Discrete Applied Mathematics
Fast algorithms for detecting overlapping functional modules in protein-protein interaction networks
CIBCB'09 Proceedings of the 6th Annual IEEE conference on Computational Intelligence in Bioinformatics and Computational Biology
A graph-theoretic method for mining overlapping functional modules in protein interaction networks
ISBRA'08 Proceedings of the 4th international conference on Bioinformatics research and applications
A hybrid clustering algorithm for identifying modules in Protein Protein Interaction networks
International Journal of Data Mining and Bioinformatics
FRINGE: a new approach to the detection of overlapping communities in graphs
ICCSA'11 Proceedings of the 2011 international conference on Computational science and its applications - Volume Part III
Computational Biology and Chemistry
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
A vertex similarity probability model for finding network community structure
PAKDD'12 Proceedings of the 16th Pacific-Asia conference on Advances in Knowledge Discovery and Data Mining - Volume Part I
International Journal of Bioinformatics Research and Applications
CMSB'12 Proceedings of the 10th international conference on Computational Methods in Systems Biology
Community Detection in Social Networks Using Information Diffusion
ASONAM '12 Proceedings of the 2012 International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2012)
Module-based breast cancer classification
International Journal of Data Mining and Bioinformatics
Proceedings of the 22nd ACM international conference on Conference on information & knowledge management
A unified community detection algorithm in complex network
Neurocomputing
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Motivation: Identification of functional modules in protein interaction networks is a first step in understanding the organization and dynamics of cell functions. To ensure that the identified modules are biologically meaningful, network-partitioning algorithms should take into account not only topological features but also functional relationships, and identified modules should be rigorously validated. Results: In this study we first integrate proteomics and microarray datasets and represent the yeast protein--protein interaction network as a weighted graph. We then extend a betweenness-based partition algorithm, and use it to identify 266 functional modules in the yeast proteome network. For validation we show that the functional modules are indeed densely connected subgraphs. In addition, genes in the same functional module confer a similar phenotype. Furthermore, known protein complexes are largely contained in the functional modules in their entirety. We also analyze an example of a functional module and show that functional modules can be useful for gene annotation. Contact: yuan.33@osu.edu Supplementary Information: Supplementary data are available at Bioinformatics online