James J Chen

Summary

Affiliation: Food and Drug Administration
Country: USA

Publications

  1. ncbi request reprint Classification ensembles for unbalanced class sizes in predictive toxicology
    J J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    SAR QSAR Environ Res 16:517-29. 2005
  2. ncbi request reprint Decision threshold adjustment in class prediction
    J J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    SAR QSAR Environ Res 17:337-52. 2006
  3. ncbi request reprint A probabilistic framework for non-cancer risk assessment
    James J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Regul Toxicol Pharmacol 48:45-50. 2007
  4. ncbi request reprint The simultaneous analysis of discrete and continuous outcomes in a dose-response study: using desirability functions
    Todd Coffey
    Department of Biostatistics, Virginia Commonwealth University, PO Box 980032, Richmond, VA 23298, USA
    Regul Toxicol Pharmacol 48:51-8. 2007
  5. ncbi request reprint Weighted p-value adjustments for animal carcinogenicity trend test
    J J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Biometrics 56:586-92. 2000
  6. ncbi request reprint Analysis of variance components in gene expression data
    James J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicology Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Bioinformatics 20:1436-46. 2004
  7. ncbi request reprint Significance analysis of groups of genes in expression profiling studies
    James J Chen
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
    Bioinformatics 23:2104-12. 2007
  8. ncbi request reprint Multi-class clustering and prediction in the analysis of microarray data
    Chen An Tsai
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration NCTR FDA HFT 20 Jefferson, AR 72079, USA
    Math Biosci 193:79-100. 2005
  9. pmc Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data
    James J Chen
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 8:412. 2007
  10. doi request reprint The genetic toxicology of methylphenidate hydrochloride in non-human primates
    Suzanne M Morris
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, United States
    Mutat Res 673:59-66. 2009

Collaborators

Detail Information

Publications88

  1. ncbi request reprint Classification ensembles for unbalanced class sizes in predictive toxicology
    J J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    SAR QSAR Environ Res 16:517-29. 2005
    ..The abatement method appears to perform well in balancing sensitivity and specificity...
  2. ncbi request reprint Decision threshold adjustment in class prediction
    J J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    SAR QSAR Environ Res 17:337-52. 2006
    ..Three example data sets were analyzed for illustrations...
  3. ncbi request reprint A probabilistic framework for non-cancer risk assessment
    James J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Regul Toxicol Pharmacol 48:45-50. 2007
    ..The proposed approach is based on the use of the BMDL (lower confidence limit on the benchmark dose) as a POD (point of departure) for risk assessment of non-cancer effects...
  4. ncbi request reprint The simultaneous analysis of discrete and continuous outcomes in a dose-response study: using desirability functions
    Todd Coffey
    Department of Biostatistics, Virginia Commonwealth University, PO Box 980032, Richmond, VA 23298, USA
    Regul Toxicol Pharmacol 48:51-8. 2007
    ....
  5. ncbi request reprint Weighted p-value adjustments for animal carcinogenicity trend test
    J J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Biometrics 56:586-92. 2000
    ..Both weighted analyses showed a significant dose-related trend for one rare tumor...
  6. ncbi request reprint Analysis of variance components in gene expression data
    James J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicology Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Bioinformatics 20:1436-46. 2004
    ..Each week there were reference and test samples with a dye-flip replicate in two hybridization days. The variance components included week-to-week, animal-to-animal and between-array and within-array variances...
  7. ncbi request reprint Significance analysis of groups of genes in expression profiling studies
    James J Chen
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
    Bioinformatics 23:2104-12. 2007
    ..These two hypotheses are related but not equivalent...
  8. ncbi request reprint Multi-class clustering and prediction in the analysis of microarray data
    Chen An Tsai
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration NCTR FDA HFT 20 Jefferson, AR 72079, USA
    Math Biosci 193:79-100. 2005
    ..With respect to prediction, the overall accuracy for the gene set omega(I) using the nearest neighbors algorithm to predict 55 samples into one of the nine treatments is 85%...
  9. pmc Reproducibility of microarray data: a further analysis of microarray quality control (MAQC) data
    James J Chen
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    BMC Bioinformatics 8:412. 2007
    ....
  10. doi request reprint The genetic toxicology of methylphenidate hydrochloride in non-human primates
    Suzanne M Morris
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, United States
    Mutat Res 673:59-66. 2009
    ..3 microg/ml. No significant increases in the frequencies of MN-RETs, HPRT mutants, or chromosome aberrations were detected in the treated animals compared to the control animals over the 20-month exposure period...
  11. doi request reprint Effect of p53 genotype on gene expression profiles in murine liver
    Suzanne M Morris
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, United States
    Mutat Res 640:54-73. 2008
    ..This may indicate that alternate pathways are brought into play in the unperturbed liver when loss or reduction in p53 levels occurs...
  12. pmc Meta-analysis of pulsed-field gel electrophoresis fingerprints based on a constructed Salmonella database
    Wen Zou
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas, United States of America
    PLoS ONE 8:e59224. 2013
    ..The presence of distinct, serotype specific patterns may provide useful information to aid in the distribution of serotypes in the population and potentially reduce the need for laborious analyses, such as traditional serotyping...
  13. doi request reprint Identifying high-dimensional biomarkers for personalized medicine via variable importance ranking
    Songjoon Baek
    Division of Personalized Nutrition and Medicine Biometry Branch, National Center for Toxicological Research, FDA, Jefferson, Arkansas, USA
    J Biopharm Stat 18:853-68. 2008
    ....
  14. ncbi request reprint On the use of hierarchical probabilistic models for characterizing and managing uncertainty in risk/safety assessment
    Ralph L Kodell
    Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 7199, USA
    Risk Anal 27:433-7. 2007
    ..The empirical probability distributions of the numerator and denominator can be combined to produce an empirical human-equivalent distribution for an animal-derived benchmark dose in external-exposure units...
  15. ncbi request reprint Sample size for gene expression microarray experiments
    Chen An Tsai
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Bioinformatics 21:1502-8. 2005
    ..The sample size problem is formulated as: the number of arrays needed in order to achieve the desired fraction of the specified measure at the desired family-wise power at the given type I error and (standardized) effect size...
  16. doi request reprint Evaluation of p53 genotype on gene expression in the testis, liver, and heart from male C57BL/6 mice
    Dayton M Petibone
    Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, FDA, Jefferson, AR, USA
    Transgenic Res 21:257-63. 2012
    ..These data indicate that gene expression in unperturbed tissue is influenced by the status of p53 genotype, and relates, at least partially, to the function of the tissue...
  17. ncbi request reprint Sample size for identifying differentially expressed genes in microarray experiments
    Sue Jane Wang
    Division of Biometrics II, Office of Biostatistics, Center for Drug Evaluation and Research, Food and Drug Administration, 5600 Fishers Lane, Rockville, Maryland 20857, USA
    J Comput Biol 11:714-26. 2004
    ..An example dataset is used to illustrate the use of the proposed approach to plan microarray experiments...
  18. pmc Gene selection with multiple ordering criteria
    James J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
    BMC Bioinformatics 8:74. 2007
    ..These two selection criteria often result in incompatible selected gene sets. Also, in a two-factor, say, treatment by time experiment, the investigator may be interested in one gene list that responds to both treatment and time effects...
  19. pmc Assessment of performance of survival prediction models for cancer prognosis
    Hung Chia Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    BMC Med Res Methodol 12:102. 2012
    ..Although this approach has several drawbacks, it does provide natural performance metrics such as positive and negative predictive values to enable unambiguous assessments...
  20. pmc Prediction system for rapid identification of Salmonella serotypes based on pulsed-field gel electrophoresis fingerprints
    Wen Zou
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA
    J Clin Microbiol 50:1524-32. 2012
    ..Additionally, this system also works well for isolates that are serotyped as "unknown" by conventional methods, and it is useful for a laboratory where standard serotyping is not available...
  21. ncbi request reprint A generalized additive model for microarray gene expression data analysis
    Chen An Tsai
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Biopharm Stat 14:553-73. 2004
    ..Two toxicogenomic experiment data sets and a simulated data set are used to contrast the proposed method with the commonly known lowess fit and ANOVA methods...
  22. ncbi request reprint Alterations in gene expression profiles and the DNA-damage response in ionizing radiation-exposed TK6 cells
    Gregory S Akerman
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Environ Mol Mutagen 45:188-205. 2005
    ....
  23. ncbi request reprint Multiple-testing strategy for analyzing cDNA array data on gene expression
    Robert R Delongchamp
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
    Biometrics 60:774-82. 2004
    ..Two functional genomics studies that were designed to assess a treatment effect are used to illustrate how the methods allowed the investigators to determine a cutoff to suit their research goals...
  24. ncbi request reprint Influence of dietary antioxidants on the mutagenicity of 7,12-dimethylbenz[a]anthracene and bleomycin in female rats
    M Khaidakov
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, FDA Jefferson Laboratories, Jefferson, AR 72079, USA
    Mutat Res 480:163-70. 2001
    ..Pending molecular analysis of mitochondrial DNA mutations will also indicate whether there is a shift in the mutational spectra produced by the carcinogens in the presence of antioxidants...
  25. pmc Identification of bicluster regions in a binary matrix and its applications
    Hung Chia Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas, United States of America
    PLoS ONE 8:e71680. 2013
    ..However, dichotomization using different signal level thresholds usually leads to different sets of biclusters; this also occurs in the present analysis. ..
  26. ncbi request reprint Database composition can affect the structure-activity relationship prediction
    John F Young
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079 9502, USA
    J Toxicol Environ Health A 69:1527-40. 2006
    ..The numbers of chemicals in the various data sets ranged from 187 to 999 and appeared to have no affect on any of the 3 predictors of sensitivity, specificity, or concordance...
  27. doi request reprint The genetic toxicity of methylphenidate: a review of the current literature
    Suzanne M Morris
    Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    J Appl Toxicol 32:756-64. 2012
    ..Published 2012. This article is a US Government work and is in the public domain in the USA...
  28. ncbi request reprint A comparison of microbial dose-response models fitted to human data
    Hojin Moon
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, 3900 NCTR Road, Jefferson, AR 72079, USA
    Regul Toxicol Pharmacol 40:177-84. 2004
    ..The model uncertainty analysis proposed by Kang et al. [Regulat. Toxicol. Pharmacol. 32 (2000) 68] using four two-parameter models was reinforced...
  29. ncbi request reprint The false discovery rate: a key concept in large-scale genetic studies
    James J Chen
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Food and Drug Administration, HFT 20, Jefferson, AR 72079, USA
    Cancer Control 17:58-62. 2010
    ..When more than one test is conducted, use of a significance level intended for use by a single test typically leads to a large chance of false-positive findings...
  30. pmc Power and sample size estimation in microarray studies
    Wei Jiun Lin
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
    BMC Bioinformatics 11:48. 2010
    ..A permutation method using a small pilot dataset to estimate sample size is proposed. This method accounts for correlation and effect size heterogeneity among genes...
  31. ncbi request reprint Significance analysis of ROC indices for comparing diagnostic markers: applications to gene microarray data
    Chen An Tsai
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    J Biopharm Stat 14:985-1003. 2004
    ..The selected gene sets from three ROC summary indices and the commonly used two-sample t-statistic are applied to the sample classification to evaluate the predictability of the four discrimination measures...
  32. ncbi request reprint Normalization methods for analysis of microarray gene-expression data
    Yi Ju Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Biopharm Stat 13:57-74. 2003
    ..The method that combines a subset approach (median or lowess fit) for location adjustment with a global lowess fit for intensity adjustment appears to perform well...
  33. doi request reprint Using dietary exposure and physiologically based pharmacokinetic/pharmacodynamic modeling in human risk extrapolations for acrylamide toxicity
    Daniel R Doerge
    National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, Jefferson, Arkansas 72079, USA
    J Agric Food Chem 56:6031-8. 2008
    ..These results suggest that a more holistic analysis of dietary cancer risks may be appropriate, by which potential risks from AA should be considered in conjunction with other risks and benefits from foods...
  34. doi request reprint Development of biomarker classifiers from high-dimensional data
    Songjoon Baek
    National Center for Toxicological Research, U S Food and Drug Administration, USA
    Brief Bioinform 10:537-46. 2009
    ..In each of the four classifiers the feature predictor set selected by the frequency approach is more stable than the feature set selected by the conventional approach...
  35. pmc A novel procedure on next generation sequencing data analysis using text mining algorithm
    Weizhong Zhao
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, HFT 20, Jefferson, AR, 72079, USA
    BMC Bioinformatics 17:213. 2016
    ..Topic modeling is an active research field in machine learning and has been mainly used as an analytical tool to structure large textual corpora for data mining...
  36. 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...
  37. pmc Assessment of reproducibility of cancer survival risk predictions across medical centers
    Hung Chia Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, AR 72079, USA
    BMC Med Res Methodol 13:25. 2013
    ..We present approaches for assessment of reproducibility of survival risk score predictions across medical centers...
  38. pmc Testing for differentially expressed genes with microarray data
    Chen An Tsai
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Nucleic Acids Res 31:e52. 2003
    ..For data from independent samples, such as the one-channel array or two-channel array experiment using reference design, the two-sample t-tests appear more powerful than the one-sample t-tests...
  39. ncbi request reprint Model averaging using the Kullback information criterion in estimating effective doses for microbial infection and illness
    Hojin Moon
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Drive, Jefferson, AR 72079, USA
    Risk Anal 25:1147-59. 2005
    ..The proposed procedures for incorporating model uncertainties and making inferences are illustrated with human infection/illness dose-response data sets...
  40. ncbi request reprint Estimation of false discovery rates in multiple testing: application to gene microarray data
    Chen An Tsai
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
    Biometrics 59:1071-81. 2003
    ..The bootstrap procedure appears to perform reasonably well, even when the alternative hypotheses are correlated (rho = .25). An example from a toxicogenomic microarray experiment is presented for illustration...
  41. ncbi request reprint Key aspects of analyzing microarray gene-expression data
    James J Chen
    US FDA, Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Pharmacogenomics 8:473-82. 2007
    ..Development of a prediction model involves two components: model building and performance assessment. It also describes two additional data analysis methods: gene-class testing and multiple ordering criteria...
  42. ncbi request reprint Statistics for risk assessment of chemical carcinogens
    James J Chen
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
    J Environ Sci Health C Environ Carcinog Ecotoxicol Rev 25:281-312. 2007
    ..This paper reviews statistical principles and procedures for qualitative and quantitative approaches to human risk assessment...
  43. ncbi request reprint Gene selection for sample classifications in microarray experiments
    Chen An Tsai
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    DNA Cell Biol 23:607-14. 2004
    ..OmegaF has slightly higher accuracy rates than omegaT. The overall predicted accuracies are above 70% for the external crossvalidation; the two gene sets omegaT and omegaF performed equally well...
  44. pmc Evaluation of pulsed-field gel electrophoresis profiles for identification of Salmonella serotypes
    Wen Zou
    Division of Personalized Nutrition and Medicine HFT 20, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, AR 72079, USA
    J Clin Microbiol 48:3122-6. 2010
    ..Discriminatory DNA band class markers were identified for distinguishing Salmonella serotype Heidelberg, Javiana, Typhimurium, and Newport isolates...
  45. pmc Dye bias correction in dual-labeled cDNA microarray gene expression measurements
    Barry A Rosenzweig
    Center for Drug Evaluation and Research, Division of Applied Pharmacology Research, U S Food and Drug Administration, 10903 New Hampshire Avenue, Life Sciences Building 64, Silver Spring, MD 20993, USA
    Environ Health Perspect 112:480-7. 2004
    ..These data support a practical and more efficient experimental design to measure and mathematically correct for dye bias...
  46. ncbi request reprint A mechanistic approach to modelling the risk of liver tumours in mice exposed to fumonisin B1 in the diet
    R L Kodell
    National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Food Addit Contam 18:237-53. 2001
    ..The model was able to reproduce reasonably well the observed tumour rates in both female and male mice, predicting substantially increased rates above background only at the highest doses of fumonisin B1 in females...
  47. ncbi request reprint Bioassays of shortened duration for drugs: statistical implications
    R L Kodell
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Toxicol Sci 55:415-32. 2000
    ..For the 21-month stopping time, the results showed that, unless pure promotion can be ruled out a priori as a potential carcinogenic mode of action, the loss of power is too great to warrant early stopping...
  48. ncbi request reprint Attenuation of bleomycin-induced Hprt mutant frequency in female and male rats by calorie restriction
    A Aidoo
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Mutat Res 430:155-63. 1999
    ..The results indicate that calorie intake of 60% reduced the mutagenic response of BLM, a compound known to induce oxidative DNA damage, and suggest a possible decrease in ROS as a function of calorie restriction...
  49. ncbi request reprint Evaluation of the genotoxicity of the phytoestrogen, coumestrol, in AHH-1 TK(+/-) human lymphoblastoid cells
    O E Domon
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research (NCTR, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    Mutat Res 474:129-37. 2001
    ..Taken together, these results suggest that coumestrol exhibits both mutagenic and clastogenic properties in cultured human lymphoblastoid cells...
  50. ncbi request reprint Aflatoxin B1-induced Hprt mutations in splenic lymphocytes of Fischer 344 rats. Results of an intermittent feeding trial
    S M Morris
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, Food and Drug Administration, Department of Health and Human Services, 3900 NCTR Road, Jefferson, AR 72079, USA
    Mutat Res 423:33-8. 1999
    ..These results indicate that the rat lymphocyte/Hprt assay is useful for detecting chronic low level exposures. Further, these data suggest that an intermittent, low-level exposure to AFB1 may present a human health risk...
  51. ncbi request reprint p53, mutations, and apoptosis in genistein-exposed human lymphoblastoid cells
    S M Morris
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Mutat Res 405:41-56. 1998
    ..Our results may be interpreted that genistein is a chromosomal mutagen and that p53 functional status affects the recovery of chromosomal mutants, possibly by signalling cells into the apoptosis pathways...
  52. ncbi request reprint Relative contribution of calories from dietary fat, carbohydrate, and fiber in the promotion of DMBA-induced mammary tumors in Sprague-Dawley rats
    C D Jackson
    National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR 72079, USA
    Nutr Cancer 30:194-200. 1998
    ..The statistical model derived from these results also indicates a significant synergistic interaction of dietary fat and carbohydrate on final body weight and tumor incidence...
  53. ncbi request reprint A role for apoptosis in the toxicity and mutagenicity of bleomycin in AHH-1 tk+/- human lymphoblastoid cells
    S M Morris
    Department of Health and Human Services, Food and Drug Administration, Jefferson, AR 72079, USA
    Mutat Res 357:143-65. 1996
    ....
  54. ncbi request reprint Effect of dietary genistein on cell replication indices in C57BL6 mice
    S M Morris
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, HFT 120 DGRT NCTR, 3900 NCTR Road, Jefferson, AR 72079, USA
    Cancer Lett 195:139-45. 2003
    ..Thus, genistein appears to accumulate to a sufficient level to affect topo-II activity in the small intestine...
  55. ncbi request reprint Hierarchical models for probabilistic dose-response assessment
    R L Kodell
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Regul Toxicol Pharmacol 45:265-72. 2006
    ..In addition, the complexity of a PK model of internal dose does not affect how the variability in risk is measured via the ultimate endpoint...
  56. pmc Text mining for identifying topics in the literatures about adolescent substance use and depression
    Shi Heng Wang
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, 3900 NCTR Road, HFT 20, Jefferson, AR, 72079, USA
    BMC Public Health 16:279. 2016
    ..Topic modeling offers a computational tool to find relevant topics by capturing meaningful structure among collections of documents...
  57. pmc A composite model for subgroup identification and prediction via bicluster analysis
    Hung Chia Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, Arkansas, United States of America Graduate Institute of Biostatistics and Biostatistics Center, China Medical University, Taichung, Taiwan
    PLoS ONE 9:e111318. 2014
    ..Each subgroup can represent different pathogen serotypes of microorganisms, different tumor subtypes in cancer patients, or different genetic makeups of patients related to treatment response...
  58. doi request reprint Quantitative benefit-risk analysis for evaluating drug therapies
    Ralph L Kodell
    Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
    J Biopharm Stat 23:231-8. 2013
    ....
  59. doi request reprint Pharmacokinetics, dose-range, and mutagenicity studies of methylphenidate hydrochloride in B6C3F1 mice
    Mugimane G Manjanatha
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, USA
    Environ Mol Mutagen 49:585-93. 2008
    ..05). There was no significant increase in either the Hprt mutant frequency or the micronucleus frequency in the treated animals. These results indicated that although MPH induced liver hypertrophy in mice, no genotoxicity was observed...
  60. doi request reprint ClassRHO: a platform for classification of bacterial rieske non-heme iron ring-hydroxylating oxygenases
    Songjoon Baek
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, AR 72079, USA
    J Microbiol Methods 76:307-9. 2009
    ..Pre-computed classifications were implemented for 42 standard RHO sequences. These 42 RHO sequences can be flexibly selected based on user requests. ClassRHO provides users with many options to view and analyze RHO sequences...
  61. doi request reprint An approach to identifying preclinical biomarkers of susceptibility to drug-induced toxicity
    Wei Jiun Lin
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    Pharmacogenomics 12:493-501. 2011
    ..This article presents a statistical model and an approach for identifying pharmacogenomic biomarkers of susceptibility to drug-induced toxicity for detecting the susceptible subpopulations...
  62. pmc Reordering hierarchical tree based on bilateral symmetric distance
    Minho Chae
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, United States of America
    PLoS ONE 6:e22546. 2011
    ..The relationship between objects is lost, however, because clusters rather than individual objects are compared. This results in a tree that is hard to interpret...
  63. pmc Classification methods for the development of genomic signatures from high-dimensional data
    Hojin Moon
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, FDA, NCTR Road, Jefferson, AR 72079, USA
    Genome Biol 7:R121. 2006
    ..CERP performs consistently well compared to the other classification algorithms. The predictive accuracy can be improved by adding some relevant clinical/histopathological measurements to the genomic data...
  64. doi request reprint Predictive biomarkers for treatment selection: statistical considerations
    James J Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Biomark Med 9:1121-35. 2015
    ....
  65. pmc Identification of reproducible gene expression signatures in lung adenocarcinoma
    Tzu Pin Lu
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration Jefferson, Little Rock, Arkansas, USA
    BMC Bioinformatics 14:371. 2013
    ..In this study, we proposed an approach by identifying predictive genes through pathways...
  66. pmc Comparison of the global gene expression of choroid plexus and meninges and associated vasculature under control conditions and after pronounced hyperthermia or amphetamine toxicity
    John F Bowyer
    Division of Neurotoxicology, National Center for Toxicological Research, U, S, Food and Drug Administration, Jefferson, AR 72079 9502, USA
    BMC Genomics 14:147. 2013
    ..Since AMPH and EIH are so disruptive to vasculature, genes related to vasculature integrity and function were of interest...
  67. doi request reprint Pharmacogenomic biomarkers for personalized medicine
    James J Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US FDA, 3900 NCTR Road, HFT 20, Jefferson, AR 72079, USA
    Pharmacogenomics 14:969-80. 2013
    ..This review describes the use of the two personalized medicine biomarkers, prognostic and predictive, to classify patients into subgroups for treatment recommendation...
  68. pmc Identification and categorization of liver toxicity markers induced by a related pair of drugs
    Ching Wei Chang
    Division of Personalized Nutrition and Medicine, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA E mail
    Int J Mol Sci 12:4609-24. 2011
    ..The gene Vars2 (valyl-tRNA synthetase 2) was identified in both animals and the pathway to which it belongs, the aminoacyl-tRNA biosynthesis pathway, was one of the three most significant tolcapone-specific pathways identified...
  69. ncbi request reprint Gene expression profiles and genetic damage in benzo(a)pyrene diol epoxide-exposed TK6 cells
    G S Akerman
    Division of Genetic and Reproductive Toxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
    Mutat Res 549:43-64. 2004
    ..001) was minimal. Alterations in gene expression were more robust at doses associated with cellular toxicity and induction of mutations...
  70. doi request reprint Ensemble survival trees for identifying subpopulations in personalized medicine
    Yu Chuan Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U S Food and Drug Administration, Jefferson, AR, 72079, USA
    Biom J 58:1151-63. 2016
    ..A simulation study is conducted to compare the performance between our proposed method and the multivariate Cox model. The applications of our proposed method to two public cancer data sets are also conducted for illustration. ..
  71. doi request reprint Identification of drug-induced toxicity biomarkers for treatment determination
    Tzu Pin Lu
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, Jefferson, AR, USA
    Pharm Stat 14:284-93. 2015
    ..When the proportion of susceptible subpopulation is 1% or less, a very large sample size is needed to ensure observing sufficient number of DIOT responses for biomarker and/or subpopulation identifications...
  72. doi request reprint Biomarker identification from next-generation sequencing data for pathogen bacteria characterization and surveillance
    Weizhong Zhao
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079, USA
    Biomark Med 9:1253-64. 2015
    ..The purpose was to develop an analytical pipeline for specific gene analysis and biomarker discovery from next generation sequencing (NGS) data...
  73. pmc Subgroup identification for treatment selection in biomarker adaptive design
    Tzu Pin Lu
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, HFT 20, Jefferson, AR, 72079, USA
    BMC Med Res Methodol 15:105. 2015
    ..We propose utilization of classification methods to identity patient subgroups and present a statistical testing strategy to detect treatment effects...
  74. doi request reprint Class-imbalanced classifiers for high-dimensional data
    Wei Jiun Lin
    Department of Applied Mathematics, Feng Chia University, Taiwan
    Brief Bioinform 14:13-26. 2013
    ..The SVM-THR performs well if the imbalance is severe and predictors are highly correlated. The DLDA with a feature selection can perform well without using the ensemble correction...
  75. doi request reprint Data mining for signal detection of adverse event safety data
    Hung Chia Chen
    Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    J Biopharm Stat 23:146-60. 2013
    ..Significance of each bicluster can be tested using disproportionality analysis. Individual drug-event combination can be further tested. A safety data set consisting of 193 drugs with 8453 adverse events is analyzed as an illustration...
  76. ncbi request reprint Mutagenicity of food-derived carcinogens and the effect of antioxidant vitamins
    Beverly A Montgomery
    Division of Genetic and Reproductive Toxicology, Division of Biometry and Risk Assessment, National Center for Toxicological Research, Jefferson, AR 72079, USA
    Nutr Cancer 43:103-10. 2002
    ....
  77. 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...
  78. ncbi request reprint Selection of differentially expressed genes in microarray data analysis
    J J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA
    Pharmacogenomics J 7:212-20. 2007
    ..The P-value and the fold-change can be pictorially shown simultaneously in a volcano plot. We also address several issues on gene selection...
  79. ncbi request reprint Using dose addition to estimate cumulative risks from exposures to multiple chemicals
    J J Chen
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Regul Toxicol Pharmacol 34:35-41. 2001
    ..An example data set of four drugs representing four chemicals is used to illustrate the proposed procedure and compare it to the HI, PODI, and TEF methods...
  80. ncbi request reprint An approximate unconditional test of non-inferiority between two proportions
    S H Kang
    Division of Biometry and Risk Assessment, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 72079, USA
    Stat Med 19:2089-100. 2000
    ..The performance of the tests depends on the sample size and the range of plausible values of the nuisance parameter. Published in 2000 by John Wiley & Sons, Ltd...
  81. ncbi request reprint Probe rank approaches for gene selection in oligonucleotide arrays with a small number of replicates
    Dung Tsa Chen
    Biostatistics and Bioinformatics Unit, Comprehensive Cancer Center, University of Alabama at Birmingham, 153 Wallace Tumor Institute, 1824 6th Avenue South, Birmingham, AL 35294, USA
    Bioinformatics 21:2861-6. 2005
    ..The probe level approach takes into account non-homogenous treatment effects and reduces possible cross-hybridization effects across a set of probes...
  82. ncbi request reprint Microarrays in pharmacogenomics
    James J Chen
    J Biopharm Stat 14:535-7. 2004
  83. ncbi request reprint A two-stage binomial test approach of gene identification in oligonucleotide arrays
    Dung Tsa Chen
    Biostatistics Division, Moffitt Cancer Center and Research Institute, University of South Florida, Tampa, Florida 12902, USA
    J Biopharm Stat 17:903-18. 2007
    ..In the breast cancer dataset, the approach also identified one potential alternative splicing gene...
  84. ncbi request reprint Comparison of methods for estimating the number of true null hypotheses in multiplicity testing
    Huey Miin Hsueh
    Department of Statistics, National Chengchi University, Taipei, Taiwan
    J Biopharm Stat 13:675-89. 2003
    ..These two methods control the FWE properly when the number of nontrue null hypotheses is small. A data set from a toxicogenomic microarray experiment is used for illustration...
  85. ncbi request reprint Age-adjusted exact trend tests in the event of rare occurrences
    Jessica Y Mancuso
    Pfizer Global Research and Development, Groton, Connecticut 06340, USA
    Biometrics 58:403-12. 2002
    ..The proposed age-adjusted exact test does not require COD, and it is shown to compare favorably to the COD tests via an extensive Monte Carlo simulation. Applications of the methods to two real data sets are included...
  86. ncbi request reprint An integrated tree-based classification approach to prognostic grouping with application to localized melanoma patients
    Chen An Tsai
    Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
    J Biopharm Stat 17:445-60. 2007
    ..This approach performs more efficiently than the standard tree methods and has made improvement over the current AJCC melanoma staging system...
  87. ncbi request reprint Ensemble methods for classification of patients for personalized medicine with high-dimensional data
    Hojin Moon
    Department of Mathematics and Statistics, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA 90840, USA
    Artif Intell Med 41:197-207. 2007
    ..An objective is to find a novel classification algorithm that can be used for prediction of response to therapy in order to help individualize clinical assignment of treatment...
  88. ncbi request reprint Tests for equivalence or non-inferiority for paired binary data
    Jen Pei Liu
    Division of Biostatistics and Bioinformatics, National Health Research Institutes, Taipei, Taiwan
    Stat Med 21:231-45. 2002
    ..15, a minimal sample size of 120 is needed. The RMLE-based test without the continuity correction performs well at the boundary point 0. A numerical example illustrates the proposed procedures...