Zhijin Wu

Summary

Affiliation: Brown University
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. doi 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

Collaborators

Detail Information

Publications14

  1. 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...
  2. 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...
  3. 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...
  4. 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...
  5. 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...
  6. 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...
  7. 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
    ....
  8. 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...
  9. 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...
  10. doi 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...
  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. 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...
  13. 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...
  14. 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...