Pairwise Global Alignment of Protein Interaction Networks by Matching Neighborhood Topology

By Rohit Singh, Jinbo Xu, Bonnie Berger. Annual International Conference on Research in Computational Molecular Biology, 2007

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IsoRankN: spectral methods for global alignment of multiple protein networks (2009, background): “Most notably, these include NetworkBLAST-M (Kalaev et al ., 2008), Græmlin 2.0 (Flannick et al ., 2008) and IsoRank (Singh 2003, 2004; Koyuturk et al ., 2005; Sharan et al ., 2005; Srinivasan et al ., 2006).”
Inferring anchor links across multiple heterogeneous social networks (2013, background): “Network alignment problem has also been studied by many works in recent years, which has many applications bioinformatics [11, 19].”
Predict Anchor Links across Social Networks via an Embedding Approach (2016, background): “…approaches cope with the anchor link prediction problem as a problem of network alignment, which is generally an NP-hard combinatorial optimization problem [Singh et al. , 2007; Klau, 2009; Kollias et al. , 2012], and solve it by ﬁnding certain structural similarity between nodes across networks.”
Topsy-Turvy: integrating a global view into sequence-based PPI prediction (2022, result): “As our dataset and evaluation approach is the same as in Sledzieski et al. (2021), we also include results reported there for two other state-of-the-art sequence-based PPI prediction methods, PIPR (Chen et al.”
PageRank beyond the Web (2014, background): “Singh et al. [2007] proposes a PageRank problem to estimate how much of a match the two nodes are in a diﬀusion sense.”