Leming Shi

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. 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
  2. ncbi request reprint Reproducibility Probability Score--incorporating measurement variability across laboratories for gene selection
    Guixian Lin
    Nat Biotechnol 24:1476-7. 2006
  3. pmc Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map
    Zhining Wen
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, United States of America
    PLoS ONE 6:e18278. 2011
  4. pmc Transcriptional profiling of Chinese medicinal formula Si-Wu-Tang on breast cancer cells reveals phytoestrogenic activity
    Mandy Liu
    Department of Pharmaceutical Sciences and Center for Advancement of Drug Research, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
    BMC Complement Altern Med 13:11. 2013
  5. pmc Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile
    Chen Zhao
    The Center for Bioinformatics and The institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
    BMC Genomics 12:S3. 2011
  6. pmc Effect of training-sample size and classification difficulty on the accuracy of genomic predictors
    Vlad Popovici
    Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Genopode Building, Quartier Sorge, Lausanne CH 1015, Switzerland
    Breast Cancer Res 12:R5. 2010
  7. pmc The genomic features that affect the lengths of 5' untranslated regions in multicellular eukaryotes
    Chun Hsi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, 350 Taiwan, Republic of China
    BMC Bioinformatics 12:S3. 2011
  8. ncbi request reprint Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential
    Leming Shi
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCRT Road, Jefferson, AR 72079, USA
    Curr Opin Biotechnol 19:10-8. 2008
  9. 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
  10. 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

Collaborators

Detail Information

Publications70

  1. 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...
  2. ncbi request reprint Reproducibility Probability Score--incorporating measurement variability across laboratories for gene selection
    Guixian Lin
    Nat Biotechnol 24:1476-7. 2006
  3. pmc Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map
    Zhining Wen
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, United States of America
    PLoS ONE 6:e18278. 2011
    ....
  4. pmc Transcriptional profiling of Chinese medicinal formula Si-Wu-Tang on breast cancer cells reveals phytoestrogenic activity
    Mandy Liu
    Department of Pharmaceutical Sciences and Center for Advancement of Drug Research, College of Pharmacy, Western University of Health Sciences, Pomona, CA, USA
    BMC Complement Altern Med 13:11. 2013
    ..In our previous study, the microarray gene expression profiles of SWT on breast cancer cell line MCF-7 were found similar to the effect of ╬▓-estradiol (E2) on MCF-7 cells in the Connectivity Map database...
  5. pmc Maximum predictive power of the microarray-based models for clinical outcomes is limited by correlation between endpoint and gene expression profile
    Chen Zhao
    The Center for Bioinformatics and The institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
    BMC Genomics 12:S3. 2011
    ..Fine-tuning of model parameters and optimizing each step of the modeling process often results in over-fitting problems without improving performance...
  6. pmc Effect of training-sample size and classification difficulty on the accuracy of genomic predictors
    Vlad Popovici
    Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Genopode Building, Quartier Sorge, Lausanne CH 1015, Switzerland
    Breast Cancer Res 12:R5. 2010
    ....
  7. pmc The genomic features that affect the lengths of 5' untranslated regions in multicellular eukaryotes
    Chun Hsi Chen
    Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, 350 Taiwan, Republic of China
    BMC Bioinformatics 12:S3. 2011
    ..Furthermore, different selective constraints between vertebrates and invertebrates may lead to differences in the determinants of 5'UTR length, which have not been systematically analyzed...
  8. ncbi request reprint Reproducible and reliable microarray results through quality control: good laboratory proficiency and appropriate data analysis practices are essential
    Leming Shi
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCRT Road, Jefferson, AR 72079, USA
    Curr Opin Biotechnol 19:10-8. 2008
    ..The widespread collaboration aims to assess achievable technical performance of microarrays and capabilities and limitations of methods for microarray data analysis...
  9. 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...
  10. 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...
  11. ncbi request reprint QA/QC: challenges and pitfalls facing the microarray community and regulatory agencies
    Leming Shi
    US Food and Drug Administration, Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, HFT 020, 3900 NCTR Road, Jefferson, AR 72079, USA
    Expert Rev Mol Diagn 4:761-77. 2004
    ..These fundamental issues must be adequately addressed before microarray technology can be transformed from a research tool to clinical practices...
  12. 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...
  13. pmc Gene expression profiles distinguish the carcinogenic effects of aristolochic acid in target (kidney) and non-target (liver) tissues in rats
    Tao Chen
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    BMC Bioinformatics 7:S20. 2006
    ..To evaluate whether microarray analysis can be used for distinguishing the tissue-specific carcinogenicity of AA, we examined gene expression profiles in kidney and liver of rats treated with carcinogenic doses of AA...
  14. 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...
  15. pmc Genomic analysis of microRNA time-course expression in liver of mice treated with genotoxic carcinogen N-ethyl-N-nitrosourea
    Zhiguang Li
    Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
    BMC Genomics 11:609. 2010
    ..However, there is little information as to if or when expression changes of miRNAs occur in normal tissues after carcinogen exposure...
  16. doi request reprint ArrayTrack: an FDA and public genomic tool
    Hong Fang
    Z Tech Corporation, ICF International Company, Jefferson, AR, USA
    Methods Mol Biol 563:379-98. 2009
    ..ArrayTrack is publicly available online ( http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/index.htm ) and the prospective user can also request a local installation version by contacting the authors...
  17. 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
    ....
  18. ncbi request reprint Self-self hybridization as an alternative experiment design to dye swap for two-color microarrays
    Hong Fang
    Division of Bioinformatics, Z Tech Corporation, Jefferson, Arkansas, USA
    OMICS 11:14-24. 2007
    ..For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design...
  19. 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...
  20. ncbi request reprint Rat toxicogenomic study reveals analytical consistency across microarray platforms
    Lei Guo
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Nat Biotechnol 24:1162-9. 2006
    ....
  21. 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...
  22. 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...
  23. 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...
  24. pmc Selecting a single model or combining multiple models for microarray-based classifier development?--a comparative analysis based on large and diverse datasets generated from the MAQC-II project
    Minjun Chen
    Center for Bioinformatics, Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas, USA
    BMC Bioinformatics 12:S3. 2011
    ..Both the nominated and candidate models from MAQC-II provide benchmarks to assess other methodologies for developing microarray-based predictive models...
  25. 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...
  26. 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...
  27. 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...
  28. 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...
  29. 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)...
  30. doi request reprint Correlation analysis of external RNA controls reveals its utility for assessment of microarray assay
    Xiaohui Fan
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Anal Biochem 385:203-7. 2009
    ..The proposed approach is sensitive to identifying outlying assays and is not dependent on the choice of normalization method...
  31. pmc Analysis of gene expression changes in relation to toxicity and tumorigenesis in the livers of Big Blue transgenic rats fed comfrey (Symphytum officinale)
    Nan Mei
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
    BMC Bioinformatics 7:S16. 2006
    ..Our previous study suggested that comfrey induces liver tumors by a genotoxic mechanism and that the pyrrolizidine alkaloids in the plant are responsible for mutation induction and tumor initiation in rat liver...
  32. 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...
  33. pmc Technical reproducibility of genotyping SNP arrays used in genome-wide association studies
    Huixiao Hong
    Center of Excellence for Bioinformatics, Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arizona, United States of America
    PLoS ONE 7:e44483. 2012
    ..e. the odds ratio) and the minor allele frequencies are low...
  34. pmc Differential gene expression in mouse primary hepatocytes exposed to the peroxisome proliferator-activated receptor alpha agonists
    Lei Guo
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    BMC Bioinformatics 7:S18. 2006
    ..The activation of PPARalpha leads to a cascade of events that result in the pharmacological (hypolipidemic) and adverse (carcinogenic) effects in rodent liver...
  35. 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...
  36. 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...
  37. pmc Similarities and differences in the expression of drug-metabolizing enzymes between human hepatic cell lines and primary human hepatocytes
    Lei Guo
    Division of Biochemical Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Drug Metab Dispos 39:528-38. 2011
    ....
  38. ncbi request reprint Evaluation of external RNA controls for the assessment of microarray performance
    Weida Tong
    National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas 72079, USA
    Nat Biotechnol 24:1132-9. 2006
    ..This multiplatform investigation of the behavior and utility of ERCs provides a basis for articulating specific recommendations for their future use in evaluating assay performance across multiple platforms...
  39. pmc Gene expression variability in human hepatic drug metabolizing enzymes and transporters
    Lun Yang
    Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America
    PLoS ONE 8:e60368. 2013
    ..Expression variability of human hepatic DMET genes may affect drug-gene interactions and disease susceptibility, with concomitant clinical implications...
  40. doi request reprint Cytotoxicity and inhibitory effects of low-concentration triclosan on adipogenic differentiation of human mesenchymal stem cells
    Li Wu Guo
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Toxicol Appl Pharmacol 262:117-23. 2012
    ..Our study demonstrates that TCS inhibits adipocyte differentiation of hMSCs under concentrations that are not cytotoxic and in the range observed in human blood...
  41. pmc Improvement in the reproducibility and accuracy of DNA microarray quantification by optimizing hybridization conditions
    Tao Han
    Center for Functional Genomics, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    BMC Bioinformatics 7:S17. 2006
    ..A successful microarray experiment, however, involves many steps: well-designed oligonucleotide probes, printing, RNA extraction and labeling, hybridization, and imaging. Optimization is essential to generate reliable microarray data...
  42. 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...
  43. ncbi request reprint Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project
    Tucker A Patterson
    National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, Arkansas 72079, USA
    Nat Biotechnol 24:1140-50. 2006
    ....
  44. 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...
  45. doi request reprint Molecular biomarkers: a US FDA effort
    Huixiao Hong
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US FDA 3900 NCTR Road, Jefferson, AR, USA
    Biomark Med 4:215-25. 2010
    ..Specific FDA programs and research projects related to molecular biomarkers are also discussed for supporting regulatory review in the future...
  46. ncbi request reprint QA/QC issues to aid regulatory acceptance of microarray gene expression data
    James C Fuscoe
    Center for Functional Genomics, Division of Systems Toxicology, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Environ Mol Mutagen 48:349-53. 2007
    ..All data are available free of cost and the reference RNA samples are available for proficiency testing. Thus, current microarray technology appears to provide both reliability and consistency for regulatory submissions...
  47. 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...
  48. ncbi request reprint Phytoestrogens and mycoestrogens bind to the rat uterine estrogen receptor
    William S Branham
    Division of Genetic and Reproductive Toxicology, Jefferson Laboratories, National Center for Toxicological Research, Jefferson, AR 72079, USA
    J Nutr 132:658-64. 2002
    ..00008; E(2) = 100). These data can be utilized before animal testing to rank order estimates of the potential for in vivo estrogenic activity of a wide range of untested plant chemicals (as well as other chemicals) based on ER binding...
  49. ncbi request reprint Differences in hepatotoxicity and gene expression profiles by anti-diabetic PPAR gamma agonists on rat primary hepatocytes and human HepG2 cells
    Lei Guo
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Mol Divers 10:349-60. 2006
    ..Our work suggests that microarray analysis together with toxicological observations can be used to rank drugs for hepatotoxicity and to evaluate the safety of new compounds...
  50. 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...
  51. pmc Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation
    Xiaohui Fan
    National Center for Toxicological Research NCTR, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079, USA
    BMC Proc 3:S4. 2009
    ..We conclude that the MAQC recommendation should be considered when reproducibility is an important study objective...
  52. ncbi request reprint Structure-activity relationship approaches and applications
    Weida Tong
    Center for Toxicoinformatics, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    Environ Toxicol Chem 22:1680-95. 2003
    ..g., median lethal dose [LD50] dose). The reader is also referred to a companion paper in this issue that discusses quantitative structure-activity relationship (QSAR) methods that have advanced markedly over the past decade...
  53. doi request reprint Estimating relative noise to signal in DNA microarray data
    Huixiao Hong
    Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Int J Bioinform Res Appl 9:433-48. 2013
    ..Relative noise was estimated for both data sets, and the results were consistent with the observations in the original papers, demonstrating the proposed method is reliable for estimating relative noise in microarray data. ..
  54. doi request reprint Methysticin and 7,8-dihydromethysticin are two major kavalactones in kava extract to induce CYP1A1
    Yan Li
    Division of Systems Biology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Toxicol Sci 124:388-99. 2011
    ..The induction of CYP1A1 indicates a potential interaction between kava or kavalactones and CYP1A1-mediated chemical carcinogenesis...
  55. pmc The EDKB: an established knowledge base for endocrine disrupting chemicals
    Don Ding
    Division of Bioinformatics, Z Tech Corporation, ICF International Company at NCTR FDA, Jefferson, AR 72079, USA
    BMC Bioinformatics 11:S5. 2010
    ..This paper demonstrates the utility of EDKB database, an integral part of the EDKB project, for understanding and prioritizing EDs for testing...
  56. doi request reprint Voluntary exploratory data submissions to the US FDA and the EMA: experience and impact
    Federico M Goodsaid
    Genomics Group, Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, US FDA, Building 51, 10903 New Hampshire Avenue, Silver Spring, Maryland 20903 002, USA
    Nat Rev Drug Discov 9:435-45. 2010
    ....
  57. ncbi request reprint Classification of cDNA array genes that have a highly significant discriminative power due to their unique distribution in four brain regions
    Hong Fang
    Northrop Grumman Information Technology, Jefferson, Arkansas, USA
    DNA Cell Biol 23:661-74. 2004
    ....
  58. pmc A microarray study of MPP+-treated PC12 Cells: Mechanisms of toxicity (MOT) analysis using bioinformatics tools
    Zengjun Xu
    Division of Neurotoxicology, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 6:S8. 2005
    ..MPP+ depletes dopamine content and elicits cell death in PC12 cells. However, the mechanism of MPP+-induced neurotoxicity is still unclear...
  59. 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...
  60. ncbi request reprint Evaluation of DNA microarray results with quantitative gene expression platforms
    Roger D Canales
    Applied Biosystems, 850 Lincoln Centre Dr, Foster City, California 94404, USA
    Nat Biotechnol 24:1115-22. 2006
    ....
  61. ncbi request reprint 3D QSAR studies on peroxisome proliferator-activated receptor gamma agonists using CoMFA and CoMSIA
    Chenzhong Liao
    Chipscreen Biosciences Ltd, Research Institute of Tsinghua University, Suite C301, P O Box 28, 518057 Shenzhen, Guangdong, China
    J Mol Model 10:165-77. 2004
    ....
  62. ncbi request reprint Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models
    Yongxi Tan
    Burns and Allen Research Institute Microarray Core, Cedars Sinai Medical Center, David Geffen School of Medicine, UCLA, Los Angeles, CA 90048, USA
    Comput Biol Chem 28:235-44. 2004
    ....
  63. pmc Multi-class cancer classification by total principal component regression (TPCR) using microarray gene expression data
    Yongxi Tan
    Department of Medicine, Cedars Sinai Medical Center, David Geffen School of Medicine UCLA, Los Angeles, CA 90048, USA
    Nucleic Acids Res 33:56-65. 2005
    ..A fast kernel algorithm was applied to decrease the computation time dramatically. (MATLAB source code is available upon request.)...
  64. pmc Using RNA sample titrations to assess microarray platform performance and normalization techniques
    Richard Shippy
    GE Healthcare, 7700 S River Pkwy, Suite 2603, Tempe, Arizona 85284, USA
    Nat Biotechnol 24:1123-31. 2006
    ..In summary, titration samples may be regarded as a valuable tool, not only for assessing microarray platform performance and different analysis methods, but also for determining some underlying biological features of the samples...
  65. ncbi request reprint The External RNA Controls Consortium: a progress report
    Shawn C Baker
    Illumina, Inc, 9885 Towne Centre Drive, San Diego, California 92121, USA
    Nat Methods 2:731-4. 2005
    ..The External RNA Controls Consortium (ERCC) is developing commonly agreed-upon and tested controls for use in expression assays, a true industry-wide standard control...
  66. ncbi request reprint Integrating time-course microarray gene expression profiles with cytotoxicity for identification of biomarkers in primary rat hepatocytes exposed to cadmium
    Yongxi Tan
    Cedars Sinai Research Institute, Cedars Sinai Medical Center Los Angeles, CA 90048, USA
    Bioinformatics 22:77-87. 2006
    ..It is important to investigate the multi-scale biological system in a systematic way to better understand the gene regulation networks and signal transduction pathways involved in the cellular responses to environmental factors...
  67. ncbi request reprint Design, synthesis, and evaluation of a new class of noncyclic 1,3-dicarbonyl compounds as PPARalpha selective activators
    Zhibin Li
    Chipscreen Biosciences, Ltd, Research Institute of Tsinghua University, Suite C301, PO Box 28, Shenzhen 518057, China
    Bioorg Med Chem Lett 14:3507-11. 2004
    ..The data strongly support further testing of these lead compounds in other relevant disease animal models to evaluate their potential therapeutic benefits...
  68. ncbi request reprint Quantitative structure-activity relationship study of histone deacetylase inhibitors
    Aihua Xie
    Institute of Process Engineering, Chinese Academy of Sciences, P O Box 353, Beijing 100080, China
    Curr Med Chem Anticancer Agents 4:273-99. 2004
    ..The QSAR and classification models provided direct guidance to our internal programs of identifying and optimizing HDAC inhibitors. Limitations of the models were also discussed...
  69. ncbi request reprint Eigenvalue analysis of peroxisome proliferator-activated receptor gamma agonists
    Chenzhong Liao
    Chipscreen Biosciences, Ltd, Research Institute of Tsinghua University, Suite C301, PO Box 28, Shenzhen, Guangdong 518057, China
    J Chem Inf Comput Sci 44:230-8. 2004
    ..614 for AM1 and 0.822 for PM3 methods, set a successful example for applying a similar approach in building QSAR models for PPARalpha and -delta that could potentially offer a new opportunity in the design of novel PPAR modulators...
  70. ncbi request reprint Construction of a virtual combinatorial library using SMILES strings to discover potential structure-diverse PPAR modulators
    Chenzhong Liao
    Chipscreen Biosciences, Ltd Research Institute of Tsinghua University, Suite C301, P O Box 28, Shenzhen, Guangdong 518057, China
    Eur J Med Chem 40:632-40. 2005
    ..The method to construct virtual combinatorial library using SMILES strings was further visualized by Visual Basic.net that can facilitate the needs of generating other type virtual combinatorial libraries...