Complexity issues in color-preserving graph embeddings
Theoretical Computer Science
Neighborhood based fast graph search in large networks
Proceedings of the 2011 ACM SIGMOD International Conference on Management of data
Tutorial on biological networks
Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery
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ACM Transactions on Knowledge Discovery from Data (TKDD)
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Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
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Summary: NetAlign is a web-based tool designed to enable comparative analysis of protein interaction networks (PINs). NetAlign compares a query PIN with a target PIN by combining interaction topology and sequence similarity to identify conserved network substructures (CoNSs), which may derive from a common ancestor and disclose conserved topological organization of interactions in evolution. To exemplify the application of NetAlign, we perform two genome-scale comparisons with (1) the Escherichia coli PIN against the Helicobacter pylori PIN and (2) the Saccharomyces cerevisiae PIN against the Caenorrhabditis elegans PIN. Many of the identified CoNSs correspond to known complexes; therefore, cross-species PIN comparison provides a way for discovery of conserved modules. In addition, based on the species-to-species differences in CoNSs, we reformulate the problems of protein--protein interaction (PPI) prediction and species divergence from a network perspective. Availability: http://www1.ustc.edu.cn/lab/pcrystal/NetAlign Supplementary Data: Supplementary data are available at Bioinformatics online. Contact:mkteng@ustc.edu.cn, lwniu@ustc.edu.cn