Weida Tong

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. pmc Translating clinical findings into knowledge in drug safety evaluation--drug induced liver injury prediction system (DILIps)
    Zhichao Liu
    Division of Systems Biology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arizona, USA
    PLoS Comput Biol 7:e1002310. 2011
  2. ncbi request reprint An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative
    Weida Tong
    Center for Toxicoinformatics, National Center for Toxicological Research, FDA, Jefferson, AR, USA Electronic
    Drug Discov Today Technol 4:3-8. 2007
  3. pmc Consistency of predictive signature genes and classifiers generated using different microarray platforms
    X Fan
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
    Pharmacogenomics J 10:247-57. 2010
  4. pmc Investigating drug repositioning opportunities in FDA drug labels through topic modeling
    Halil Bisgin
    Department of Information Science, University of Arkansas at Little Rock, 2801 S, University Ave, Little Rock, AR 72204 1099, USA
    BMC Bioinformatics 13:S6. 2012
  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 Maximizing biomarker discovery by minimizing gene signatures
    Chang Chang
    The Center for Bioinformatics and Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
    BMC Genomics 12:S6. 2011
  7. pmc ebTrack: an environmental bioinformatics system built upon ArrayTrack
    Minjun Chen
    Department of Environmental and Occupational Medicine, UMDNJ RWJMS, 675 Hoes Lane, Piscataway, NJ 08854, USA
    BMC Proc 3:S5. 2009
  8. pmc Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)
    Pierre R Bushel
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    BMC Proc 3:S1. 2009
  9. pmc Mining FDA drug labels using an unsupervised learning technique--topic modeling
    Halil Bisgin
    Department of Information Science, University of Arkansas at Little Rock, 2801 S, University Ave, Little Rock, AR 72204 1099, USA
    BMC Bioinformatics 12:S11. 2011
  10. 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

Collaborators

Detail Information

Publications81

  1. pmc Translating clinical findings into knowledge in drug safety evaluation--drug induced liver injury prediction system (DILIps)
    Zhichao Liu
    Division of Systems Biology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arizona, USA
    PLoS Comput Biol 7:e1002310. 2011
    ..We expect that the methodology can be also applied to other drug safety endpoints, such as renal or cardiovascular toxicity...
  2. ncbi request reprint An integrated bioinformatics infrastructure essential for advancing pharmacogenomics and personalized medicine in the context of the FDA's Critical Path Initiative
    Weida Tong
    Center for Toxicoinformatics, National Center for Toxicological Research, FDA, Jefferson, AR, USA Electronic
    Drug Discov Today Technol 4:3-8. 2007
    ..ArrayTrack is used in the routine review of genomic data submitted to the FDA; here, three hypothetical examples of its use in the Voluntary eXploratory Data Submission (VXDS) program are illustrated.: ..
  3. pmc Consistency of predictive signature genes and classifiers generated using different microarray platforms
    X Fan
    College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
    Pharmacogenomics J 10:247-57. 2010
    ..The study reveals an opportunity for possible translation of biomarkers identified using microarrays to clinically validated non-array gene expression assays...
  4. pmc Investigating drug repositioning opportunities in FDA drug labels through topic modeling
    Halil Bisgin
    Department of Information Science, University of Arkansas at Little Rock, 2801 S, University Ave, Little Rock, AR 72204 1099, USA
    BMC Bioinformatics 13:S6. 2012
    ..Therefore, our drug repositioning approach can take the advantage of more comprehensive safety information comparing with conventional de novo approach...
  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 Maximizing biomarker discovery by minimizing gene signatures
    Chang Chang
    The Center for Bioinformatics and Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
    BMC Genomics 12:S6. 2011
    ....
  7. pmc ebTrack: an environmental bioinformatics system built upon ArrayTrack
    Minjun Chen
    Department of Environmental and Occupational Medicine, UMDNJ RWJMS, 675 Hoes Lane, Piscataway, NJ 08854, USA
    BMC Proc 3:S5. 2009
    ..The design of ebTrack is presented in detail and steps involved in its application are summarized through an illustrative application...
  8. pmc Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)
    Pierre R Bushel
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    BMC Proc 3:S1. 2009
    ....
  9. pmc Mining FDA drug labels using an unsupervised learning technique--topic modeling
    Halil Bisgin
    Department of Information Science, University of Arkansas at Little Rock, 2801 S, University Ave, Little Rock, AR 72204 1099, USA
    BMC Bioinformatics 12:S11. 2011
    ..Consequently, this task has largely relied on the manual reading of the full text by experts, which is time consuming and labor intensive...
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. ncbi request reprint Quantitative structure-activity relationship models for predicting drug-induced liver injury based on FDA-approved drug labeling annotation and using a large collection of drugs
    Minjun Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079
    Toxicol Sci 136:242-9. 2013
    ....
  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. 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...
  19. 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...
  20. 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
    ....
  21. 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...
  22. 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%...
  23. doi request reprint Comparative analysis of predictive models for nongenotoxic hepatocarcinogenicity using both toxicogenomics and quantitative structure-activity relationships
    Zhichao Liu
    Center of Excellence for Bioinformatics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    Chem Res Toxicol 24:1062-70. 2011
    ..55). Permutation tests confirmed the statistical significance of the model's prediction performance. The study concluded that a short-term 5-day TGx animal model holds the potential to predict nongenotoxic hepatocarcinogenicity...
  24. 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...
  25. doi request reprint A decade of toxicogenomic research and its contribution to toxicological science
    Minjun Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Toxicol Sci 130:217-28. 2012
    ..Finally, we provide a perspective on the future direction of toxicogenomics and how new technologies such as RNA-Seq may impact this field...
  26. 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...
  27. 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...
  28. 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...
  29. 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...
  30. 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...
  31. 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...
  32. 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)...
  33. pmc Shifting from population-wide to personalized cancer prognosis with microarrays
    Li Shao
    Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
    PLoS ONE 7:e29534. 2012
    ..Ascribing a confidence level to prognosis with the clinical confidence metric provides the clinician an objective, personalized basis for decisions, such as choosing the severity of the treatment...
  34. 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...
  35. 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...
  36. pmc Cross-platform comparison of microarray-based multiple-class prediction
    Xiaohui Fan
    Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
    PLoS ONE 6:e16067. 2011
    ..Further studies are needed to confirm the feasibility of microarray-based cross-platform prediction, especially using independent datasets...
  37. 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
    ....
  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. 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...
  40. 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...
  41. 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...
  42. 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...
  43. 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...
  44. doi request reprint A unifying ontology to integrate histological and clinical observations for drug-induced liver injury
    Yuping Wang
    Divisions of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Am J Pathol 182:1180-7. 2013
    ..In conclusion, DILIo entrains different algorithms for an efficient meta-analysis of published findings for an improved understanding of mechanisms and clinical characteristics of DILI...
  45. ncbi request reprint FDA-approved drug labeling for the study of drug-induced liver injury
    Minjun Chen
    Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    Drug Discov Today 16:697-703. 2011
    ..The method is transparent and reproducible with a potential to serve as a common practice to study the DILI of marketed drugs for supporting drug discovery and biomarker development...
  46. 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...
  47. 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...
  48. 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...
  49. 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...
  50. pmc ArrayTrack: a free FDA bioinformatics tool to support emerging biomedical research--an update
    Joshua Xu
    Z Tech Corporation, an ICF International Company at the National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079, USA
    Hum Genomics 4:428-34. 2010
    ..Other extensions have been added to manage and analyse genomics data related to bacterial food-borne pathogens...
  51. ncbi 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. ..
  52. doi request reprint DNA microarrays are predictive of cancer prognosis: a re-evaluation
    Xiaohui Fan
    Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
    Clin Cancer Res 16:629-36. 2010
    ..We set to investigate the reality of microarrays for predicting cancer prognosis by using the same data sets with commonly accepted data analysis approaches...
  53. 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...
  54. doi request reprint Rat α-Fetoprotein binding affinities of a large set of structurally diverse chemicals elucidated the relationships between structures and binding affinities
    Huixiao Hong
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, AK 72079, USA
    Chem Res Toxicol 25:2553-66. 2012
    ..The data assist in elucidating binding interactions and mechanisms between chemicals and rat AFP and, in turn, assist in the evaluation of the endocrine disrupting potential of chemicals...
  55. 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...
  56. 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...
  57. 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...
  58. ncbi request reprint A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the 'rule-of-two' model
    Minjun Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, 72079, USA
    Arch Toxicol 88:1439-49. 2014
    ..Taken collectively, the proposed testing strategy can significantly improve the prediction of in vitro assays for detecting DILI liability in an early drug discovery phase. ..
  59. 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...
  60. 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...
  61. 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...
  62. 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...
  63. 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...
  64. 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
    ....
  65. 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...
  66. doi request reprint In silico drug repositioning: what we need to know
    Zhichao Liu
    ICF International at FDA National Center for Toxicological Research, Jefferson, AR 72079, USA
    Drug Discov Today 18:110-5. 2013
    ....
  67. pmc Two new ArrayTrack libraries for personalized biomedical research
    Joshua Xu
    Z Tech Corporation, ICF International company at NCTR, National Center for Toxicological Research, 3900 NCTR Rd, Jefferson, AR 72079, USA
    BMC Bioinformatics 11:S6. 2010
    ..An efficient data mining strategy and a set of sophisticated tools are necessary to help better understand and utilize the findings from genetic association studies...
  68. pmc Meta-analysis of microarray data using a pathway-based approach identifies a 37-gene expression signature for systemic lupus erythematosus in human peripheral blood mononuclear cells
    Dhivya Arasappan
    National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    BMC Med 9:65. 2011
    ..However, meta-analysis approaches with microarray data have not been well-explored in SLE...
  69. 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...
  70. 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...
  71. doi request reprint Assessing consistency between versions of genotype-calling algorithm Birdseed for the Genome-Wide Human SNP Array 6.0 using HapMap samples
    Huixiao Hong
    Center for Toxicoinformatics, Division of Systems Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Adv Exp Med Biol 680:355-60. 2010
    ..Our results revealed that genotypes called from version-1 and version-2 of Birdseed were slightly different and the inconsistency in genotypes propagated to the downstream association analysis...
  72. 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...
  73. 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...
  74. 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
    ....
  75. doi request reprint 2012 Global Summit on Regulatory Science (GSRS-2012)--modernizing toxicology
    Margaret A Miller
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Toxicol Sci 131:9-12. 2013
    ....
  76. doi request reprint High lipophilicity and high daily dose of oral medications are associated with significant risk for drug-induced liver injury
    Minjun Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
    Hepatology 58:388-96. 2013
    ..Conclusion: Apart from dose, lipophilicity contributes significantly to risk for hepatotoxicity. Applying the rule-of-two is an appropriate means of estimating risk for DILI compared with dose alone...
  77. doi request reprint Is toxicogenomics a more reliable and sensitive biomarker than conventional indicators from rats to predict drug-induced liver injury in humans?
    Min Zhang
    Center of Excellence for Bioinformatics, Division of Systems Biology, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, United States
    Chem Res Toxicol 25:122-9. 2012
    ..The study will facilitate further research to understand the role of genomic biomarkers from rats for assessing human hepatotoxicity...
  78. 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...
  79. 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
    ....
  80. 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...
  81. pmc Identification of New SRF Binding Sites in Genes Modulated by SRF Over-Expression in Mouse Hearts
    Xiaomin Zhang
    Donald W Reynolds Department of Geriatrics, The University of Arkansas for Medical Sciences and Geriatric Research, Education, and Clinical Center, Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
    Gene Regul Syst Bio 5:41-59. 2011
    ....