PUBLICATIONS

Authors Year Title Journal Links Topic
Jaffe, Storey, Ji, Leek 2013 Gene set bagging for estimating replicability of gene set analyses arXiv:1301.3933 [stat.ME] [PDF] [Web] StatGen
Marstrand, Storey 2012 Identifying and mapping cell-type specific chromatin programming of gene expression arXiv:1210.3313 [q-bio.QM] [PDF] [Web] Genomics
Desai, Storey 2012 Cross-dimensional inference of dependent high-dimensional data J Am Stat Assoc, 107: 135-151 [PDF] [Web] Statistics
Leek, Johnson, Parker, Jaffe, Storey 2012 The sva package for removing batch effects and other unwanted variation in high-throughput experiments Bioinformatics, 28(6): 882-883 [PDF] [Web] Software
Xiao, ... Storey, ... Davis, Tompkins 2011 A genomic storm in critically injured humans J Exp Med, 208(13): 2581-2590 [Web] Genomics
Desai*, Tan*, Leek, Maier, Tompkins, Storey 2011 Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study PLoS Medicine, 8(9): e1001093 [PDF] [Web] [Data] Genomics
Kanodia, ... Storey, ... Shvartsman 2011 A computational statistics approach for estimating the spatial range of morphogen gradients Development, 138: 4867-4874 [PDF] [Web] StatGen
Mak, Storey 2011 Interview with Nature Biotechnology: New statistical methods for high-throughput sequencing Nature Biotech [PDF] [Web] Genomics
Leek, Storey 2011 The joint null criterion for multiple hypothesis tests Stat Appl Gen and Mol Bio, 10: Art 28. [PDF] [Web] Statistics
Xu, ... Storey, ... Davis, Xiao 2011 Human transcriptome array for high-throughput clinical studies Proc Natl Acad Sci, 108: 3707-3712 [PDF] [Web] Genomics
Woo, Leek, Storey 2011 A computationally efficient modular optimal discovery procedure Bioinformatics, 27: 509-515 [PDF] [Web] Statistics
Gresham, ... Storey, Botstein 2011 System-level analysis of genes and functions affecting survival during nutrient starvation in Saccharomyces cerevisiae Genetics, 187: 299-317 [PDF] [Web] Genomics
Mecham, Nelson, Storey 2010 Supervised normalization of microarrays Bioinformatics, 26: 1308-1315 [PDF] [Web]
[R]
StatGen
Storey 2010 False discovery rates In International Encyclopedia of Statistical Science [PDF] [Web] Statistics
Kruglyak, Storey 2009 Cause and express Nature Biotech, 27: 544-545 [Web] Genomics
Kall, Storey, Noble 2009 QVALITY: non-parametric estimation of q-values and posterior error probabilities Bioinformatics, 25: 964-966 [Web] Proteomics
Leek, Storey 2008 A general framework for multiple testing dependence Proc Natl Acad Sci, 105: 18718-18723 [PDF] [Web]
[R]
Statistics
Chen, Storey 2008 Eigen-R2 for dissecting variation in high-dimensional studies Bioinformatics, 24: 2260-2262 [PDF] [Web] [Supp]
[R]
StatGen
Kall, Storey, Noble 2008 Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry Bioinformatics, 24: i42-i48 [PDF] [Web]
[Soft]
Proteomics
Hao, Schadt, Storey 2008 Calibrating the performance of SNP arrays for whole genome association studies PLoS Genetics, 4: e1000109 [PDF] [Web] Genomics
Biswas, Storey, Akey 2008 Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis BMC Bioinf, 9: 244 [PDF] [Web] Genomics
Schadt, Molony, ... , Storey, et al. 2008 Mapping the genetic architecture of gene expression in human liver PLoS Biology, 6: e107 [PDF] [Web] Genomics
Idaghdour, Storey, Jadallah, Gibson 2008 A genome-wide gene expression signature of lifestyle in peripheral blood of Moroccan Amazighs PLoS Genetics, 4: e1000052 [PDF] [Web] Genomics
Kall, Storey, MacCoss, Noble 2008 Assigning significance to peptides identified by tandem mass spectrometry using decoy databases J Proteome Res, 7: 29-34 [PDF] [Web] Proteomics
Kall, Storey, MacCoss, Noble 2008 Posterior error probabilities and false discovery rates: two sides of the same coin J Proteome Res, 7: 40-44 [PDF] [Web] Proteomics
Chen, Emmert-Streib, Storey 2007 Harnessing naturally randomized transcription to infer regulatory relationships among genes Genome Biology, 8: R219 [PDF] [Web]
[R]
StatGen
Dabney, Storey 2007 Optimality driven nearest centroid classification from genomic data PLoS ONE, 2(10): e1002 [PDF] [Web]
[R]
StatGen
Leek, Storey 2007 Capturing heterogeneity in gene expression studies by surrogate variable analysis PLoS Genetics, 3: e161 [PDF] [Web] [Supp]
[R]
StatGen
Akey, Biswas, Leek, Storey 2007 On the design and analysis of expression studies in human populations Nature Genetics, 39: 807-808 [PDF] [Web] Genomics
Dabney, Storey 2007 Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships Genome Biology, 8: R44 [PDF] [Web]
[R]
StatGen
Storey, ... Akey 2007 Gene expression variation within and among human populations Am J Hum Gen, 80: 502-509 [PDF] [Web] Genomics
Storey 2007 The optimal discovery procedure: A new approach to simultaneous significance testing J Roy Stat Soc, Ser B, 69: 347-368 [PDF] [Web] Statistics
Storey, Dai, Leek 2007 The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments Biostatistics, 8: 414-432 [PDF] [Web] [Supp]
[R]
StatGen
Dabney, Storey 2007 A new approach to intensity-dependent normalization of two-channel microarrays Biostatistics, 8: 128-139 [PDF] [Web] StatGen
Chen, Storey 2006 Relaxed significance criteria for linkage analysis Genetics, 173: 2371-2381 [PDF] [Web] StatGen
Dabney, Storey 2006 A reanalysis of a published Affymetrix GeneChip control dataset Genome Biology, 7: 401 [PDF] [Web] Genomics
Leek, Monsen, Dabney, Storey 2006 EDGE: Extraction and analysis of differential gene expression Bioinformatics, 22: 507-508 [PDF]
[R]
Software
Storey, Xiao, Leek, Tompkins, Davis 2005 Significance analysis of time course microarray experiments Proc Natl Acad Sci, 102: 12837-12842 [PDF] [Web]
[R]
StatGen
Storey*, Brem*, Whittle, Kruglyak 2005 Genetic interactions between polymorphisms that affect gene expression in yeast Nature, 436: 701-703 [PDF] Genomics
Storey, Akey, Kruglyak 2005 Multiple locus linkage analysis of genomewide expression in yeast PLoS Biology, 3(8): 1380-1390 [PDF] [Web] StatGen
Vaszar, ... Storey, ... Kao 2004 Longitudinal transcriptional analysis of developing neointimal vascular occlusion and pulmonary hypertension in rats Physiological Genomics, 17: 150-156 [PDF] Genomics
Storey, Taylor, Siegmund 2004 Strong control, conservative point estimation, and simultaneous conservative consistency of false discovery rates: A unified approach J Roy Stat Soc, Ser B, 66: 187-205 [PDF]
[R]
Statistics
Storey 2003 The positive false discovery rate: A Bayesian interpretation and the q-value Ann Stat, 31: 2013-2035 [PDF] Statistics
Storey, Tibshirani 2003 Statistical significance for genome-wide studies Proc Natl Acad Sci, 100: 9440-9445 [PDF] [Web] [Supp]
[R]
StatGen
Arava, Wang, Storey, Brown, Herschlag 2003 Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae Proc Natl Acad Sci, 100: 3889-3894 [PDF] [Supp] Genomics
Storey, Tibshirani 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 [Web] StatGen
Storey, Tibshirani 2003 Statistical methods for detecting differential gene expression In Functional Genomics: Methods and Protocols [Web] StatGen
Efron, Storey, Tibshirani 2002 Microarrays, empirical Bayes methods, and false discovery rates Tech Report 2001-217, Dept Stat, Stanford University [PDF] Statistics
Storey 2002 A direct approach to false discovery rates J Roy Stat Soc, Ser B, 64: 479-498 [PDF] [Supp]
[R]
Statistics
Wang, Liu, Storey, ... Brown 2002 Precision and functional specificity in mRNA decay Proc Natl Acad Sci, 99: 5860-5865 [PDF] [Supp] Genomics
Clement, ... Storey, ... Langin 2002 In vivo regulation of human skeletal muscle gene expression by thyroid hormone Genome Research, 12: 281-291 [PDF] Genomics
Efron, Tibshirani, Storey, Tusher 2001 Empirical Bayes analysis of a microarray experiment J Am Stat Assoc, 96: 1151-1160 [PDF] StatGen
Storey, Tibshirani 2001 Estimating false discovery rates under dependence, with applications to DNA microarrays Tech Report 2001-28, Dept Stat, Stanford Univ [PDF] Statistics
Storey, Siegmund 2001 Approximate p-values for local sequence alignments: numerical studies J Comp Bio, 8: 549-556 [PDF] StatGen
Gilbert, Kolesar, Reiter, Storey 2001 Function digraphs of quadratic maps modulo p Fibonacci Quarterly, 39: 32-49 [PDF] Maths