Shyamal D Peddada

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. ncbi request reprint Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference
    Shyamal D Peddada
    Biostatistics Branch, Laboratory of Molecular Carcinogenesis, Research Triangle Park, NC 27709, USA
    Bioinformatics 19:834-41. 2003
  2. doi request reprint Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancer
    Arun R Pandiri
    Cellular and Molecular Pathology Branch, National Toxicology Program NTP, National Institute of Environmental Health Sciences NIEHS, Research Triangle Park, North Carolina, USA
    Toxicol Pathol 40:1141-59. 2012
  3. pmc A random-periods model for expression of cell-cycle genes
    Delong Liu
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, P O Box 12233, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 101:7240-5. 2004
  4. pmc Phase analysis of circadian-related genes in two tissues
    Delong Liu
    Biostatistics Branch, National Institute of Environmental Health Sciences, MD A3 03, 111 TW Alexander Dr, Research Triangle Park, NC 27709, USA
    BMC Bioinformatics 7:87. 2006
  5. ncbi request reprint Estradiol regulates the thioredoxin antioxidant system in the mouse uterus
    Bonnie J Deroo
    Receptor Biology Section, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Endocrinology 145:5485-92. 2004
  6. doi request reprint Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer
    Mark J Hoenerhoff
    Cellular and Molecular Pathology Branch, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Toxicol Pathol 39:678-99. 2011
  7. ncbi request reprint A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions
    Delong Liu
    Biostatistics Branch, MD A3 03, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC 27709, USA
    Bioinformatics 20:2521-8. 2004
  8. pmc Points to consider on the statistical analysis of rodent cancer bioassay data when incorporating historical control data
    Susan A Elmore
    National Toxicology Program, National Institute of Environmental Health Sciences, Cellular and Molecular Pathology Branch Research Triangle Park, North Carolina 27709, USA
    Toxicol Pathol 37:672-6. 2009
  9. pmc Analysis of nonlinear regression models: a cautionary note
    Shyamal D Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Dose Response 3:342-52. 2005
  10. pmc A survival-adjusted quantal-response test for analysis of tumor incidence rates in animal carcinogenicity studies
    Shyamal D Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
    Environ Health Perspect 114:537-41. 2006

Collaborators

Detail Information

Publications22

  1. ncbi request reprint Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference
    Shyamal D Peddada
    Biostatistics Branch, Laboratory of Molecular Carcinogenesis, Research Triangle Park, NC 27709, USA
    Bioinformatics 19:834-41. 2003
    ..In this example, our method was able to identify several biologically interesting genes that previous analyses failed to reveal...
  2. doi request reprint Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancer
    Arun R Pandiri
    Cellular and Molecular Pathology Branch, National Toxicology Program NTP, National Institute of Environmental Health Sciences NIEHS, Research Triangle Park, North Carolina, USA
    Toxicol Pathol 40:1141-59. 2012
    ....
  3. pmc A random-periods model for expression of cell-cycle genes
    Delong Liu
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, P O Box 12233, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 101:7240-5. 2004
    ..The model permits estimation of and hypothesis testing about biologically meaningful parameters that characterize cycling genes...
  4. pmc Phase analysis of circadian-related genes in two tissues
    Delong Liu
    Biostatistics Branch, National Institute of Environmental Health Sciences, MD A3 03, 111 TW Alexander Dr, Research Triangle Park, NC 27709, USA
    BMC Bioinformatics 7:87. 2006
    ..These interesting biological observations prompt a statistical question regarding how to distinguish the synchronized genes from genes that are systematically lagged in phase/peak expression time across two tissues...
  5. ncbi request reprint Estradiol regulates the thioredoxin antioxidant system in the mouse uterus
    Bonnie J Deroo
    Receptor Biology Section, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Endocrinology 145:5485-92. 2004
    ..We conclude that the rapid E2-mediated activation of the Txn pathway is an important step in the response of the mammalian uterus to estrogen...
  6. doi request reprint Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer
    Mark J Hoenerhoff
    Cellular and Molecular Pathology Branch, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
    Toxicol Pathol 39:678-99. 2011
    ....
  7. ncbi request reprint A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions
    Delong Liu
    Biostatistics Branch, MD A3 03, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC 27709, USA
    Bioinformatics 20:2521-8. 2004
    ..Our proposed methodology is illustrated by applying it to a HeLa cell-cycle gene-expression data...
  8. pmc Points to consider on the statistical analysis of rodent cancer bioassay data when incorporating historical control data
    Susan A Elmore
    National Toxicology Program, National Institute of Environmental Health Sciences, Cellular and Molecular Pathology Branch Research Triangle Park, North Carolina 27709, USA
    Toxicol Pathol 37:672-6. 2009
    ..The various options for the statistical analysis of HCD presented here do not necessarily represent standard practice...
  9. pmc Analysis of nonlinear regression models: a cautionary note
    Shyamal D Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
    Dose Response 3:342-52. 2005
    ..Sometimes they could underestimate the true nominal level and are thus liberal. Hence one needs to be cautious in using the usual linearized standard errors of MLE and the associated confidence intervals...
  10. pmc A survival-adjusted quantal-response test for analysis of tumor incidence rates in animal carcinogenicity studies
    Shyamal D Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
    Environ Health Perspect 114:537-41. 2006
    ..The trend test and the multiple pairwise comparisons test are demonstrated using an example from a study conducted by the NTP...
  11. pmc Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome
    Alejandro Colaneri
    Laboratory of Neurobiology, Library and Information Services, and Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA
    Proc Natl Acad Sci U S A 108:9715-20. 2011
    ..About 50% of MSCC-defined unmethylated regions do not overlap algorithm-defined CGIs and offer a novel search space in which new functionalities of DNA may be found in health and disease...
  12. doi request reprint Aloe vera non-decolorized whole leaf extract-induced large intestinal tumors in F344 rats share similar molecular pathways with human sporadic colorectal tumors
    Arun R Pandiri
    Cellular and Molecular Pathology Branch, National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    Toxicol Pathol 39:1065-74. 2011
    ..In conclusion, the AVNWLE-induced large intestinal tumors in F344 rats share several similarities with hCRC at the morphological and molecular levels...
  13. pmc Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays
    Jun Lu
    Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, SRA International, Inc and Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 39:e86. 2011
    ..We demonstrate that PVAC exhibits equal or better performance than several widely used filtering methods. Furthermore, a data-driven approach that guides the selection of the filtering threshold value is also proposed...
  14. pmc Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle
    Pierre R Bushel
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    BMC Syst Biol 3:93. 2009
    ..It has only been partially characterized. As a result, important regulatory cascades in budding yeast have no known or complete counterpart in fission yeast...
  15. pmc Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories
    Wenge Guo
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Biometrics 66:485-92. 2010
    ..2002) and Peddada et al. (2003, Bioinformatics 19, 834-841). Although some of our findings overlap with previous findings, we identify several other genes that complement the results of Lobenhofer et al. (2002)...
  16. pmc Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species
    Miguel A Fernandez
    Department of Statistics and Operations Research, Universidad de Valladolid, Prado de Magdalena s n, 47005 Valladolid, Spain
    Nucleic Acids Res 40:2823-32. 2012
    ....
  17. pmc A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments
    Shyamal D Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences Research Triangle Park, NC 27709, USA
    BMC Bioinformatics 10:438. 2009
    ..1 is inefficient compared to the publicly available JAVA implementation. Our results on the false positive rate of ORIOGEN suggest some error in Figure three of Liu et al. 1, perhaps due to a programming error...
  18. ncbi request reprint Comparison of NTP historical control tumor incidence rates in female Harlan Sprague Dawley and Fischer 344/N Rats
    Gregg E Dinse
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
    Toxicol Pathol 38:765-75. 2010
    ..When vehicle was included as an additional matching criterion, the number of comparable F344/N rat studies dropped to four, but similar results were obtained...
  19. pmc Short-term change in growth of uterine leiomyoma: tumor growth spurts
    Donna Day Baird
    Epidemiology Branch, Laboratory of Women s Health, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Fertil Steril 95:242-6. 2011
    ..To describe the short-term changes in growth of uterine leiomyomas (fibroids)...
  20. pmc Male sex hormones promote vagally mediated reflex airway responsiveness to cholinergic stimulation
    Jeffrey W Card
    Division of Intramural Research, National Institute of Environmental Health Sciences, 111 T W Alexander Dr, Bldg 101, Rm D236, Research Triangle Park, NC 27709, USA
    Am J Physiol Lung Cell Mol Physiol 292:L908-14. 2007
    ..Together, these data indicate that male sex hormones promote cholinergic airway responsiveness via a vagally mediated reflex mechanism that may be important in the regulation of airway tone in the normal and diseased lung...
  21. ncbi request reprint Mutant Brca2/p53 mice exhibit altered radiation responses in the developing mammary gland
    Christopher D Houle
    Laboratory of Women s Health, National Institute of Environmental Health Sciences, NIH, P O Box 12233, Research Triangle Park, NC 27709, USA
    Exp Toxicol Pathol 57:105-15. 2005
    ..We also demonstrate distinct spatial differences in the cellular functions of Brca2 and p53 and show that combined mutation of both genes is more detrimental than loss of either gene alone...
  22. ncbi request reprint Hemostatic activation in a chemically induced rat model of severe hemolysis and thrombosis
    Deborah A Lewis
    Hemostasis and Thrombosis Center, Department of Medicine, Duke University Medical Center, Duke University Health System, Box 3422 Durham, NC 27710, USA
    Thromb Res 118:747-53. 2006
    ....