Zhijin Wu

Summary

Affiliation: Brown University
Country: USA

Publications

  1. pmc A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
    Hao Wu
    Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
    Biostatistics 14:232-43. 2013
  2. pmc Removing technical variability in RNA-seq data using conditional quantile normalization
    Kasper D Hansen
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
    Biostatistics 13:204-16. 2012
  3. pmc Subset quantile normalization using negative control features
    Zhijin Wu
    Center for Statistical Sciences and Department of Community Health, Brown University, Providence, Rhode Island 02912, USA
    J Comput Biol 17:1385-95. 2010
  4. doi request reprint Quantitative assessment of hit detection and confirmation in single and duplicate high-throughput screenings
    Zhijin Wu
    Center for Statistical Sciences, Department of Community Health, Brown University, Providence, RI 02903, USA
    J Biomol Screen 13:159-67. 2008
  5. pmc A review of statistical methods for preprocessing oligonucleotide microarrays
    Zhijin Wu
    Center for Statistical Sciences and Department of Community Health, Brown University, RI 02912, USA
    Stat Methods Med Res 18:533-41. 2009
  6. pmc Accurate genome-scale percentage DNA methylation estimates from microarray data
    Martin J Aryee
    Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231, USA
    Biostatistics 12:197-210. 2011
  7. pmc Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences
    Srinivasan Yegnasubramanian
    Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    BMC Genomics 12:313. 2011
  8. ncbi request reprint Comparison of Affymetrix GeneChip expression measures
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205, USA
    Bioinformatics 22:789-94. 2006
  9. pmc Molecular alterations underlying the enhanced disruption of spermatogenesis by 2,5-hexanedione and carbendazim co-exposure
    Sarah N Campion
    Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
    Reprod Toxicol 33:382-9. 2012
  10. pmc Background adjustment for DNA microarrays using a database of microarray experiments
    Yunxia Sui
    Department of Community Health, Brown University, Providence, Rhode Island 02912, USA
    J Comput Biol 16:1501-15. 2009

Detail Information

Publications21

  1. pmc A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data
    Hao Wu
    Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA
    Biostatistics 14:232-43. 2013
    ..We present a new empirical Bayes shrinkage estimate of the dispersion parameters and demonstrate improved DE detection...
  2. pmc Removing technical variability in RNA-seq data using conditional quantile normalization
    Kasper D Hansen
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
    Biostatistics 13:204-16. 2012
    ....
  3. pmc Subset quantile normalization using negative control features
    Zhijin Wu
    Center for Statistical Sciences and Department of Community Health, Brown University, Providence, Rhode Island 02912, USA
    J Comput Biol 17:1385-95. 2010
    ..It does not require an equal number of features in all samples and tolerates missing data...
  4. doi request reprint Quantitative assessment of hit detection and confirmation in single and duplicate high-throughput screenings
    Zhijin Wu
    Center for Statistical Sciences, Department of Community Health, Brown University, Providence, RI 02903, USA
    J Biomol Screen 13:159-67. 2008
    ..However, false discovery rate based on empirically estimated null distribution is very close to observed false discovery proportion...
  5. pmc A review of statistical methods for preprocessing oligonucleotide microarrays
    Zhijin Wu
    Center for Statistical Sciences and Department of Community Health, Brown University, RI 02912, USA
    Stat Methods Med Res 18:533-41. 2009
    ..In this article, we review the issues encountered in each preprocessing step and introduce the statistical models and methods in preprocessing...
  6. pmc Accurate genome-scale percentage DNA methylation estimates from microarray data
    Martin J Aryee
    Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University and Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21231, USA
    Biostatistics 12:197-210. 2011
    ..We illustrate the method on data generated to detect methylation differences between tissues and between normal and tumor colon samples...
  7. pmc Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences
    Srinivasan Yegnasubramanian
    Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    BMC Genomics 12:313. 2011
    ..This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells...
  8. ncbi request reprint Comparison of Affymetrix GeneChip expression measures
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, 615 N Wolfe Street, Baltimore, MD 21205, USA
    Bioinformatics 22:789-94. 2006
    ..A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had been submitted...
  9. pmc Molecular alterations underlying the enhanced disruption of spermatogenesis by 2,5-hexanedione and carbendazim co-exposure
    Sarah N Campion
    Department of Pathology and Laboratory Medicine, Brown University, Providence, RI 02903, USA
    Reprod Toxicol 33:382-9. 2012
    ..These findings provide candidate genes for further investigation of the testicular response to damage...
  10. pmc Background adjustment for DNA microarrays using a database of microarray experiments
    Yunxia Sui
    Department of Community Health, Brown University, Providence, Rhode Island 02912, USA
    J Comput Biol 16:1501-15. 2009
    ..An R package dbRMA implementing our method can be obtained from the authors...
  11. ncbi request reprint Stochastic models inspired by hybridization theory for short oligonucleotide arrays
    Zhijin Wu
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
    J Comput Biol 12:882-93. 2005
    ..We discuss how the proposed model can be used to obtain improved measures of expression useful for the data analysts...
  12. pmc Empirical bayes analysis of sequencing-based transcriptional profiling without replicates
    Zhijin Wu
    Center for Statistical Sciences and Department of Community Health, Box G 121S 7, Brown University, Providence RI 02912, USA
    BMC Bioinformatics 11:564. 2010
    ..However, advances in technology do not remove biological variation between replicates and this variation is often neglected in many analyses...
  13. pmc The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
    Nat Genet 41:178-86. 2009
    ....
  14. pmc DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity
    Srinivasan Yegnasubramanian
    Sidney Kimmel Comprehensive Cancer Center, School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
    Cancer Res 68:8954-67. 2008
    ....
  15. ncbi request reprint Alternative statistical parameter for high-throughput screening assay quality assessment
    Yunxia Sui
    Department of Community Health, Brown University, Providence, RI 02903, USA
    J Biomol Screen 12:229-34. 2007
    ..Studying the power of identifying true "hits" gives a more direct interpretation of assay quality and may provide guidance in assay optimization on some occasions...
  16. ncbi request reprint A benchmark for Affymetrix GeneChip expression measures
    Leslie M Cope
    Department of Mathematical Sciences, Johns Hopkins University, 104 Whitehead Hall, 3400 North Charles Street, Baltimore, MD 21218, USA
    Bioinformatics 20:323-31. 2004
    ..Those features highlighted in our suite of graphs are justified by questions of biological interest and motivated by the presence of appropriate data...
  17. pmc Suppression of radiation-induced testicular germ cell apoptosis by 2,5-hexanedione pretreatment. II. Gene array analysis reveals adaptive changes in cell cycle and cell death pathways
    Sarah N Campion
    Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
    Toxicol Sci 117:457-65. 2010
    ....
  18. ncbi request reprint Exploration, visualization, and preprocessing of high-dimensional data
    Zhijin Wu
    Center for Statistical Sciences, Brown University, Providence, RI, USA
    Methods Mol Biol 620:267-84. 2010
    ..In this chapter we review the common techniques in exploring and visualizing high-dimensional data and introduce the basic preprocessing procedures...
  19. pmc Phylogenetic analysis of gene expression
    Casey W Dunn
    Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA Department of Biostatistics and Center for Statistical Sciences, Brown University, Providence, RI 02903, USA
    Integr Comp Biol 53:847-56. 2013
    ..These topics are relevant to high-throughput phenotypic data well beyond gene expression. ..
  20. pmc Genetic variation in stearoyl-CoA desaturase 1 is associated with metabolic syndrome prevalence in Costa Rican adults
    Jian Gong
    Department of Community Health, Brown University, Providence, RI, USA
    J Nutr 141:2211-8. 2011
    ..No gene-fatty acid interactive effects were observed. Our results suggest that genetic variation in the SCD1 gene may play a role in the development of MetS...
  21. pmc Feature-level exploration of a published Affymetrix GeneChip control dataset
    Rafael A Irizarry
    Genome Biol 7:404. 2006
    ..A comment on 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...