Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks

By Jacob Scott, Trey Ideker, Richard M. Karp, Roded Sharan. Annual International Conference on Research in Computational Molecular Biology, 2005

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Network-based prediction of protein function (2007, background): “The purpose of some algorithms is the detection of molecular complexes, but others can also detect sparser structures, such as signaling pathways (Steffen et al , 2002; Yeang et al , 2005; Scott et al , 2006).”
Integrative approaches for finding modular structure in biological networks (2013, methodology): “Different scoring functions have assumed scores on network nodes 48 or edges 41,58 or both 59 ; or constrained scores by network topology 56 or signal content 44 ; or are prioritized by high-scoring ‘seed’ nodes 60 , including using strategies for computational colour coding of ‘seed’ paths 51,55 .”
Protein networks in disease. (2008, methodology): “Beyond enriched motifs, methods have been devised to identify all sorts of network structures, such as densely connected network regions (for review, see Brohee and van Helden 2006), which are suggestive of protein complexes, and paths of interactions connecting membrane proteins to transcription fa”