Detection of functional modules from protein interaction networks

By José B. Pereira-Leal, Anton J. Enright, Christos A. Ouzounis. Proteins: Structure, Function, and Bioinformatics, 2003

457 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2a51f8d5f318a63699ff62076f2417699bee8c3a

How researchers see this paper

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In Computational Theory and Mathematics

1. Stijn van Dongen
2. Min Wu
3. Oliver Mason
4. Chee Keong Kwoh
5. Mark H. A. Verwoerd
6. Ron Shamir
7. Roded Sharan
8. See-Kiong Ng

In Molecular Biology

1. Roded Sharan
2. Igor Ulitsky
3. Stijn van Dongen
4. Ron Shamir
5. Min Wu
6. Xiaoli Li
7. Chee Keong Kwoh
8. See-Kiong Ng

Citations in the corpus

• Computational approaches for detecting protein complexes from protein interaction networks: a survey (2010, methodology): “Fortunately, we have a good representative collection of implemented algorithms for comparison: MCODE [27], RNSC [57], MCL [31], DPClus [38], CFinder [43], DECAFF [16], CORE [86] and COACH [87].”
• Evaluation of clustering algorithms for protein-protein interaction networks (2006, background): “It should be mentioned that MCL and SPC can deal with weighted graphs and are likely to give better performances if the weights reflect the reliability of the links between proteins [20].”
• Network-based prediction of protein function (2007, methodology): “Notably, this comparison used unweighted networks, whereas the MCL and SPC algorithms can deal with weighted graphs and are likely to give better performances if weights are assigned to reflect the reliability of the interactions (Pereira-Leal et al , 2004).”
• Graph Clustering Via a Discrete Uncoupling Process (2008, background): “Other proteinrelated MCL applications in bioinformatics are large scale sequence space analysis [19, 37], hybrid MCL/single-link clustering [29], orthologous groups [41], kinase proteins [24], secreted proteins [7], eye proteins [39], mobile genetic elements [40], protein interaction networks [5, 54”
• A core-attachment based method to detect protein complexes in PPI networks (2009, methodology): “Meanwhile, MCL, DPClus and DECAFF cover only 6, 8 and 8 proteins of the real SAGA complex respectively.”
• Graph theory and networks in Biology. (2006, methodology): “Subsequently, in [181] this algorithm was used to identify functionally related families in the protein interaction network of S.”
• Comparative Genomics in Eukaryotes (2005, background): “Locally densely connected networks reflect stable physical complexes, whereas less connected networks correlate with signaling pathways and transient interactions (Pereira-Leal et al., 2004; Spirin and Mirny, 2003).”