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Bioinformatics Contributions to Data Mining

  • Isabelle Bichindaritz
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6171)

Abstract

The field of bioinformatics shows a tremendous growth at the crossroads of biology, medicine, information science, and computer science. Figures clearly demonstrate that today bioinformatics research is as productive as data mining research as a whole. However most bioinformatics research deals with tasks of prediction, classification, and tree or network induction from data. Bioinformatics tasks consist mainly in similarity-based sequence search, microarray data analysis, 2D or 3D macromolecule shape prediction, and phylogenetic classification. It is therefore interesting to consider how the methods of bioinformatics can be pertinent advances in data mining and to highlight some examples of how these bioinformatics algorithms can potentially be applied to domains outside biology.

Keywords

bioinformatics feature selection phylogenetic classification 

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References

  1. 1.
    DOE Human Genome Project. Genome Glossary, http://www.ornl.gov/sci/techresources/Human_Genome/glossary/glossary_b.shtml (accessed April 22, 2010)
  2. 2.
    Miller, P.: Opportunities at the Intersection of Bioinformatics and Health Informatics: A Case Study. Journal of the American Medical Informatics Association 7(5), 431–438 (2000)Google Scholar
  3. 3.
    Felsenstein, J.: Inferring Phylogenies. Sinauer Associates, Inc., Sunderland (2004)Google Scholar
  4. 4.
    Sokal, R.R., Rohlf, F.J.: Biometry. The Principles and Practice of Statistics in Biological Research. W.H. Freeman and Company, New York (2001)Google Scholar
  5. 5.
    Kuonen, D.: Challenges in Bioinformatics for Statistical Data Miners. Bulletin of the Swiss Statistical Society 46, 10–17 (2003)Google Scholar
  6. 6.
    Piatetsky-Shapiro, G., Tamayo, P.: Microarray Data Mining: Facing the Challenges. ACM SIGKDD Explorations Newsletter 5(2), 1–5 (2003)CrossRefGoogle Scholar
  7. 7.
    Annest, A., Bumgarner, R.E., Raftery, A.E., Yeung, K.Y.: Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data. BMC Bioinformatics 10, 10–72 (2009)CrossRefGoogle Scholar
  8. 8.
    Felsenstein, J.: The troubled growth of statistical phylogenetics. Systematic-Biology 50(4), 465–467 (2001)CrossRefGoogle Scholar
  9. 9.
    Maddison, W.P., Maddison, D.R.: MacClade: analysis of phylogeny and character evolution. Version 3.0. Sinauer Associates, Sunderland (1992)Google Scholar
  10. 10.
    Swofford, D.L.: PAUP: Phylogenetic Analysis Using Parcimony. Version 4. Sinauer Associates Inc. (2002)Google Scholar
  11. 11.
    Martins, E.P., Diniz-Filho, J.A., Housworth, E.A.: Adaptation and the comparative method: A computer simulation study. Evolution 56, 1–13 (2002)Google Scholar
  12. 12.
    Meacham, C.A.: A manual method for character compatibility analysis. Taxon 30(3), 591–600 (1981)CrossRefGoogle Scholar
  13. 13.
    Raftery, A.: Bayesian Model Selection in Social Research (with Discussion). In: Marsden, P. (ed.) Sociological Methodology 1995, pp. 111–196. Blackwell, Cambridge (1995)Google Scholar
  14. 14.
    Volinsky, C., Madigan, D., Raftery, A., Kronmal, R.: Bayesian Model Averaging in Proprtional Hazard Models: Assessing the Risk of a Stroke. Applied Statistics 46(4), 433–448 (1997)zbMATHGoogle Scholar
  15. 15.
    Hoeting, J., Madigan, D., Raftery, A., Volinsky, C.: Bayesian Model Averaging: A Tutorial. Statistical Science 14(4), 382–417 (1999)zbMATHCrossRefMathSciNetGoogle Scholar
  16. 16.
    Yeung, K., Bumgarner, R., Raftery, A.: Bayesian Model Averaging: Development of an Improved Multi-Class, Gene Selection and Classification Tool for Microarray Data. Bioinformatics 21(10), 2394–2402 (2005)CrossRefGoogle Scholar
  17. 17.
    Hosmer, D., Lemeshow, S., May, S.: Applied Survival Analysis: Regression Modeling of Time to Event Data, 2nd edn. Wiley Series in Probability and Statistics. Wiley Interscience, Hoboken (2008)zbMATHGoogle Scholar
  18. 18.
    O’Brien, M.J., Lyman, R.L.: Evolutionary Archaeology: Current Status and Future Prospects. Evolutionary Anthropology 11, 26–36 (2002)CrossRefGoogle Scholar
  19. 19.
    Benedetto, D., Caglioti, E., Loreto, V.: Language Trees and Zipping. Physical Review Letters 88(4), 048702-1– 048702-1 (2002)Google Scholar
  20. 20.
    Houkes, W.: Tales of Tools and Trees: Phylogenetic Analysis and Explanation in evolu-tionary Archeology. In: EPSA 2009 2nd Conference of the European Philosophy of Science Association Proceedings (2010), http://philsci-archive.pitt.edu/archive/00005238/

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Isabelle Bichindaritz
    • 1
  1. 1.Institute of Technology / Computer Science and SystemsUniversity of WashingtonTacomaUSA

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