Please use this identifier to cite or link to this item: https://doi.org/10.1109/TCBB.2013.14
Title: Maximum likelihood inference of the evolutionary history of a PPI network from the duplication history of its proteins
Authors: Li, S.
Choi, K.P. 
Wu, T.
Zhang, L. 
Keywords: Maximum likelihood inference
Network evolution
Protein-protein interaction network
Issue Date: Nov-2013
Citation: Li, S., Choi, K.P., Wu, T., Zhang, L. (2013-11). Maximum likelihood inference of the evolutionary history of a PPI network from the duplication history of its proteins. IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 (6) : 1412-1421. ScholarBank@NUS Repository. https://doi.org/10.1109/TCBB.2013.14
Abstract: Evolutionary history of protein-protein interaction (PPI) networks provides valuable insight into molecular mechanisms of network growth. In this paper, we study how to infer the evolutionary history of a PPI network from its protein duplication relationship. We show that for a plausible evolutionary history of a PPI network, its relative quality, measured by the so-called loss number, is independent of the growth parameters of the network and can be computed efficiently. This finding leads us to propose two fast maximum likelihood algorithms to infer the evolutionary history of a PPI network given the duplication history of its proteins. Simulation studies demonstrated that our approach, which takes advantage of protein duplication information, outperforms NetArch, the first maximum likelihood algorithm for PPI network history reconstruction. Using the proposed method, we studied the topological change of the PPI networks of the yeast, fruitfly, and worm. © 2013 IEEE.
Source Title: IEEE/ACM Transactions on Computational Biology and Bioinformatics
URI: http://scholarbank.nus.edu.sg/handle/10635/103535
ISSN: 15455963
DOI: 10.1109/TCBB.2013.14
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