pathway; a different notion of module may be needed for a different network (authors mentioned Y2H experiments)
benefits
extension
concepts used
benefits
extension
concepts used
chordal theory
cographs
degree of overlap between complexes can be described because of tree structure
clique tree representation of chordal graph
algorithm could fail if chordal graph not generated; could address this
benefits
extension
concepts used
split cluster graphs
monopolar graphs
solve optimization models using integer linear programming + simulated annealing
optimized solution
consider different core-periphery models
high-order common neighbor
structual similarity
distinguishes between overlapping protein and peripheral proteins
reconstruct more reliable networks with less noise