Mining coherent dense subgraphs across massive biological networks for functional discovery

By Haiyan Hu, Xifeng Yan, Yu Huang, Jiawei Han, X. Zhou. Intelligent Systems in Molecular Biology, 2005

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A core-attachment based method to detect protein complexes in PPI networks (2009, methodology): “, minimum cut and normalized cut [10]) are also used for graph partition and thus for detecting protein complexes.”
Comparing Stars: On Approximating Graph Edit Distance (2009, background): “For example, World Wide Web can be considered as a graph whose vertices correspond to static pages and edges correspond to links between pages[7]; in chem-informatics, labelled graphs are suited to express the connectivity of chemical compounds[29]; in bioinformatics, collections of DNA segments in ”
Integrating structured biological data by Kernel Maximum Mean Discrepancy (2006, methodology): “Data For our first experiment, we obtained datasets from Hu et al. (2005). These data comprise gene expression levels of 6661 genes from 39 datasets from several published studies.”