S D Peddada

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. 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
  2. pmc Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data
    Wenge Guo
    Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
    BMC Bioinformatics 13:177. 2012
  3. 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
  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. 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
  6. 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
  7. ncbi request reprint Tests for order restrictions in binary data
    S D Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Biometrics 57:1219-27. 2001
  8. ncbi request reprint ORIOGEN: order restricted inference for ordered gene expression data
    S Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences, Durham, NC 27713, USA
    Bioinformatics 21:3933-4. 2005
  9. 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
  10. 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

Collaborators

Detail Information

Publications15

  1. 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...
  2. pmc Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data
    Wenge Guo
    Department of Mathematical Sciences, New Jersey Institute of Technology, Newark, NJ 07102, USA
    BMC Bioinformatics 13:177. 2012
    ..Secondly, variables (e.g. genes) belonging to a set or a subset are potentially correlated, yet such information is often ignored and univariate methods are used. This may result in loss of power and/or inflated false positive rate...
  3. 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...
  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. 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...
  6. 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...
  7. ncbi request reprint Tests for order restrictions in binary data
    S D Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Biometrics 57:1219-27. 2001
    ..The procedure is illustrated through application to two data sets that correspond to three commonly encountered order restrictions: simple tree order, simple order, and down turn order...
  8. ncbi request reprint ORIOGEN: order restricted inference for ordered gene expression data
    S Peddada
    Biostatistics Branch, National Institute of Environmental Health Sciences, Durham, NC 27713, USA
    Bioinformatics 21:3933-4. 2005
    ..nih.gov (for statistical questions) and oriogen@constellagroup.com (for software support) SUPPLEMENTARY INFORMATION: ORIOGEN has a full set of help files. Also, an example input file is provided with the download...
  9. 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...
  10. 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...
  11. 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...
  12. 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...
  13. 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...
  14. 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...
  15. 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
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