Research Topics
Genomes and Genes | Shyamal D PeddadaSummaryAffiliation: National Institutes of Health Country: USA Publications
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Publications
Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inferenceShyamal 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...
Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancerArun 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....
A random-periods model for expression of cell-cycle genesDelong 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...- Phase analysis of circadian-related genes in two tissuesDelong 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... - Estradiol regulates the thioredoxin antioxidant system in the mouse uterusBonnie 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... - Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancerMark 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.... - A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditionsDelong 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... - Points to consider on the statistical analysis of rodent cancer bioassay data when incorporating historical control dataSusan 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... - Analysis of nonlinear regression models: a cautionary noteShyamal 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... - A survival-adjusted quantal-response test for analysis of tumor incidence rates in animal carcinogenicity studiesShyamal 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... - Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genomeAlejandro 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... - Aloe vera non-decolorized whole leaf extract-induced large intestinal tumors in F344 rats share similar molecular pathways with human sporadic colorectal tumorsArun 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... - Principal component analysis-based filtering improves detection for Affymetrix gene expression arraysJun 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... - Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cyclePierre 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... - Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categoriesWenge 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)... - Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across speciesMiguel 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.... - A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experimentsShyamal 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... - Comparison of NTP historical control tumor incidence rates in female Harlan Sprague Dawley and Fischer 344/N RatsGregg 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... - Short-term change in growth of uterine leiomyoma: tumor growth spurtsDonna 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)... - Male sex hormones promote vagally mediated reflex airway responsiveness to cholinergic stimulationJeffrey 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... - Mutant Brca2/p53 mice exhibit altered radiation responses in the developing mammary glandChristopher 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... - Hemostatic activation in a chemically induced rat model of severe hemolysis and thrombosisDeborah 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....