Skip to main content

Visualization of Influenza Protein Segment HA in Manifold Space

  • Conference paper
Intelligent Information and Database Systems (ACIIDS 2010)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 5990))

Included in the following conference series:

Abstract

Due to the lateral gene transfer, the phylogenetic tree may be inadequate for representing the evolution of Influenza A (H1N1) virus. This work employs the distance invariant manifold [3] to display the collection of influenza A (H1N1) genes in a cubic space. This space provides a global view of the evolution of the virus vividly.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Bao, Y., Bolotov, P., Dernovoy, D., et al.: The Influenza Virus Resource at the National Center for Biotechnology Information. J. Virol. 82, 596–601 (2008)

    Article  Google Scholar 

  2. Bapteste, E., Susko, E., Leigh, J.: Do Orthologous Gene Phylogenies Really Support Tree-thinking? BMC Evol. Biol. 5, 33 (2005)

    Article  Google Scholar 

  3. Cheng, W.-C., Liou, C.-Y.: A Novel Method for Manifold Construction. In: Köppen, M., Kasabov, N., Coghill, G. (eds.) ICONIP 2008, Part II. LNCS, vol. 5507, pp. 3–10. Springer, Heidelberg (2009)

    Google Scholar 

  4. Gonnet, G.H., Cohen, M.A., Benner, S.A.: Exhaustive Matching of the Entire Protein Sequence Database. Science 256, 1443–1445 (1992)

    Article  Google Scholar 

  5. Jain, R., Rivera, M.C., Lake, J.A.: Horizontal Gene Transfer among Genomes: the Complexity Hypothesis. Proc. Natl. Acad. Sci. U.S.A. 96, 3801–3806 (1999)

    Article  Google Scholar 

  6. Kohonen, T.: Self-Organized Formation of Topologically Correct Feature Maps. Biol. Cybern. 43, 59–69 (1982)

    Article  MATH  MathSciNet  Google Scholar 

  7. Larkin, M.A., Blackshields, G., Brown, N.P., et al.: Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948 (2007)

    Article  Google Scholar 

  8. Liou, C.-Y., Chen, H.-T., Huang, J.-C.: Separation of Internal Representations of the Hidden Layer. In: Proceedings of the International Computer Symposium, Workshop on Artificial Intelligence, pp. 26–34 (2000)

    Google Scholar 

  9. Liou, C.-Y., Cheng, W.-C.: Manifold Construction by Local Neighborhood Preservation. In: Ishikawa, M., Doya, K., Miyamoto, H., Yamakawa, T. (eds.) ICONIP 2007, Part II. LNCS, vol. 4985, pp. 683–692. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

  10. Roweis, S.T., Saul, L.K.: Nonlinear Dimensionality Reduction by Locally Linear Embedding. Science 290, 2323–2326 (2000)

    Article  Google Scholar 

  11. Saitou, N., Nei, M.: The Neighbor-joining Method: a New Method for Reconstructing Phylogenetic Trees. Mol. Biol. Evol. 4, 406–425 (1987)

    Google Scholar 

  12. Syvanen, M.: Cross-species Gene Transfer; Implications for a New Theory of Evolution. J. Theor. Biol. 112, 333–343 (1985)

    Article  Google Scholar 

  13. Tenenbaum, J., Silva, V., Langford, J.C.: A Global Geometric Framework for Nonlinear Dimensionality Reduction. Science 290, 2319–2323 (2000)

    Article  Google Scholar 

  14. Epidemic and Pandemic Alert and Response (EPR), Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO, http://www.who.int/csr/disease/avian_influenza/country/cases_table_2009_12_11/en/index.html

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Liou, CY., Cheng, WC. (2010). Visualization of Influenza Protein Segment HA in Manifold Space. In: Nguyen, N.T., Le, M.T., ÅšwiÄ…tek, J. (eds) Intelligent Information and Database Systems. ACIIDS 2010. Lecture Notes in Computer Science(), vol 5990. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-12145-6_16

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-12145-6_16

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-12144-9

  • Online ISBN: 978-3-642-12145-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics