W Tong

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. 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
  2. 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
  3. 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
  4. ncbi request reprint Evaluation of quantitative structure-activity relationship methods for large-scale prediction of chemicals binding to the estrogen receptor
    W Tong
    Department of Chemistry, University of Missouri St Louis 63121, USA
    J Chem Inf Comput Sci 38:669-77. 1998
  5. 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
  6. 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
  7. 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
  8. 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
  9. ncbi request reprint An integrated "4-phase" approach for setting endocrine disruption screening priorities--phase I and II predictions of estrogen receptor binding affinity
    L Shi
    R O W Sciences, Inc, Jefferson, AR 72079, USA
    SAR QSAR Environ Res 13:69-88. 2002
  10. 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

Collaborators

Detail Information

Publications65

  1. 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...
  2. 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
    ....
  3. 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...
  4. ncbi request reprint Evaluation of quantitative structure-activity relationship methods for large-scale prediction of chemicals binding to the estrogen receptor
    W Tong
    Department of Chemistry, University of Missouri St Louis 63121, USA
    J Chem Inf Comput Sci 38:669-77. 1998
    ....
  5. 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...
  6. 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...
  7. 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...
  8. 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...
  9. ncbi request reprint An integrated "4-phase" approach for setting endocrine disruption screening priorities--phase I and II predictions of estrogen receptor binding affinity
    L Shi
    R O W Sciences, Inc, Jefferson, AR 72079, USA
    SAR QSAR Environ Res 13:69-88. 2002
    ..We believe that the same integrated scheme will be equally applicable to endpoints of other endocrine disrupting mechanisms, e.g. androgen receptor binding...
  10. 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
    ....
  11. ncbi request reprint QSAR models using a large diverse set of estrogens
    L M Shi
    ROW Sciences Inc, Jefferson, Arkansas 72079, USA
    J Chem Inf Comput Sci 41:186-95. 2001
    ....
  12. ncbi request reprint The estrogen receptor relative binding affinities of 188 natural and xenochemicals: structural diversity of ligands
    R M Blair
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
    Toxicol Sci 54:138-53. 2000
    ..The current study provides the most structurally diverse ER RBA data set with the widest range of RBA values published to date...
  13. pmc Quantitative comparisons of in vitro assays for estrogenic activities
    H Fang
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research NCTR, Jefferson, Arkansas, USA
    Environ Health Perspect 108:723-9. 2000
    ..The results should provide guidance for expanded data mining examinations and the selection of appropriate assays to screen estrogenic endocrine disruptors...
  14. ncbi request reprint An in silico ensemble method for lead discovery: decision forest
    H Hong
    Z Tech at National Center for Toxicological Research, U S Food and Drug Administration, Division of Bioinformatics, Jefferson, AR 72079, USA
    SAR QSAR Environ Res 16:339-47. 2005
    ..The results show that the decision forest method is a fast, reliable and effective in silico approach, which could be useful in drug discovery...
  15. ncbi request reprint Comparative molecular field analysis (CoMFA) model using a large diverse set of natural, synthetic and environmental chemicals for binding to the androgen receptor
    H Hong
    Northrop Grumman Information Technology, Jefferson, AR 72079, USA
    SAR QSAR Environ Res 14:373-88. 2003
    ..637 logRBA. This study demonstrates the utility of this CoMFA model for real-world use in predicting the AR binding affinities of structurally diverse chemicals over a wide RBA range...
  16. 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
    ....
  17. ncbi request reprint Structure-activity relationships for a large diverse set of natural, synthetic, and environmental estrogens
    H Fang
    R.O.W. Sciences, Inc, 3900 NCTR Road, MC 910, Jefferson, Arkansas 72079, USA
    Chem Res Toxicol 14:280-94. 2001
    ..A rigid ring structure favors ER binding. The knowledge derived from this study is rationalized into a set of hierarchical rules that will be useful in guidance for identification of potential estrogens...
  18. ncbi request reprint Exploring the FDA adverse event reporting system to generate hypotheses for monitoring of disease characteristics
    H Fang
    Office of Scientific Coordination, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
    Clin Pharmacol Ther 95:496-8. 2014
    ..Although the FAERS has been predominantly used for safety signal detection, this study explored its utility for disease characteristics. ..
  19. doi request reprint The liver toxicity knowledge base: a systems approach to a complex end point
    M Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
    Clin Pharmacol Ther 93:409-12. 2013
    ..The project has also produced a centralized resource of data as well as predictive models that will be useful for research and drug regulation...
  20. 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...
  21. 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%...
  22. 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...
  23. 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...
  24. ncbi request reprint Quantitative structure-activity relationship methods: perspectives on drug discovery and toxicology
    Roger Perkins
    Logicon ROW Sciences, 3900 NCTR Road, MC 910, Jefferson, Arkansas 72079, USA
    Environ Toxicol Chem 22:1666-79. 2003
    ..The review will conclude by discussing statistical validation of QSAR models, a topic that has received sparse attention in recent years despite its critical importance...
  25. 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...
  26. 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...
  27. pmc Assessing sources of inconsistencies in genotypes and their effects on genome-wide association studies with HapMap samples
    H Hong
    Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
    Pharmacogenomics J 10:364-74. 2010
    ..Our studies show that inconsistencies between SNP arrays and between genotype calling algorithms are potential sources for the lack of reproducibility in GWAS results...
  28. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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...
  33. 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)...
  34. 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...
  35. 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
    ....
  36. 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...
  37. 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...
  38. 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...
  39. 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...
  40. 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...
  41. 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...
  42. 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...
  43. 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...
  44. 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...
  45. 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...
  46. doi request reprint Biomarkers for drug-induced liver injury
    Qiang Shi
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    Expert Rev Gastroenterol Hepatol 4:225-34. 2010
    ..This review summarizes the current practice and future perspectives for DILI biomarkers...
  47. 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...
  48. 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
    ....
  49. ncbi request reprint An integrated study of acute effects of valproic acid in the liver using metabonomics, proteomics, and transcriptomics platforms
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, 72079, USA
    OMICS 10:1-14. 2006
    ..The combined studies indicated a perturbation in the glycogenolysis pathway following administration of VPA...
  50. ncbi request reprint The liver toxicity biomarker study: phase I design and preliminary results
    Robert N McBurney
    BG Medicine, Inc, Waltham, MA 02451, USA
    Toxicol Pathol 37:52-64. 2009
    ....
  51. 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
    ....
  52. doi request reprint Evaluations of the trans-sulfuration pathway in multiple liver toxicity studies
    Laura K Schnackenberg
    Division of Systems Toxicology, National Center for Toxicological Research, Food and Drug Administration, FDA, Jefferson, AR 72079, USA
    Toxicol Appl Pharmacol 235:25-32. 2009
    ..The metabolic and transcriptomic results show that the trans-sulfuration pathway from SAMe to glutathione was disturbed due to the administration of heptatotoxicants...
  53. 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...
  54. ncbi request reprint Toward a checklist for exchange and interpretation of data from a toxicology study
    Jennifer M Fostel
    NIEHS, LMIT ITSS Contract, Research Triangle Park, North Carolina 27709 2233, USA
    Toxicol Sci 99:26-34. 2007
    ..It is anticipated that once a toxicology checklist is accepted and put into use, then toxicology databases can be configured to require and output these fields, making it straightforward to annotate data for interpretation by others...
  55. ncbi request reprint Influence of the structural diversity of data sets on the statistical quality of three-dimensional quantitative structure-activity relationship (3D-QSAR) models: predicting the estrogenic activity of xenoestrogens
    Seong Jae Yu
    Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854, USA
    Chem Res Toxicol 15:1229-34. 2002
    ..These models should be effective for predicting the endocrine disrupting potential of existing chemicals as well as prospective and newly prepared chemicals before they enter the environment...
  56. 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...
  57. ncbi request reprint Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics data
    Jennifer Fostel
    LIMT Lockheed Martin Information Technology LMIT, Research Triangle Park, NC 27709, USA
    Toxicol Sci 88:585-601. 2005
    ..To illustrate the utility of the CEBS-DD, we present an example of integrating data from two proteomics and transcriptomics studies of the response to acute acetaminophen toxicity (A. N. Heinloth et al., 2004, Toxicol. Sci. 80, 193-202)...
  58. ncbi request reprint A strategy capitalizing on synergies: the Reporting Structure for Biological Investigation (RSBI) working group
    Susanna Assunta Sansone
    EMBL EBI, European Nutrigenomics Organisation NuGO, Hinxton, Cambridge, United Kingdom
    OMICS 10:164-71. 2006
    ....
  59. ncbi request reprint Consensus analysis of multiple classifiers using non-repetitive variables: diagnostic application to microarray gene expression data
    Zhenqiang Su
    Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
    Comput Biol Chem 31:48-56. 2007
    ..Importantly, the CAMCUN algorithm employed an integrated 10-fold cross-validation and randomization test to assess the degree of confidence of the predictions for unknown samples...
  60. ncbi request reprint An approach to comparative analysis of chromatographic fingerprints for assuring the quality of botanical drugs
    Yiyu Cheng
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310027, China
    J Chem Inf Comput Sci 43:1068-76. 2003
    ..The methods are equally applicable to other botanical drugs...
  61. 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.)...
  62. pmc Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use
    Raffaella Corvi
    European Centre for the Validation of Alternative Methods, Institute for Health and Consumer Protection, Joint Research Centre of the European Commission, Ispra, Italy
    Environ Health Perspect 114:420-9. 2006
    ..In this report we summarize the discussions and describe in detail the recommendations for future direction and priorities...
  63. ncbi request reprint Current status of methods for defining the applicability domain of (quantitative) structure-activity relationships. The report and recommendations of ECVAM Workshop 52
    Tatiana I Netzeva
    EVCAM, ECB, Institute for Health and Consumer Protection, European Commission Joint Research Centre, 21020 Ispra VA, Italy
    Altern Lab Anim 33:155-73. 2005
  64. 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
    ....
  65. ncbi request reprint The first RSBI (ISA-TAB) workshop: "can a simple format work for complex studies?"
    Susanna Assunta Sansone
    EMBL EBI The European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    OMICS 12:143-9. 2008
    ..This article is part of the special issue of OMICS on the activities of the Genomics Standards Consortium (GSC)...