Predicting protein functions from redundancies in large-scale protein interaction networks

By M. Samanta, Shoudan Liang. Proceedings of the National Academy of Sciences of the United States of America, 2003

306 citations recorded by the source corpus.

Subfields: Cell Biology, Computational Theory and Mathematics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/bc582d778e456278ed36e4b357a81ecd152b4a06

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Citations in the corpus

Uncovering Biological Network Function via Graphlet Degree Signatures (2008, methodology): “Other approaches use the idea of shared neighbors (Samanta and Liang, 2003) or the network flow-based idea (Nabieva et al.”
Ribosome Biogenesis in the Yeast Saccharomyces cerevisiae (2013, background): “654 J. L. Woolford and S. J. Baserga Nop56/Ski1 NOP56; NP_006383 Box C/D Nop5, NOSIC and Nop domains; RNAP I site and KKE/D repeats Lafontaine and Tollervey (2000) Nop58/Nop5 NOP58; NP_057018 Box C/D Nop5, NOSIC, and Nop domains; CCs, RNAP I site, and KKE/D repeats Wu et al. (1998) Snu13 15.5K/NHP2-”
A Transfer Learning Approach and Selective Integration of Multiple Types of Assays for Biological Network Inference (2010, background): “The use of this approach is motivated by the observation that node A is likely to be linked with node B when they share common neighbors in molecular networks (Chua et al., 2006; Samanta & Liang, 2003; Okada et al., 2005).”
Predicting protein functions with message passing algorithms (2004, background): “Among the presently available methods that try to exploit the global PPI network structure to infer yet unknown functions for unclassiﬁed proteins whose interactions with the rest of the graph are at least partially known, there are the so called Neighboring Counting Method 16 , the χ 2 Method 17 , ”
Network-based prediction of protein function (2007, methodology): “Additional similarity measures proposed for using in a hierarchical clustering setting include Czekanovski–Dice distance (Brun et al , 2003) and the statistical signiﬁcance of the number of common interaction partners (Samanta and Liang, 2003).”
Graph theory and networks in Biology. (2006, background): “Work on the link between structural network properties and dynamics is also described, with emphasis on synchronization and disease propagation.”
How complete are current yeast and human protein-interaction networks? (2006, background): “These latter scores either exploit assay-specific features [46] or use simple, but surprisingly effective, statistical criteria for separating true from false-positive interactions [43,47,48].”