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Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History

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Bioinformatics Research and Applications (ISBRA 2012)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7292))

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Abstract

Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to inferring network evolution history from the topology of PPI networks and the duplication relationship among the paralogs. Simulations show that our approach outperforms the existing ones in terms of the accuracy of reconstruction. Moreover, the growth parameters of several real PPI networks estimated by our method are more consistent with the ones predicted in literature.

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Author information

Authors and Affiliations

  1. Department of Mathematics, National University of Singapore, Singapore, 119076

    Si Li, Kwok Pui Choi, Taoyang Wu & Louxin Zhang

  2. Department of Statistics and Applied Probability, National University of Singapore, Singapore, 119076

    Kwok Pui Choi

Authors
  1. Si Li
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  2. Kwok Pui Choi
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  3. Taoyang Wu
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  4. Louxin Zhang
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Editor information

Editors and Affiliations

  1. Departments of Bioengineering and Electrical Engineering, University of Texas at Dallas, 75080, Richardson, TX, USA

    Leonidas Bleris

  2. Department of Computer Science and Engineering, University of Connecticut, 06269, Storrs, CT, USA

    Ion Măndoiu

  3. Department of Biological Sciences, Carnegie Mellon University, 15213, Pittsburgh, PA, USA

    Russell Schwartz

  4. School of Information Science and Engineering, Central South University, 410083, Changsha, China

    Jianxin Wang

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© 2012 Springer-Verlag Berlin Heidelberg

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Li, S., Choi, K.P., Wu, T., Zhang, L. (2012). Reconstruction of Network Evolutionary History from Extant Network Topology and Duplication History. In: Bleris, L., Măndoiu, I., Schwartz, R., Wang, J. (eds) Bioinformatics Research and Applications. ISBRA 2012. Lecture Notes in Computer Science(), vol 7292. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30191-9_16

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  • DOI: https://doi.org/10.1007/978-3-642-30191-9_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-30190-2

  • Online ISBN: 978-3-642-30191-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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