John D Storey

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. ncbi request reprint The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Biostatistics 8:414-32. 2007
  2. pmc A reanalysis of a published Affymetrix GeneChip control dataset
    Alan R Dabney
    Genome Biol 7:401. 2006
  3. pmc Significance analysis of time course microarray experiments
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 102:12837-42. 2005
  4. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003
  5. pmc Multiple locus linkage analysis of genomewide expression in yeast
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, Washington, USA
    PLoS Biol 3:e267. 2005
  6. doi request reprint Gene set bagging for estimating the probability a statistically significant result will replicate
    Andrew E Jaffe
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205, USA
    BMC Bioinformatics 14:360. 2013
  7. pmc Capturing heterogeneity in gene expression studies by surrogate variable analysis
    Jeffrey T Leek
    Department of Biostatistics, University of Washington, Seattle, Washington, USA
    PLoS Genet 3:1724-35. 2007
  8. pmc Calibrating the performance of SNP arrays for whole-genome association studies
    Ke Hao
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Genet 4:e1000109. 2008
  9. pmc A computationally efficient modular optimal discovery procedure
    Sangsoon Woo
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 27:509-15. 2011
  10. pmc Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry
    LUKAS KALL
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Bioinformatics 24:i42-8. 2008

Detail Information

Publications31

  1. ncbi request reprint The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Biostatistics 8:414-32. 2007
    ..Our proposed microarray method is freely available to academic users in the open-source, point-and-click EDGE software package...
  2. pmc A reanalysis of a published Affymetrix GeneChip control dataset
    Alan R Dabney
    Genome Biol 7:401. 2006
    ..A response to Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset by SE Choe, M Boutros, AM Michelson, GM Church and MS Halfon. Genome Biology 2005, 6:R16...
  3. pmc Significance analysis of time course microarray experiments
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 102:12837-42. 2005
    ..The methodology proposed here has been implemented in the freely distributed and open-source edge software package...
  4. pmc Statistical significance for genomewide studies
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Proc Natl Acad Sci U S A 100:9440-5. 2003
    ..Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage...
  5. pmc Multiple locus linkage analysis of genomewide expression in yeast
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, Washington, USA
    PLoS Biol 3:e267. 2005
    ..In addition, we show that a two-dimensional scan does not truly allow one to test for simultaneous linkage, and the statistical significance measured from this existing method cannot be interpreted among many traits...
  6. doi request reprint Gene set bagging for estimating the probability a statistically significant result will replicate
    Andrew E Jaffe
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205, USA
    BMC Bioinformatics 14:360. 2013
    ..Gene set bagging involves resampling the original high-throughput data, performing gene-set analysis on the resampled data, and confirming that biological categories replicate in the bagged samples...
  7. pmc Capturing heterogeneity in gene expression studies by surrogate variable analysis
    Jeffrey T Leek
    Department of Biostatistics, University of Washington, Seattle, Washington, USA
    PLoS Genet 3:1724-35. 2007
    ..We apply SVA to disease class, time course, and genetics of gene expression studies. We show that SVA increases the biological accuracy and reproducibility of analyses in genome-wide expression studies...
  8. pmc Calibrating the performance of SNP arrays for whole-genome association studies
    Ke Hao
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Genet 4:e1000109. 2008
    ....
  9. pmc A computationally efficient modular optimal discovery procedure
    Sangsoon Woo
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 27:509-15. 2011
    ..However, their ODP estimator grows quadratically in computational time with respect to the number of genes. Reducing this computational burden is a key step in making the ODP practical for usage in a variety of high-throughput problems...
  10. pmc Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry
    LUKAS KALL
    Department of Genome Sciences, University of Washington, Seattle, WA, USA
    Bioinformatics 24:i42-8. 2008
    ..cult than the related problem of estimating the error rate associated with a large collection of PSMs. Existing methods for estimating PEPs rely on a parametric or semiparametric model of the underlying score distribution...
  11. pmc Gene-expression variation within and among human populations
    John D Storey
    Department of Biostatistics, University of Washington, Seattle, WA 98195 7730, USA
    Am J Hum Genet 80:502-9. 2007
    ..These results provide the first insight into how human population structure manifests itself in gene-expression levels and will help guide the search for regulatory quantitative trait loci...
  12. ncbi request reprint EDGE: extraction and analysis of differential gene expression
    Jeffrey T Leek
    Department of Biostatistics, University of Washington, Seattle 98195, USA
    Bioinformatics 22:507-8. 2006
    ..EDGE can perform both standard and time course differential expression analysis. The functions are based on newly developed statistical theory and methods. This document introduces the EDGE software package...
  13. pmc Mapping gene expression quantitative trait loci by singular value decomposition and independent component analysis
    Shameek Biswas
    Department of Genome Sciences, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA
    BMC Bioinformatics 9:244. 2008
    ..In addition, gene expression traits exhibit a complex correlation structure, which is ignored when analyzing traits individually...
  14. ncbi request reprint Assigning significance to peptides identified by tandem mass spectrometry using decoy databases
    LUKAS KALL
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    J Proteome Res 7:29-34. 2008
    ..We first describe a simple FDR inference method and then describe how estimating and taking into account the percentage of incorrectly identified spectra in the entire data set can lead to increased statistical power...
  15. pmc Relaxed significance criteria for linkage analysis
    Lin Chen
    Department of Biostatistics, University of Washington, Seattle, Washington 98195, USA
    Genetics 173:2371-81. 2006
    ..A generalized version of the GWER is proposed, called GWERk, that allows one to provide a more liberal balance between true positives and false positives at no additional cost in computation or assumptions...
  16. pmc Mapping the genetic architecture of gene expression in human liver
    Eric E Schadt
    Rosetta Inpharmatics, Seattle, Washington, United States of America
    PLoS Biol 6:e107. 2008
    ..We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process...
  17. pmc Harnessing naturally randomized transcription to infer regulatory relationships among genes
    Lin S Chen
    Department of Biostatistics, University of Washington, 1705 NE Pacific St, Seattle, WA 98195, USA
    Genome Biol 8:R219. 2007
    ..We apply the method to an experiment in yeast, in which genes known to be in the same processes and functions are recovered in the resulting transcriptional regulatory network...
  18. pmc Supervised normalization of microarrays
    Brigham H Mecham
    Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
    Bioinformatics 26:1308-15. 2010
    ..However, the most popular normalization approaches do not utilize what is known about the study, both in terms of the biological variables of interest and the known technical factors in the study, such as batch or array processing date...
  19. ncbi request reprint A new approach to intensity-dependent normalization of two-channel microarrays
    Alan R Dabney
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Biostatistics 8:128-39. 2007
    ..We show that CADS removes both dye bias and array-specific effects, and preserves the true differential expression signal for every gene under the assumptions of the model...
  20. pmc The sva package for removing batch effects and other unwanted variation in high-throughput experiments
    Jeffrey T Leek
    Department of Biostatistics, JHU Bloomberg School of Public Health, Baltimore, MD, USA
    Bioinformatics 28:882-3. 2012
    ..The sva package supports surrogate variable estimation with the sva function, direct adjustment for known batch effects with the ComBat function and adjustment for batch and latent variables in prediction problems with the fsva function...
  21. pmc Genetic interactions between polymorphisms that affect gene expression in yeast
    Rachel B Brem
    Program in Computational Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue N, M2 B876, Seattle, Washington 98109, USA
    Nature 436:701-3. 2005
    ..Our results indicate that genetic interactions are widespread in the genetics of transcript levels, and that many QTLs will be missed by single-locus tests but can be detected by two-stage tests that allow for interactions...
  22. ncbi request reprint Posterior error probabilities and false discovery rates: two sides of the same coin
    LUKAS KALL
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
    J Proteome Res 7:40-4. 2008
    ..Here, we explain how two types of scores, the q-value and the posterior error probability, are related and complementary to one another...
  23. doi request reprint Eigen-R2 for dissecting variation in high-dimensional studies
    Lin S Chen
    Lewis Sigler Institute and Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
    Bioinformatics 24:2260-2. 2008
    ..We apply eigen-R(2) to two real-life examples and compare it with simply averaging R(2) over many features...
  24. pmc Optimality driven nearest centroid classification from genomic data
    Alan R Dabney
    Department of Statistics, Texas A and M University, College Station, Texas, United States of America
    PLoS ONE 2:e1002. 2007
    ..We apply the proposed method to clinical classification based on gene-expression microarrays, demonstrating that the proposed method can outperform existing nearest centroid classifiers...
  25. pmc In vivo regulation of human skeletal muscle gene expression by thyroid hormone
    Karine Clement
    Department of Pediatrics and Genetics, Howard Hughes Medical Institute, Beckman Center, Stanford University School of Medicine, Stanford, California 94305, USA
    Genome Res 12:281-91. 2002
    ..These results define molecular signatures that help to understand the physiology and pathophysiology of thyroid hormone action...
  26. ncbi request reprint Longitudinal transcriptional analysis of developing neointimal vascular occlusion and pulmonary hypertension in rats
    Laszlo T Vaszar
    Division of Pulmonary Critical Care Medicine, Stanford University Medical Center, Stanford, California 94305 5236, USA
    Physiol Genomics 17:150-6. 2004
    ..Mast-cell-derived proteases may play a role in regulating the development of neointimal pulmonary vascular occlusion and pulmonary hypertension in response to injury...
  27. ncbi request reprint Statistical methods for identifying differentially expressed genes in DNA microarrays
    John D Storey
    Department of Statistics, Stanford University, Palo Alto, CA, USA
    Methods Mol Biol 224:149-57. 2003
  28. pmc Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae
    Yoav Arava
    Department of Biochemistry, Stanford University, Stanford, CA 94305 5307, USA
    Proc Natl Acad Sci U S A 100:3889-94. 2003
    ..Global analysis revealed an unexpected correlation: Ribosome density decreases with increasing ORF length. Models to account for this surprising observation are discussed...
  29. pmc Precision and functional specificity in mRNA decay
    Yulei Wang
    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305 5307, USA
    Proc Natl Acad Sci U S A 99:5860-5. 2002
    ..The results provide strong evidence that precise control of the decay of each mRNA is a fundamental feature of the gene expression program in yeast...
  30. pmc A genome-wide gene expression signature of environmental geography in leukocytes of Moroccan Amazighs
    Youssef Idaghdour
    North Carolina State University, Raleigh, North Carolina, United States of America
    PLoS Genet 4:e1000052. 2008
    ....
  31. ncbi request reprint On the design and analysis of gene expression studies in human populations
    Joshua M Akey
    Nat Genet 39:807-8; author reply 808-9. 2007