Qian Xie

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. pmc A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist
    W David Tolbert
    Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue, Grand Rapids, MI 49503, USA
    Proc Natl Acad Sci U S A 104:14592-7. 2007
  2. pmc Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling
    H Fang
    Division of Bioinformatics, Z Tech Corporation, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 6:S6. 2005
  3. pmc Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method
    Qian Xie
    Division of Bioinformatics, Z tech at FDA s National Center for Toxicological Research, Jefferson, AR 72079, USA
    BMC Bioinformatics 6:S4. 2005
  4. ncbi request reprint Development of public toxicogenomics software for microarray data management and analysis
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, NCTR, 3900 NCTR Road, HFT 020, Jefferson, AR 72079, USA
    Mutat Res 549:241-53. 2004
  5. pmc Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity
    Weida Tong
    Center for Toxicoinformatics, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Environ Health Perspect 112:1249-54. 2004
  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. 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
  8. 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
  9. ncbi request reprint Decision forest: combining the predictions of multiple independent decision tree models
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
    J Chem Inf Comput Sci 43:525-31. 2003
  10. ncbi request reprint Building an organ-specific carcinogenic database for SAR analyses
    John Young
    Division of Biometry and Risk Assessment, Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
    J Toxicol Environ Health A 67:1363-89. 2004

Detail Information

Publications24

  1. pmc A mechanistic basis for converting a receptor tyrosine kinase agonist to an antagonist
    W David Tolbert
    Laboratory of Structural Sciences, Van Andel Research Institute, 333 Bostwick Avenue, Grand Rapids, MI 49503, USA
    Proc Natl Acad Sci U S A 104:14592-7. 2007
    ..This strategy of antagonist design may be applicable for other growth factor receptors by selectively abolishing the receptor activation ability but not the receptor binding of the growth factors...
  2. pmc Bioinformatics approaches for cross-species liver cancer analysis based on microarray gene expression profiling
    H Fang
    Division of Bioinformatics, Z Tech Corporation, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Bioinformatics 6:S6. 2005
    ....
  3. pmc Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method
    Qian Xie
    Division of Bioinformatics, Z tech at FDA s National Center for Toxicological Research, Jefferson, AR 72079, USA
    BMC Bioinformatics 6:S4. 2005
    ....
  4. ncbi request reprint Development of public toxicogenomics software for microarray data management and analysis
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, NCTR, 3900 NCTR Road, HFT 020, Jefferson, AR 72079, USA
    Mutat Res 549:241-53. 2004
    ..ArrayTrack is publicly available online and the prospective user can also request a local installation version by contacting the authors...
  5. pmc Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity
    Weida Tong
    Center for Toxicoinformatics, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Environ Health Perspect 112:1249-54. 2004
    ....
  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. 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...
  8. 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)...
  9. ncbi request reprint Decision forest: combining the predictions of multiple independent decision tree models
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
    J Chem Inf Comput Sci 43:525-31. 2003
    ..An example will be presented for prediction of binding affinity of 232 chemicals to the estrogen receptor...
  10. ncbi request reprint Building an organ-specific carcinogenic database for SAR analyses
    John Young
    Division of Biometry and Risk Assessment, Food and Drug Administration, National Center for Toxicological Research, Jefferson, Arkansas, USA
    J Toxicol Environ Health A 67:1363-89. 2004
    ..These preliminary analyses all yielded approximately the same results with an overall predictability of about 63%, which was comprised of a sensitivity of about 30% and a specificity of about 77%...
  11. pmc Using decision forest to classify prostate cancer samples on the basis of SELDI-TOF MS data: assessing chance correlation and prediction confidence
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, National Center for Toxicological Research FDA, 3900 NCTR Road, HFT020, Jefferson, AK 72079, USA
    Environ Health Perspect 112:1622-7. 2004
    ..DF should be equally applicable to other omics data such as gene expression data or metabolomic data. The DF algorithm is available upon request...
  12. ncbi request reprint Multiclass Decision Forest--a novel pattern recognition method for multiclass classification in microarray data analysis
    Huixiao Hong
    Bioinformatics Laboratory, National Center for Toxicological Research, FDA, Jefferson, Arkansas 72079, USA
    DNA Cell Biol 23:685-94. 2004
    ..The results demonstrated that the multiclass DF is an effective classification method for analysis of gene expression data for the purpose of molecular diagnostics...
  13. 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...
  14. ncbi request reprint Study of 202 natural, synthetic, and environmental chemicals for binding to the androgen receptor
    Hong Fang
    Northrop Grumman Information Technology, Jefferson, Arkansas 72079, USA
    Chem Res Toxicol 16:1338-58. 2003
    ..The SAR studies of ligand binding characteristics for AR are compared to our previously reported results for estrogen receptor binding...
  15. ncbi request reprint Gene expression profile exploration of a large dataset on chronic fatigue syndrome
    Hong Fang
    Z Tech Corporation at NCTR, Division of Bioinformatics, 3900 NCTR Road, Jefferson, AR 72079, USA
    Pharmacogenomics 7:429-40. 2006
    ..To gain understanding of the molecular basis of chronic fatigue syndrome (CFS) through gene expression analysis using a large microarray data set in conjunction with clinically administrated questionnaires...
  16. pmc Quality control and quality assessment of data from surface-enhanced laser desorption/ionization (SELDI) time-of flight (TOF) mass spectrometry (MS)
    Huixiao Hong
    Division of Bioinformatics, Z tech at FDA s National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S5. 2005
    ..The use of SELDI data for biomarker identification requires application of rigorous procedures to detect and discard low quality spectra prior to data analysis...
  17. pmc ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research
    Weida Tong
    Center for Toxicoinformatics, Division of Biometry and Risk Assessment, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    Environ Health Perspect 111:1819-26. 2003
    ..Using ArrayTrack, we can select an analysis method from the TOOL and apply the method to selected microarray data stored in the MicroarrayDB; the analysis results can be linked directly to gene information in the LIB...
  18. 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...
  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. ncbi request reprint Models of steroid binding based on the minimum deviation of structurally assigned 13C NMR spectra analysis (MiDSASA)
    Richard D Beger
    Division of Chemistry, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079 9502, USA
    J Chem Inf Comput Sci 44:1489-96. 2004
    ..88. A MiDSASA template model for 50 steroids binding the aromatse enzyme based on the average activity of the four nearest compounds had a correlation of 0.71...
  21. pmc Prediction of estrogen receptor binding for 58,000 chemicals using an integrated system of a tree-based model with structural alerts
    Huixiao Hong
    R O W Sciences, Inc, Jefferson, Arkansas 72079, USA
    Environ Health Perspect 110:29-36. 2002
    ..The general approach for predicting ER binding reported here may be applied to other receptors and/or reversible binding mechanisms involved in endocrine disruption...
  22. ncbi request reprint Three new consensus QSAR models for the prediction of Ames genotoxicity
    Joseph R Votano
    ChemSilico LLC, 48 Baldwin Street, Tewksbury, MA 01876, USA
    Mutagenesis 19:365-77. 2004
    ..Substantially higher specificity was achieved with these new models as compared with MULTICASE or DEREK with comparable sensitivities among all models...
  23. ncbi request reprint [Influence of the inhibitor of c-Met on the growth and motility of hepatocellular carcinoma cells]
    Bi Hua Chen
    Experimental Research Center of Zhongshan Hospital, Fudan University, Shanghai 200032, China
    Zhonghua Gan Zang Bing Za Zhi 11:487-9. 2003
    ....
  24. ncbi request reprint Geldanamycin derivative inhibition of HGF/SF-mediated Met tyrosine kinase receptor-dependent urokinase-plasminogen activation
    Yuehai Shen
    Department of Physiology, Michigan State University, East Lansing, MI 48864, USA
    Bioorg Med Chem 13:4960-71. 2005
    ..Assessment is made of structural requirements for such an activity and evidence is given that distinguishes the target of such an activity from that of heat shock protein 90...