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