Zhenyu Jia

Summary

Affiliation: University of California
Country: USA

Publications

  1. 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
  2. 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
  3. pmc 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
  4. 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
  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 The identification of trans-associations between prostate cancer GWAS SNPs and RNA expression differences in tumor-adjacent stroma
    Xin Chen
    Genomics Center, Loma Linda University, Loma Linda, California, 92354, United States of America
    Oncotarget 6:1865-73. 2015
  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. 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
  9. pmc A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors
    Farah B Rahmatpanah
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
    Oncotarget 6:1286-301. 2015
  10. pmc Role of the adjacent stroma cells in prostate cancer development and progression: synergy between TGF-β and IGF signaling
    Chung Lee
    Department of Urology, Northwestern University Feinberg School of Medicine, Tarry Building, Room 16 733, 303 East Chicago Avenue, Chicago, IL 60611, USA Department of Urology, University of California at Irvine, Medical Center, Orange, CA 92868, USA Department of Pathology and Laboratory Medicine, University of California at Irvine, Medical Surgery Building I, Room 168, Irvine, CA 92697, USA Department of Surgery, NorthShore University Healthsystem, Evanston, IL 60201, USA
    Biomed Res Int 2014:502093. 2014

Collaborators

Detail Information

Publications17

  1. 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...
  2. 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...
  3. pmc 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...
  4. 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...
  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 The identification of trans-associations between prostate cancer GWAS SNPs and RNA expression differences in tumor-adjacent stroma
    Xin Chen
    Genomics Center, Loma Linda University, Loma Linda, California, 92354, United States of America
    Oncotarget 6:1865-73. 2015
    ..Potentially, a combination of SNPs and associated expression differences in prostate stroma may increase the power of risk assessment for individuals, and for cancer progression. ..
  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. 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...
  9. pmc A class of genes in the HER2 regulon that is poised for transcription in breast cancer cell lines and expressed in human breast tumors
    Farah B Rahmatpanah
    Department of Pathology and Laboratory Medicine, University of California, Irvine, CA, USA
    Oncotarget 6:1286-301. 2015
    ....
  10. pmc Role of the adjacent stroma cells in prostate cancer development and progression: synergy between TGF-β and IGF signaling
    Chung Lee
    Department of Urology, Northwestern University Feinberg School of Medicine, Tarry Building, Room 16 733, 303 East Chicago Avenue, Chicago, IL 60611, USA Department of Urology, University of California at Irvine, Medical Center, Orange, CA 92868, USA Department of Pathology and Laboratory Medicine, University of California at Irvine, Medical Surgery Building I, Room 168, Irvine, CA 92697, USA Department of Surgery, NorthShore University Healthsystem, Evanston, IL 60201, USA
    Biomed Res Int 2014:502093. 2014
    ..A continuous input from TGF-β and IGF in the tumor microenvironment will result in cancer progression. Understanding of these events can help prevention, diagnosis, and therapy of prostate cancer. ..
  11. 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...
  12. 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...
  13. pmc Alterations in gene array patterns in dendritic cells from aged humans
    Jia Ning Cao
    Division of Basic and Clinical Immunology, Department of Medicine, University of California Irvine, Irvine, California, United States of America
    PLoS ONE 9:e106471. 2014
    ..These changes in gene expression provide molecular based evidence for age-associated functional abnormalities in human DCs that may be responsible for the defects in adaptive immunity observed in the elderly. ..
  14. 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
    ....
  15. 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...
  16. 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. ..
  17. 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...