Modular organization of cellular networks

By Alexander Rives, Timothy Galitski. Proceedings of the National Academy of Sciences of the United States of America, 2003

729 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c9123dd0a12b6aca7411a5df9be6c9a9ff9c97c2

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In Molecular Biology

Citations in the corpus

Detecting functional modules in the yeast protein-protein interaction network (2006, neutral): “In another study, using shortest-distance as a metric, Rives and Galitski applied a hierarchical clustering algorithm to reveal the modular organization of yeast signaling networks (Rives and Galitski, 2003).”
PINA v2.0: mining interactome modules (2011, background): “It is well established that densely interconnected regions of a global PPI network often correspond to functionally related groups of genes/proteins that can be identified as modules (4).”
Approaches for extracting practical information from gene co-expression networks in plant biology. (2007, background): “1A), there are substructures such as modules (Rives and Galitski 2003), motifs (Milo et al. 2002) and pathways, characterized by topological properties such as degree distribution (Barabasi and Albert 1999), network density (Barnes 1969) and clustering coefficient (Watts and Strogatz 1998).”
Robustness of Cellular Functions (2004, neutral): “(Ravasz et al., 2002), protein-protein interaction (Rives and Galitski, 2003), gene regulatory robustness (Freeman, 2000).”
Estimating the size of the human interactome (2008, neutral): “E(p) = -?TA- = E(pi) = (p), [13]”
Functional classification of proteins for the prediction of cellular function from a protein-protein interaction network (2003, methodology): “For this purpose, we evaluated PRODISTIN against the MRA [28] and two networks-based methods, the GOM [18] and the Rives and Galitski method (RGM [17]).”
Automated Network Analysis Identifies Core Pathways in Glioblastoma (2010, background): “As has been noted by others, clustering of networks into modules can be used to direct experimental research by providing a functional context for previously uncharacterized genes [23].”
clusterMaker: a multi-algorithm clustering plugin for Cytoscape (2011, methodology): “Such network clustering algorithms include Molecular Complex Detection (MCODE) [4], Restricted Neighborhood Search Clustering (RNSC) [5], Super Paramagnetic Clustering (SPC) [6], Markov Clustering (MCL) [7,8], and hierarchical clustering [9].”
CFinder: locating cliques and overlapping modules in biological networks (2006, background): “To identify such modules, a common approach is to search for groups of densely interconnected nodes in the cell’s protein association network (Bader and Hogue, 2003; Rives and Galitski, 2003).”
Integrative approaches for finding modular structure in biological networks (2013, background): “Clustering based on network topology alone has proven instrumental in defining basic principles of modular network organization 7,77,78 .”