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A Method for Querying Conserved Subnetwork in a Large-Scale Biomolecular Network

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High Performance Computing and Applications

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5938))

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Abstract

To uncover conserved pathways using systems biology methods, comparing various kinds of networks among different species or within a species becomes an increasingly important problem. With more and more molecular data being available, most of the current methods cannot deal with the large-scale networks owing to the computational scale limitation on a single PC or workstation. In this paper, we adopted an Immediate Neighbors-in-first Method for the biomolecular network querying problem. In contrast to other methods, we developed the parallel computing algorithm to treat large-scale networks. The efficient parallel performance of the present method is shown by Parkinson’s Disease related protein interaction network.

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Author information

Authors and Affiliations

  1. School of Computer Engineering and Science, Shanghai University, Shanghai, 200072, China

    Jiang Xie, Weibing Feng, Songbei Li, Luwen Zhang & Wu Zhang

  2. Institute of Systems Biology, Shanghai University, Shanghai, 200444, China

    Jiang Xie, Tieqiao Wen & Wu Zhang

  3. CAS, Academy of Mathematics and Systems Science, Beijing, 100080, China

    Shihua Zhang

  4. Department of Electronic Information and Electric Engineering, Changzhou Institute of Technology, Changzhou, 213002, China

    Guoyong Mao

Authors
  1. Jiang Xie
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  2. Weibing Feng
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  3. Shihua Zhang
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  4. Songbei Li
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  5. Guoyong Mao
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  6. Luwen Zhang
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  7. Tieqiao Wen
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  8. Wu Zhang
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Editor information

Editors and Affiliations

  1. School of Computer Engineering and Science, Shanghai University, 200072, Shanghai, P.R. China

    Wu Zhang  & Weiqin Tong  & 

  2. Schulich School of Engineering, University of Calgary, T2N 1N4, Calgary, AB, Canada

    Zhangxin Chen

  3. Department of Mathematics, University of Wyoming, 1000 University Avenue, 82071-3036, Laramie, WY, USA

    Craig C. Douglas

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Xie, J. et al. (2010). A Method for Querying Conserved Subnetwork in a Large-Scale Biomolecular Network. In: Zhang, W., Chen, Z., Douglas, C.C., Tong, W. (eds) High Performance Computing and Applications. Lecture Notes in Computer Science, vol 5938. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-11842-5_65

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  • DOI: https://doi.org/10.1007/978-3-642-11842-5_65

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-11841-8

  • Online ISBN: 978-3-642-11842-5

  • eBook Packages: Computer ScienceComputer Science (R0)

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