Parsimonious reconstruction of network evolution
WABI'11 Proceedings of the 11th international conference on Algorithms in bioinformatics
Statistical model selection methods applied to biological networks
Transactions on Computational Systems Biology III
Comparative analysis of protein networks: hard problems, practical solutions
Communications of the ACM
Reconstruction of network evolutionary history from extant network topology and duplication history
ISBRA'12 Proceedings of the 8th international conference on Bioinformatics Research and Applications
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Molecular interaction networks have emerged as a powerful data source for answering a plethora of biological questions ranging from how cells make decisions to how species evolve. The availability of such data from multiple organisms allows for their analysis from an evolutionary perspective. Indeed, work has emerged recently on network alignment, ancestral network reconstruction, and phylogenetic inference based on networks. In this paper, we address two central issues in the area of evolutionary analysis of molecular interaction networks, namely (1) correcting genetic distances derived from observed differences between networks, and (2) reconstructing ancestral networks from extant ones. We address both issues computationally under the link dynamics and duplication-mutation with complementarity (DMC) evolutionary models. We demonstrate the utility and accuracy of our methods on biological and simulated data.