42. Kruglyak L and Storey JD. (2009) Cause and express. Nature Biotechnology, 27: 544-545. [Web Site]
41. Käll L, Storey JD, and Noble WS. (2009) QVALITY: non-parametric estimation of q-values and posterior error probabilities. Bioinformatics, 25: 964-966. [Web Site]
40. Leek JT and Storey JD. (2008) A general framework for multiple testing dependence. Proceedings of the National Academy of Sciences, 105: 18718-18723. [PDF] [Web Site] [Supp Info] [Software]
39. Chen LS and Storey JD. (2008) Eigen-R2 for dissecting variation in high-dimensional studies. Bioinformatics, 24: 2260-2262. [PDF] [Web Site] [Software] [Supp Info]
38. Kall L, Storey JD, and Noble WS. (2008) Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry. Bioinformatics, 24: i42-i48. [PDF] [Web Site] [Software]
37. Hao K, Schadt EE, and Storey JD. (2008) Calibrating the performance of SNP arrays for whole genome association studies. PLoS Genetics, 4: e1000109. [PDF] [Web Site]
36. Biswas S, Storey JD, and Akey JM. (2008) Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis. BMC Bioinformatics, 9: 244. [PDF] [Web Site]
35. Schadt EE, Molony C, Chudin E, Hao K, Yang X, Lum PY, Kasarskis A, Zhang B, Wang S, Suver C, Zhu J, Millstein J, Sieberts S, Lamb J, Guhathakurta G, Derry J, Storey JD, Avila-Campillo I, Kruger MJ, Johnson JM, Rohl CA, van Nas A, Mehrabian M, Drake TA, Lusis AJ, Smith RC, Guengerich FP, Strom SC, Schuetz E, Rushmore TH, and Ulrich R. (2008) Mapping the genetic architecture of gene expression in human liver. PLoS Biology, 6: e107. [PDF] [Web Site]
34. Idaghdour Y, Storey JD, Jadallah S, and Gibson G. (2008) A genome-wide gene expression signature of lifestyle in peripheral blood of Moroccan Amazighs. PLoS Genetics, 4: e1000052. [PDF] [Web Site]
33. Kall L, Storey JD, MacCoss MJ, and Noble WS. (2008) Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. Journal of Proteome Research, 7: 29-34. [PDF] [Web Site]
32. Kall L, Storey JD, MacCoss MJ, and Noble WS. (2008) Posterior error probabilities and false discovery rates: two sides of the same coin. Journal of Proteome Research, 7: 40-44. [PDF] [Web Site]
31. Chen LS, Emmert-Streib F, and Storey JD. (2007) Harnessing naturally randomized transcription to infer regulatory relationships among genes. Genome Biology, 8: R219. [PDF] [Web Site]
30. Dabney AR and Storey JD. (2007) Optimality driven nearest centroid classification from genomic data. PLoS ONE, 2(10): e1002. [PDF] [Web Site] [Software]
29. Leek JT and Storey JD. (2007) Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genetics, 3: e161. [PDF] [Web Site] [Supp Info] [Software]
28. Akey JM, Biswas S, Leek JT, and Storey JD. (2007) On the design and analysis of expression studies in human populations. Nature Genetics, 39: 807-808. [PDF] [Web Site]
27. Dabney AR and Storey JD. (2007) Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships. Genome Biology, 8: R44. [PDF] [Web Site] [Software]
26. Storey JD, Madeoy J, Strout JL, Wurfel M, Ronald J, and Akey JM. (2007) Gene expression variation within and among human populations. American Journal of Human Genetics, 80: 502-509. [PDF] [Web Site] [Synopsis]
25. Storey JD. (2007) The optimal discovery procedure: A new approach to simultaneous significance testing. Journal of the Royal Statistical Society, Series B, 69: 347-368. [PDF] [Web Site]
24. Storey JD, Dai JY, and Leek JT. (2007) The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments. Biostatistics, 8: 414-432. [PDF] [Web Site] [Supp Info] [Software]
23. Dabney AR and Storey JD. (2007) A new approach to intensity-dependent normalization of two-channel microarrays. Biostatistics, 8: 128-139. [PDF] [Web Site]
22. Chen L and Storey JD. (2006) Relaxed significance criteria for linkage analysis. Genetics, 173: 2371-2381. [PDF] [Web Site]
21. Dabney AR and Storey JD. (2006) A reanalysis of a published Affymetrix GeneChip control dataset. Genome Biology, 7: 401. [PDF] [Web Site]
20. Leek JT, Monsen EC, Dabney AR, and Storey JD. (2006) EDGE: Extraction and analysis of differential gene expression. Bioinformatics, 22: 507-508. [PDF] [Software]
19. Storey JD, Xiao W, Leek JT, Tompkins RG, and Davis RW. (2005) Significance analysis of time course microarray experiments. Proceedings of the National Academy of Sciences, 102: 12837-12842. [PDF] [Web Site] [Software]
18. Brem RB*, Storey JD*, Whittle J, and Kruglyak L. (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature, 436: 701-703. *Equal contributors. [PDF]
17. Storey JD, Akey JM, and Kruglyak L. (2005) Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biology, 3(8): 1380-1390. [PDF] [Web Site] [Synopsis]
16. Vaszar LT, Nishimura T, Storey JD, Zhao G, Qiu D, Faul JL, Pearl RG, and Kao PN. (2004) Longitudinal transcriptional analysis of developing neointimal vascular occlusion and pulmonary hypertension in rats. Physiological Genomics, 17: 150-156. [PDF]
15. Storey JD, Taylor JE, and Siegmund D. (2004) Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: A unified approach. Journal of the Royal Statistical Society, Series B, 66: 187-205. [PDF] [Software]
14. Storey JD. (2003) The positive false discovery rate: A Bayesian interpretation and the q-value. Annals of Statistics, 31: 2013-2035. [PDF]
13. Storey JD and Tibshirani R. (2003) Statistical significance for genome-wide studies. Proceedings of the National Academy of Sciences, 100: 9440-9445. [PDF] [Software] [Supp Info]
12. Storey JD. (2003) Invited comment on 'Resampling-based multiple testing for DNA microarray data analysis' by Ge, Dudoit, and Speed. Test, 12: 1-77. [PDF] [Full Paper]
11. Arava Y, Wang Y, Storey JD, Brown PO, and Herschlag D. (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences, 100: 3889-3894. [PDF] [Supp Info]
10. Storey JD and Tibshirani R. (2003) SAM thresholding and false discovery rates for detecting differential gene expression in DNA microarrays. In The Analysis of Gene Expression Data: Methods and Software, by G Parmigiani, ES Garrett, RA Irizarry and SL Zeger (editors). Springer, New York. [Buy Here]
9. Storey JD and Tibshirani R. (2003) Statistical methods for detecting differential gene expression. In Functional Genomics: Methods and Protocols, by MJ Brownstein and AB Khodursky (editors). Methods in Molecular Biology series, Humana Press, Totowa, NJ. [Buy Here]
8. Efron B, Storey JD, and Tibshirani R. (2002) Microarrays, empirical Bayes methods, and false discovery rates. Technical Report 2001-217, Department of Statistics, Stanford University. NOTE: This also appeared in a special issue of Genetic Epidemiology where I was not listed as an author.
7. Storey JD. (2002) A direct approach to false discovery rates. Journal of the Royal Statistical Society, Series B, 64: 479-498. [PDF] [Software] [Supp Info]
6. Wang Y, Liu CL, Storey JD, Tibshirani RJ, Herschlag D, and Brown PO. (2002) Precision and functional specificity in mRNA decay. Proceedings of the National Academy of Sciences, 99: 5860-5865. [PDF] [Supp Info]
5. Clement K, Viguerie N, Diehn M, Alizadeh A, Barbe P, Thalamas C, Storey JD, Brown PO, Barsh GS, and Langin D. (2002) In vivo regulation of human skeletal muscle gene expression by thyroid hormone. Genome Research, 12: 281-291. [PDF]
4. Efron B, Tibshirani R, Storey JD, and Tusher V. (2001) Empirical Bayes analysis of a microarray experiment. Journal of the American Statistical Association, 96: 1151-1160. [PDF]
3. Storey JD and Tibshirani R. (2001) Estimating false discovery rates under dependence, with applications to DNA microarrays. Technical Report 2001-28, Department of Statistics, Stanford University. [PDF] NOTE: This paper was reconceived and rewritten into Storey and Tibshirani (2003) PNAS, which is listed above.
2. Storey JD and Siegmund D. (2001) Approximate p-values for local sequence alignments: numerical studies. Journal of Computational Biology, 8: 549-556. [PDF]
1. Gilbert CL, Kolesar JD, Reiter CA, and Storey JD. (2001) Function digraphs of quadratic maps modulo p. Fibonacci Quarterly, 39: 32-49. [PDF]