Zhenyu Jia

Summary

Affiliation: University of California
Country: USA

Publications

  1. pmc An accurate prostate cancer prognosticator using a seven-gene signature plus Gleason score and taking cell type heterogeneity into account
    Xin Chen
    Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, USA
    PLoS ONE 7:e45178. 2012
  2. pmc A sample selection strategy to boost the statistical power of signature detection in cancer expression profile studies
    Zhenyu Jia
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
    Anticancer Agents Med Chem 13:203-11. 2013
  3. pmc Expression changes in the stroma of prostate cancer predict subsequent relapse
    Zhenyu Jia
    Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 7:e41371. 2012
  4. ncbi request reprint In silico estimates of tissue components in surgical samples based on expression profiling data
    Yipeng Wang
    Department of Pathology and Laboratory Medicine, Vaccine Research Institute of San Diego, University of California, Irvine, Irvine, California 92067, USA
    Cancer Res 70:6448-55. 2010
  5. pmc Diagnosis of prostate cancer using differentially expressed genes in stroma
    Zhenyu Jia
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
    Cancer Res 71:2476-87. 2011
  6. pmc Mapping quantitative trait loci for expression abundance
    Zhenyu Jia
    Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Genetics 176:611-23. 2007
  7. pmc Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip
    Shilpi Arora
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
    Genome Biol 9:R166. 2008
  8. ncbi request reprint Clustering expressed genes on the basis of their association with a quantitative phenotype
    Zhenyu Jia
    Department of Botany and Plant Sciences, University of California, Riverside, 92521, USA
    Genet Res 86:193-207. 2005
  9. pmc Early growth response 3 (Egr3) is highly over-expressed in non-relapsing prostate cancer but not in relapsing prostate cancer
    Rebecca Pio
    Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 8:e54096. 2013
  10. pmc Genomewide analysis of epistatic effects for quantitative traits in barley
    Shizhong Xu
    Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Genetics 175:1955-63. 2007

Detail Information

Publications13

  1. pmc An accurate prostate cancer prognosticator using a seven-gene signature plus Gleason score and taking cell type heterogeneity into account
    Xin Chen
    Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, USA
    PLoS ONE 7:e45178. 2012
    ..The strategy could have applications for improving marker performance in other cancers and other diseases...
  2. pmc A sample selection strategy to boost the statistical power of signature detection in cancer expression profile studies
    Zhenyu Jia
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
    Anticancer Agents Med Chem 13:203-11. 2013
    ..This strategy can be generally applied to profiling studies where the level of sample heterogeneity can be measured or estimated...
  3. pmc Expression changes in the stroma of prostate cancer predict subsequent relapse
    Zhenyu Jia
    Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 7:e41371. 2012
    ..This is the first general tumor microenvironment-based prognostic classifier. These results indicate that the prostate cancer microenvironment exhibits reproducible changes useful for predicting outcomes for patients...
  4. ncbi request reprint In silico estimates of tissue components in surgical samples based on expression profiling data
    Yipeng Wang
    Department of Pathology and Laboratory Medicine, Vaccine Research Institute of San Diego, University of California, Irvine, Irvine, California 92067, USA
    Cancer Res 70:6448-55. 2010
    ..A web service, "CellPred," has been designed for the in silico prediction of sample tissue components based on expression data...
  5. pmc Diagnosis of prostate cancer using differentially expressed genes in stroma
    Zhenyu Jia
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
    Cancer Res 71:2476-87. 2011
    ....
  6. pmc Mapping quantitative trait loci for expression abundance
    Zhenyu Jia
    Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Genetics 176:611-23. 2007
    ..In the experiment, approximately 40,000 transcripts and 145 codominant markers are investigated for their associations. A program written in SAS/IML is available from the authors on request...
  7. pmc Egr1 regulates the coordinated expression of numerous EGF receptor target genes as identified by ChIP-on-chip
    Shilpi Arora
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
    Genome Biol 9:R166. 2008
    ..We examined the hypothesis that Egr1 regulates genes that mediate this process by use of a chip-on-chip protocol in human tumorigenic prostate M12 cells...
  8. ncbi request reprint Clustering expressed genes on the basis of their association with a quantitative phenotype
    Zhenyu Jia
    Department of Botany and Plant Sciences, University of California, Riverside, 92521, USA
    Genet Res 86:193-207. 2005
    ..The method was verified by analysing two simulated datasets, and further demonstrated using real data generated in a microarray experiment for the study of gene expression associated with Alzheimer's disease...
  9. pmc Early growth response 3 (Egr3) is highly over-expressed in non-relapsing prostate cancer but not in relapsing prostate cancer
    Rebecca Pio
    Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 8:e54096. 2013
    ..These Egr3-correlated genes were enriched with Egr binding sites in their promoters. The gene list contains inflammatory genes such as IL-6, IL-8, IL1β and COX-2, which have extensive connections to prostate cancer...
  10. pmc Genomewide analysis of epistatic effects for quantitative traits in barley
    Shizhong Xu
    Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Genetics 175:1955-63. 2007
    ..This invalidates the common practice of epistatic analysis in which epistatic effects are estimated only for pairs of loci of which both have main effects...
  11. doi request reprint Age-related alterations of gene expression patterns in human CD8+ T cells
    Jia Ning Cao
    Division of Basic and Clinical Immunology, Department of Medicine, University of California, Medical Sciences I, C 240 Irvine, CA 92697, USA
    Aging Cell 9:19-31. 2010
    ....
  12. pmc A gradient boosting algorithm for survival analysis via direct optimization of concordance index
    Yifei Chen
    Department of Computer Science, University of California Irvine, Irvine, CA 92697, USA
    Comput Math Methods Med 2013:873595. 2013
    ..Our experiment shows that GBMCI consistently outperforms other methods based on a number of covariate settings. GBMCI is implemented in R and is freely available online. ..
  13. pmc Bayesian mixture model analysis for detecting differentially expressed genes
    Zhenyu Jia
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
    Int J Plant Genomics 2008:892927. 2008
    ..Using simulated data as well as data from a real microarray experiment, we demonstrate that the new method outperforms all methods commonly used in differential expression analysis...