Topological structure analysis of the protein-protein interaction network in budding yeast.

By Dongbo Bu, Yi Zhao, Lun Cai, Hong Xue, Xiaopeng Zhu, Hongchao Lu, Jingfen Zhang, Shiwei Sun, L. Ling, Nan Zhang and 2 more. Nucleic Acids Research, 2003

803 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8bb59186aeb4c89fef881284be4877e237e753bc

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In Computational Theory and Mathematics

In Molecular Biology

Citations in the corpus

Toward link predictability of complex networks (2015, background): “We consider the following 10 real-world networks drawn from disparate fields: ( i ) Jazz (37), a collaboration network of jazz musicians consists of 198 nodes and 2742 interactions; ( ii ) Metabolic (38), the metabolic network of Caenorhabditis elegans ; ( iii ) Neural (32), the neural network of C.”
Reconstruction of cellular signalling networks and analysis of their properties (2005, background): “At the level of individual protein function, SPECTRAL ANALYSIS defined groups of protein–protein interactions that had functional significance in the yeast proteom”
Network Properties Revealed through Matrix Functions (2010, neutral): “In Figure 8 we show results for a yeast protein-protein interaction network, taken from [12] based on data from [69].”
Computational approaches for detecting protein complexes from protein interaction networks: a survey (2010, background): “The statistical significance of the occurrence of a protein cluster (predicted protein complex) with respect to a given functional annotation can be computed by the following hypergeometric distribution in equation (9) [88,89]:”
Network-based prediction of protein function (2007, methodology): “Additional graph clustering techniques applied include clique percolation (Adamcsek et al , 2006), graph ﬂow simulation (Pereira-Leal et al , 2004), edge-betweenness clustering (Dunn et al , 2005) and spectral methods (Bu et al , 2003).”
Infinite multiple membership relational modeling for complex networks (2011, neutral): “4 Protein-protein interacti on network [18] USPower 4,941 6,594 0.”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “Motifs proved to be efficient in predicting protein function, protein–protein interactions and development of drug screening techniques (Bu et al., 2003; Albert & Albert, 2004; Luni et al., 2010; Cloutier & Wang, 2011).”
Graph theory and networks in Biology. (2006, methodology): “Finally, we note that in [182], a technique for identifying quasi-cliques in protein interaction networks based on the eigenvectors of the network’s adjacency matrix was described and applied to the yeast interaction network.”
Functional topology in a network of protein interactions (2004, methodology): “A larger study on 11 855 interactions among 2617 proteins in budding yeast used a spectral analysis method to predict function of 76 uncharacterized proteins (Bu et al., 2003).”
Analysis of global control of Escherichia coli carbohydrate uptake (2007, neutral): “The idea of using a variant of the singular value decomposition for decomposing an adjacency matrix has been proposed by several authors [42-45].”
Protein complex prediction via cost-based clustering (2004, methodology): “This is also true for dense regions of PPI networks (Bu et al., 2003; Př zulj et al., 2004).”