S D Peddada
Affiliation: National Institutes of Health
- 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...
- Linear mixed effects models under inequality constraints with applicationsLaura Farnan
Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States of America
PLoS ONE 9:e84778. 2014..We illustrate the proposed methodology by re-analyzing a clinical trial data on blood mercury level. The methodology introduced in this paper can be easily extended to other settings such as nonlinear and generalized regression models. ..
- Gene expression in uterine leiomyoma from tumors likely to be growing (from black women over 35) and tumors likely to be non-growing (from white women over 35)Barbara J Davis
Biomedical Sciences, Cummings School of Veterinary Medicine at Tufts University, North Grafton, Massachusetts, United States of America
PLoS ONE 8:e63909. 2013..To our knowledge, this is the first study to compare two groups of tumors that are likely to have different growth rates in order to reveal molecular signals likely to be influential in tumor growth...
- Novel developmental analyses identify longitudinal patterns of early gut microbiota that affect infant growthRichard A White
Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Oslo, Norway
PLoS Comput Biol 9:e1003042. 2013....
- 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....
- Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic dataWenge 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...
- 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...
- 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...
- 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...
- 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...
- ORIOGEN: order restricted inference for ordered gene expression dataS Peddada
Biostatistics Branch, National Institute of Environmental Health Sciences, Durham, NC 27713, USA
Bioinformatics 21:3933-4. 2005..In particular, ORIOGEN is useful for analyzing data obtained from time-course or dose-response type experiments...
- Tests for order restrictions in binary dataS 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...
- 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...
- 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...
- 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...
- 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...
- 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....
- 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...
- 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...