Augmenting the bootstrap to analyze high dimensional genomic data

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Volumn 17, Issue 1, 2008, Pages 1-18

  Tyekucheva, Svitlana ^a   Chiaromonte, Francesca ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Genomics; Inverse covariance; Large p small n; Resampling

Indexed keywords

EID: 40949165781     PISSN: 11330686     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11749-008-0098-6     Document Type: Article

References (31)

1. Breiman L (1996) Bagging predictors. Mach Learn 24(2):123-140
2. Buhlmann P, Yu B (2002) Analyzing bagging. Ann Stat 30(4):927-961
3. Carrel L, Willard HF (2005) X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434:400-404
4. Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, Makova KD (2006) Genomic environment predicts expression patterns on the human inactive x chromosome. PLoS Genet 2(9):1477-1486
5. Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D (1997) Genetic and physical maps of saccharomyces cerevisiae. Nature 387:67-73
6. Cook RD, Li B, Chiaromonte F (2007) Dimension reduction in regression without matrix inversion. Biometrika 94(3):569-584
7. De Angelis D, Young GA (1992) Smoothing the bootstrap. Int Stat Rev 60(1):45-56
8. Efron B (1979) Bootstrap methods: another look at jackknife. Ann Stat 7:1-26
9. Fernholz L (1983) Von Mises calculus for statistical functionals. Lecture notes in statistics, vol 19. Springer, New York
10. Friedman J, Hall P (2000) On bagging and nonlinear estimation. Preprint
11. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11(12):4241-4257
12. Gunsalus K, Ge H, Schetter A, Goldberg D, Han JDJ, Hao T, Berriz G, Bertin N, Huang J, Chuang LS, Li N, Mani R, Hyman A, Sonnichsen B, Echeverri C, Roth F, Vidal M, Piano F (2005) Predictive models of molecular machines involved in caenorhabditis elegans early embryogenesis. Nature 436:861-865
13. Hall P, DiCiccio T, Romano JP (1989) On smoothing and the bootstrap. Ann Stat 17(2):692-704
14. Hastie T, Tibshirani R, Friedman J (2001) The elements of statistical learning: data mining, inference, and prediction. Springer, New York
15. Helland IS (1990) On structure of partial least squares regression. Scand J Stat 17:97-114
16. Kamat AR (1981) Incomplete and absolute moments of the multivariate normal distribution with some applications. Biometrika 40(1/2):20-34
17. Lashkari DA, De Risi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. PNAS USA 94(24):13057-13062
18. Ledoit O, Wolf M (2003) Improved estimation of the covariance matrix of stock returns with an application to portfolio selection. J Empir Finance 10:603-621
19. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, Zeitlinger J, Jennings EG, Murray HL, Gordon DB, Ren B, Wyrick JJ, Tagne JB, Volkert TL, Fraenkel E, Gifford DK, Young RA (2002) Transcriptional regulatory networks in saccharomyces cerevisiae. Science 298(5594):799-804
20. Lezon TR, Banavar JR, Cieplak M, Maritan A, Fedoroff NV (2006) Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. PNAS USA 103:19033-19038
21. Li KC (1991) Sliced inverse regression for dimension reduction. JASA 86(414):316-327
22. Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford
23. Penrose RA (1955) A generalized inverse for matrices. Proc Camb Philos Soc 51:406-413
24. Rao CR, Mitra SK (1971) Generalized inverse of matrices and its applications. Wiley, New York
25. Raudys S, Duin RPW (1998) Expected classification error of the Fisher linear classifier with pseudoinverse covariance matrix. Pattern Recogn Lett 19:385-392
26. Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K, Muzny D, Platzer M, Howell GR, Burrows C, Bird CP et al. (2005) The DNA sequence of the human X chromosome. Nature 434:325-337
27. Schäfer J, Strimmer K (2005a) An empirical Bayes approach to inferring large-scale gene association networks. Bioinformatics 21(6):754-764
28. Schäfer J, Strimmer K (2005b) A shrinkage approach to large-scale covariance matrix estimation and implications for functional genomics. Stat Appl Genet Mol Biol 4(1):32
29. Silverman BW, Young GA (1987) The bootstrap: to smooth or not to smooth? Biometrika 74:469-479
30. Werner-Washburne M, Braun E, Johnston GC, Singer RA (1993) Stationary phase in the yeast saccharomyces cerevisiae. Microbiol Mol Biol Rev 57(2):383-401
31. Whittaker J (1990) Graphical models in applied multivariate statistics. Wiley, New York