Effect of sampling on topology predictions of protein-protein interaction networks

By Jing-Dong J. Han, D. Dupuy, Nicolas Bertin, Michael E. Cusick, Marc Vidal. Nature Biotechnology, 2005

352 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bc57e0d433d814143eeaea20005973e3af9ded64

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Citations in the corpus

IsoRankN: spectral methods for global alignment of multiple protein networks (2009, background): “Given a pair of PPI networks, networks, the problem is extended to ﬁnding clusters of The search for such an alignment h p :/ m is motivated by the intuition that evolution of genes occurs within the context of the larger cellular they are part of.”
Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006, background): “Although all currently available networks represent only samples of the complete interactomes [8], the investigation of such partial networks is a first step toward a systems-biology understanding of cells and organisms.”
A human protein-protein interaction network: a resource for annotating the proteome. (2005, positive): “Sixteen interactions from the HPRD data were directly recapitulated in our Y2H data (3%), which is in agreement with currently expected overlap rates between data sets (Formstecher et al., 2005; Han et al., 2005 ).”
Graph theory and networks in Biology. (2006, neutral): “In this subsection, we shall discuss four classical concepts of centrality which have recently been applied to biological interaction networks: (i) Degree centrality; (ii) Closeness centrality; (iii) Betweenness centrality; (iv) Eigenvector centrality.”
Evaluation of clustering algorithms for protein-protein interaction networks (2006, background): “These analyses have led to the observation of some apparently recurrent properties of biological networks: power-law degree distribution, small world, high clustering coefficients, and modularity [10-15].”
Flexible nets (2005, neutral): “[14].”
Structure and dynamics of molecular networks: A novel paradigm of drug discovery: A comprehensive review (2012, background): “Since complex networks are not homogenous, their segments may display different properties than the whole network (Han et al., 2005; Stumpf et al., 2005; Tanaka et al., 2005; Stumpf & Wiuf, 2010; Annibale & Coolen, 2011; Son et al., 2012).”
Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps (2007, background): “This finding is important because light sampling of an ER network (and networks with other degree distributions) can yield a bias toward a power law degree distribution [10,47].”
Evolutionary and Physiological Importance of Hub Proteins (2006, neutral): “action network [1] and the relationship between dispens-”
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners (2008, background): “Also, network coverage to date [21,21-24] is not sufficient to prove scale-free architecture [25].”
Interactome: gateway into systems biology. (2005, background): “Even though existing interactome maps are still far from complete ( 57 ), some of their topological properties are already evident.”