Zhenqiang Su

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. doi request reprint Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys
    Zhenqiang Su
    ICF International at FDA s National Center for Toxicological Research, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    Chem Res Toxicol 24:1486-93. 2011
  2. pmc Constructing a robust protein-protein interaction network by integrating multiple public databases
    Venkata Swamy Martha
    Department of Information Science, University of Arkansas at Little Rock, 2801 S, University Ave, Little Rock, AR 72204 1099, USA
    BMC Bioinformatics 12:S7. 2011
  3. pmc Very Important Pool (VIP) genes--an application for microarray-based molecular signatures
    Zhenqiang Su
    Center for Toxicoinformatics, National Center for Toxicological Research NCTR, U, S, Food and Drug Administration FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S9. 2008
  4. doi request reprint Next-generation sequencing and its applications in molecular diagnostics
    Zhenqiang Su
    Z Tech, an ICF International Company at US FDA s National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA
    Expert Rev Mol Diagn 11:333-43. 2011
  5. ncbi request reprint Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    J Genet 89:55-64. 2010
  6. pmc Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential
    Leming Shi
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S12. 2005
  7. doi request reprint Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine
    Huixiao Hong
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Sci China Life Sci 56:110-8. 2013
  8. pmc The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S10. 2008
  9. pmc Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S17. 2008
  10. pmc Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples
    Zhining Wen
    Division of Systems Biology, National Center for Toxicological Research NCTR, US Food and Drug Administration FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 11:S10. 2010

Detail Information

Publications20

  1. doi request reprint Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys
    Zhenqiang Su
    ICF International at FDA s National Center for Toxicological Research, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    Chem Res Toxicol 24:1486-93. 2011
    ..However, there is clearly a need for future investigations to better understand the advantages and limitations of RNA-Seq in toxicogenomics studies and environmental health research...
  2. pmc Constructing a robust protein-protein interaction network by integrating multiple public databases
    Venkata Swamy Martha
    Department of Information Science, University of Arkansas at Little Rock, 2801 S, University Ave, Little Rock, AR 72204 1099, USA
    BMC Bioinformatics 12:S7. 2011
    ..There are many PPI databases publicly available, each with a specific focus. The challenge is how to effectively combine their contents to generate a robust and biologically relevant PPI network...
  3. pmc Very Important Pool (VIP) genes--an application for microarray-based molecular signatures
    Zhenqiang Su
    Center for Toxicoinformatics, National Center for Toxicological Research NCTR, U, S, Food and Drug Administration FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S9. 2008
    ..However, improving the ability to identify differentiating genes remains a challenge in bioinformatics...
  4. doi request reprint Next-generation sequencing and its applications in molecular diagnostics
    Zhenqiang Su
    Z Tech, an ICF International Company at US FDA s National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA
    Expert Rev Mol Diagn 11:333-43. 2011
    ..The challenges in the analysis of NGS data and their potential applications in clinical diagnosis are also discussed...
  5. ncbi request reprint Evaluating variations of genotype calling: a potential source of spurious associations in genome-wide association studies
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    J Genet 89:55-64. 2010
    ..The effect of the threshold was much larger than the effect of the size. Moreover, the heterozygous calls had lower consistency compared to the homozygous calls...
  6. pmc Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential
    Leming Shi
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S12. 2005
    ..Nucleic Acids Res., 31, 5676-5684, 2003), portrays a disturbingly negative picture of the cross-platform comparability, and, hence, the reliability of microarray technology...
  7. doi request reprint Critical role of bioinformatics in translating huge amounts of next-generation sequencing data into personalized medicine
    Huixiao Hong
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Sci China Life Sci 56:110-8. 2013
    ..We review some key bioinformatics tasks, issues, and challenges in contexts of IT requirements, data quality, analysis tools and pipelines, and validation of biomarkers...
  8. pmc The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S10. 2008
    ..The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists...
  9. pmc Assessing batch effects of genotype calling algorithm BRLMM for the Affymetrix GeneChip Human Mapping 500 K array set using 270 HapMap samples
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 9:S17. 2008
    ..In this paper, we analyzed both the batch size and batch composition for effects on the genotype calling algorithm BRLMM using raw data of 270 HapMap samples analyzed with the Affymetrix Human Mapping 500 K array set...
  10. pmc Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples
    Zhining Wen
    Division of Systems Biology, National Center for Toxicological Research NCTR, US Food and Drug Administration FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 11:S10. 2010
    ..Experiments were conducted to answer these questions...
  11. pmc The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
    Nat Biotechnol 28:827-38. 2010
    ..The conclusions and recommendations from MAQC-II should be useful for regulatory agencies, study committees and independent investigators that evaluate methods for global gene expression analysis...
  12. pmc Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles
    Zhiguang Li
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, U, S, Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 10:S12. 2009
    ..In this study, we investigated whether different platforms had a high consistency from the biologically functional perspective...
  13. pmc atBioNet--an integrated network analysis tool for genomics and biomarker discovery
    Yijun Ding
    ICF International at FDA s National Center for Toxicological Research, Jefferson, AR 72079, USA
    BMC Genomics 13:325. 2012
    ....
  14. doi request reprint Mold(2), molecular descriptors from 2D structures for chemoinformatics and toxicoinformatics
    Huixiao Hong
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Chem Inf Model 48:1337-44. 2008
    ..High reproducibility and reliability are expected because Mold (2) does not require 3D structures. Mold (2) is freely available to the public ( http://www.fda.gov/nctr/science/centers/toxicoinformatics/index.htm)...
  15. doi request reprint The accurate prediction of protein family from amino acid sequence by measuring features of sequence fragments
    Huixiao Hong
    Division of Systems Toxicology, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Comput Biol 16:1671-88. 2009
    ..9941 was achieved. This study demonstrates that SVM based methods can accurately recognize and predict the protein family to which a sequence belongs based solely on its primary amino acid sequence...
  16. pmc An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays
    Hong Fang
    Z Tech Corporation, ICF International Company at National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
    BMC Bioinformatics 11:S4. 2010
    ..ArrayTrack™ has been widely adopted by the research community and used for pharmacogenomics data review in the FDA's Voluntary Genomics Data Submission program...
  17. doi request reprint Studies on abacavir-induced hypersensitivity reaction: a successful example of translation of pharmacogenetics to personalized medicine
    Yongli Guo
    Division of Systems Biology, National Center for Toxicological Research, The US Food and Drug Administration, Jefferson, AR 72079, USA
    Sci China Life Sci 56:119-24. 2013
    ..The studies of abacavir-induced HSR and the implementation of the HLA-B*57:01 screening in the clinic represent a successful example of the use of pharmacogenetics for personalized diagnosis and therapy...
  18. doi request reprint Identification of urinary microRNA profiles in rats that may diagnose hepatotoxicity
    Xi Yang
    Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Toxicol Sci 125:335-44. 2012
    ..In conclusion, the patterns of urinary miRNA may hold promise as biomarkers of hepatotoxicant-induced liver injury...
  19. pmc Microarray scanner calibration curves: characteristics and implications
    Leming Shi
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S11. 2005
    ..Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration curve can be nonlinear...
  20. pmc The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements
    Leming Shi
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Nat Biotechnol 24:1151-61. 2006
    ..This study provides a resource that represents an important first step toward establishing a framework for the use of microarrays in clinical and regulatory settings...