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Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models

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Part of the Lecture Notes in Computer Science book series (LNBI,volume 7534)

Abstract

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.

Keywords

  • Neighbor Join
  • Link Dynamic
  • Corrected Distance
  • Network Alignment
  • Ancestral Reconstruction

These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Zhu, Y., Nakhleh, L. (2012). Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. In: Raphael, B., Tang, J. (eds) Algorithms in Bioinformatics. WABI 2012. Lecture Notes in Computer Science(), vol 7534. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33122-0_5

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  • DOI: https://doi.org/10.1007/978-3-642-33122-0_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-33121-3

  • Online ISBN: 978-3-642-33122-0

  • eBook Packages: Computer ScienceComputer Science (R0)