Reference point logistic regression and the identification of DNA functional sites

Journal of Classification

Volumn 18, Issue 1, 2001, Pages 81-107

  Hooper, Peter M ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Classification; DNA sequence analysis; Logistic regression; Neural networks; Pattern recognition

Indexed keywords

EID: 0035534112     PISSN: 01764268     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00357-001-0006-1     Document Type: Article

References (38)

1. BANKS, W. J. (1991), "New Solution Algorithms for the Classification Problem," unpublished doctoral thesis, McMaster University, Hamilton, Ontario, Canada.
2. BANKS, W. J., and ABAD, P. L. (1994), "On the Performance of Linear Programming Heuristics Applied on a Quadratic Transformation in the Classification Problem," European Journal of Operational Research, 74, 23-28.
3. BENVENISTE, A., MÉTIVIER, M., and PRIOURET, P. (1990), Adaptive Algorithms and Stochastic Approximations, New York: Springer-Verlag.
4. BREIMAN, L. (1998), "ARCing Classifiers," Annals of Statistics, 26, 801-849.
5. BRIDLE, J. S. (1990), "Probabilistic Interpretation of Feedforward Classification Network Out-puts, with Relationships to Statistical Pattern Recognition," in Neuro-computing: Algorithms, Architectures and Applications, eds F. Fogleman Soulié and J. Hérault, 227-236, Berlin: Springer-Verlag.
6. BURGE, C., and KARLIN, S. (1997), "Prediction of Complete Gene Structures in Human Genomic DNA," Journal of Molecular Biology, 268, 78-94.
7. BURSET, M., and GUIGÓ, R. (1996), "Evaluation of Gene Structure Prediction Programs," Genomics, 34, 353-367.
8. COX, D. R., and SNELL, E. J. (1989), Analysis of Binary Data, New York: Chapman and Hall.
9. CHENG, B., and TITTERINGTON, D. M. (1994), "Neural Networks: A Review from a Statistical Perspective," Statistical Science, 9, 2-30.
10. DUARTE SILVA, A. P. (1995), "Minimizing the Misclassification Costs in Two-Group Classification Analysis," unpublished doctoral dissertation, University of Georgia, Terry College of Business.
11. DUARTE SILVA, A. P., and STAM, A. (1994), "Second Order Mathematical Programming Formulations for Classification in Two-Group Discriminant Analysis," European Journal of Operational Research, 72, 4-22.
12. DUARTE SILVA, A. P., and STAM, A. (1998), "Nonparametric Two-Group Classification: Concepts and a SAS-Based Software Package," American Statistician, 52, 185-197.
13. FICKETT, J. W. (1996), "Finding Genes by Computer: the State of the Art," Trends in Genetics, 12(8), 316-320.
14. FLURY, B. D. (1990), "Principal Points," Biometrika, 77, 33-41.
15. FRIEDMAN, J., HASTIE, T., and TIBSHIRANI, R. (2000), "Additive logistic regression: A statistical view of boosting," Annals of Statistics, 28, 337-407.
16. GLICK, N. (1976), "Sample-Based Classification Procedures Related to Empiric Distributions," IEEE Transactions on Information Theory, IT-22, 454-461.
17. GONICK, L., and WHEELIS, M. (1991), The Cartoon Guide to Genetics, New York: Harper Perennial.
18. GRIFFITHS, A. J. F., MILLER, J. H., SUZUKI, D. T., LEWONTIN, R. C., and GELBART, W. M. (1996), An Introduction to Genetic Analysis, 6th edition, New York: Freeman.
19. HOOPER, P. M. (1999), "Reference Point Logistic Classfication," Journal of Classification, 16, 91-116.
20. HOOPER, P. M. (2001), "Flexible regression modeling with adaptive logistic basis functions," Canadian Journal of Statistics, to appear.
21. HOOPER, P. M., ZHANG, H., and WISHART, D. S. (2000), "Prediction of Genetic Structure in Genomic DNA, using Reference Point Logistic Regression Models and Sequence Alignment," Bioinformatics, 16, 425-438.
22. KOEHLER, G. J., and ERENGUC, S. S. (1990), "Minimizing Misclassifications in Linear Discriminant Analysis," Decision Sciences, 21, 63-85.
23. KOHONEN, T. (1995), Self-Organizing Maps, New York: Springer-Verlag.
24. KULP, D., HAUSSIER, D., REESE, M. G., and EECKMAN, F. H. (1996), "A Generalized Hidden Markov Model for the Recognition of Human Genes in DNA," in Proceedings of the Fourth International Conference on Intelligent System for Molecular Biology, AAAI Press, Menlo Park, CA.
25. MACQUEEN, J. (1967), "Some Methods for Classification and Analysis f Multivariate Observations," in Proceedings of the Fifth Berkeley Symposium on Mathematical Statistics and Probabilty, eds L. M.Le Cam and J. Neyman, 1, 281-297, University of California Press: Berkeley, CA.
26. MICHIE, D., SPIEGELHALTER, D. J., and TAYLOR, C. C. (Eds.) (1994), Machine Learning, Neural and Statistical Classification, New York: Ellis Horwood.
27. MOODY, J. E., and DARKEN, C. (1989), "Fast Learning in Networks of Locally-tuned Processing Units," Neural Computation, 1, 281-294.
28. RIPLEY, B. D. (1996), Pattern Recognition and Neural Networks, Cambridge: Cambridge University Press.
29. ROBBINS, H., and MONRO, S. (1951), "A stochastic approximation method," Annals of Mathematical Statistics, 22, 400-407.
30. ROGOZIN, I. B., and MILANESI, L. (1997), "Analysis of Donor Splice Sites in Different Eukaryotic Organisms," Journal of Molecular Evolution, 45, 50-59.
31. SENAPATHY, P., SHAPIRO, M. B., and HARRIS, N. L. (1990), "Splice Junctions, Branch Point Sites, and Exons: Sequence Statistics, Identification, and Applications to the Genome Project," Methods in Enzymology, 183, 252-278.
32. SNYDER, E. E., and STORMO, G. D. (1995), "Identification of Protein Coding Regions in Genomic DNA," Journal of Molecular Biology, 248, 1-18.
33. SOLOVYEV, V. V., SALAMOV, A. A., and LAWRENCE, C. B. (1994), "Predicting Internal Exons by Oligonucleotide Composition and Discriminant Analysis of Spliceable Open Reading Frames," Nucleic Acids Research, 22, 5156-5163.
34. STADEN, R. (1984), "Computer Methods to Locate Signals in Nucleic Acid Sequences," Nucleic Acids Research, 12, 505-519.
35. STAM, A., and JOACHIMSTHALER, E. A. (1990), "Comparison of a Robust Mixed-Integer Approach to Existing Methods for Establishing Classification Rules for the Discriminant Problem," European Journal of Operational Research, 46, 113-122.
36. STAM, A., and JONES, D. G. (1990), "Classification Performance of Mathematical Programming Techniques in Discriminant Analysis: Results for Small and Medium Sample Sizes," Managerial and Decision Economics, 11, 243-253.
37. TAKANE, Y., BOZDOGAN, H., and SHIBAYAMA, T. (1987), "Ideal Point Discriminant Analysis," Psychometrika, 52, 371-392.
38. ZHANG, M. Q., and MARR, T. G. (1993), "A Weight Array Method for Splicing Signal Analysis," Computer Applications in the Biosciences, 9(5), 499-509.