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List of works by Shyamal D Peddada

2-Butoxyethanol female-rat model of hemolysis and disseminated thrombosis: X-ray characterization of osteonecrosis and growth-plate suppression.

scientific article

450K epigenome-wide scan identifies differential DNA methylation in newborns related to maternal smoking during pregnancy

scientific article published on 31 July 2012

A Bootstrap Based Measure Robust to the Choice of Normalization Methods for Detecting Rhythmic Features in High Dimensional Data

scientific article published on 2 February 2018

A HIERARCHICAL FUNCTIONAL DATA ANALYTIC APPROACH FOR ANALYZING PHYSIOLOGICALLY BASED PHARMACOKINETIC MODELS.

scientific article

A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions

scientific article

A minimal set of tissue-specific hypomethylated CpGs constitute epigenetic signatures of developmental programming

scientific article

A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies

scientific article

A random-periods model for expression of cell-cycle genes.

scientific article

A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments

scientific article published on 22 December 2009

A survival-adjusted quantal-response test for analysis of tumor incidence rates in animal carcinogenicity studies

scientific article

A systematic assessment of normalization approaches for the Infinium 450K methylation platform

scientific article

Accounting for Uncertainty in Heteroscedasticity in Nonlinear Regression

scientific article published on May 2012

Adaptive choice of the number of bootstrap samples in large scale multiple testing.

scientific article published on 24 March 2008

Age and dose sensitivities in the 2-butoxyethanol F344 rat model of hemolytic anemia and disseminated thrombosis

scientific article published on 29 January 2007

Aloe vera non-decolorized whole leaf extract-induced large intestinal tumors in F344 rats share similar molecular pathways with human sporadic colorectal tumors.

scientific article published on 21 September 2011

American Gut: an Open Platform for Citizen Science Microbiome Research

article

Analysis of Correlated Gene Expression Data on Ordered Categories.

scientific article

Analysis of Microbiome Data in the Presence of Excess Zeros

scientific article

Analysis of composition of microbiomes: a novel method for studying microbial composition

scientific article published on 29 May 2015

Analysis of high dimensional data using pre-defined set and subset information, with applications to genomic data

scientific article

Analysis of microbial compositions: a review of normalization and differential abundance analysis

scientific article published on 02 December 2020

Analysis of nonlinear regression models: a cautionary note

scientific article published on January 2005

Assessment of lead exposure and associated risk factors in urban children in Silesia, Poland.

scientific article published on June 2004

Best practices for use of historical control data of proliferative rodent lesions

scientific article

Biomarkers of oxidative stress study VI. Endogenous plasma antioxidants fail as useful biomarkers of endotoxin-induced oxidative stress.

scientific article published on 19 January 2015

Cellular senescence in usual type uterine leiomyoma

scientific article published on 03 June 2010

Chemical Exacerbation of Light-induced Retinal Degeneration in F344/N Rats in National Toxicology Program Rodent Bioassays

scientific article published on 26 May 2016

Circular piecewise regression with applications to cell-cycle data ⬇️

scientific article

Comparing tumor rates in current and historical control groups in rodent cancer bioassays

scientific article

Comparison of NTP historical control tumor incidence rates in female Harlan Sprague Dawley and Fischer 344/N Rats ⬇️

scientific article published on 9 July 2010

Controlling false discoveries in multidimensional directional decisions, with applications to gene expression data on ordered categories

scientific article

DNA Methylation Score as a Biomarker in Newborns for Sustained Maternal Smoking during Pregnancy

scientific article published on 21 June 2016

Designs for single- or multiple-agent phase I trials

scientific article

Determination of Temporal Order among the Components of an Oscillatory System.

scientific article published on 7 July 2015

Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancer

scientific article published on 11 June 2012

Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle

scientific article published on 16 September 2009

Efficacy of succimer chelation of mercury at background exposures in toddlers: a randomized trial

scientific article

Epididymal sperm granuloma induced by chronic administration of 2-methylimidazole in B6C3F1 mice

scientific article published in January 2005

Estradiol regulates the thioredoxin antioxidant system in the mouse uterus

scientific article published on 2 September 2004

Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome

scientific article

Exposures Related to House Dust Microbiota in a U.S. Farming Population.

scientific article published in June 2018

F344/NTac Rats Chronically Exposed to Bromodichloroacetic Acid Develop Mammary Adenocarcinomas With Mixed Luminal/Basal Phenotype and Tgfβ Dysregulation.

scientific article published on 2 March 2015

Factors affecting the thickness of the cervical prevertebral soft tissues.

scientific article published in January 1993

Fat and vitamin intakes during pregnancy have stronger relations with a pro-inflammatory maternal microbiota than does carbohydrate intake

scientific article published on 19 October 2016

Forestomach tumor induction by 2,4-hexadienal in F344N rats and B6C3F1 mice.

scientific article published on 18 July 2003

Gender Differences in Chemical Carcinogenesis in National Toxicology Program 2-Year Bioassays ⬇️

scientific article published on May 14, 2012

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)

scientific article

Gene expression of mesothelioma in vinylidene chloride-exposed F344/N rats reveal immune dysfunction, tissue damage, and inflammation pathways

scientific article

Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference

scientific article published on May 2003

Genetic alterations in cancer knowledge system: analysis of gene mutations in mouse and human liver and lung tumors

scientific article published on 12 January 2006

Genomic Profiling Reveals Unique Molecular Alterations in Hepatoblastomas and Adjacent Hepatocellular Carcinomas in B6C3F1 Mice.

scientific article

Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer

scientific article

Growth of uterine leiomyomata among premenopausal black and white women

scholarly article

Hemostatic activation in a chemically induced rat model of severe hemolysis and thrombosis

scientific article published on 6 January 2006

Hepatocellular carcinomas in B6C3F1 mice treated with Ginkgo biloba extract for two years differ from spontaneous liver tumors in cancer gene mutations and genomic pathways

scientific article published on 21 December 2012

Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across species.

scientific article published in December 2011

Immunization with a heat-killed preparation of the environmental bacterium Mycobacterium vaccae promotes stress resilience in mice

scientific article published on 16 May 2016

Incorporating Historical Control Data When Comparing Tumor Incidence Rates

scientific article

Individual and joint prevalence of three nonmotor symptoms of PD in the US general population

scientific article

Interleukin-1beta-induced mucin production in human airway epithelium is mediated by cyclooxygenase-2, prostaglandin E2 receptors, and cyclic AMP-protein kinase A signaling.

scientific article

Intraobserver variability in fibroid size measurements: estimated effects on assessing fibroid growth.

scientific article

Linear and nonlinear correlation estimators unveil undescribed taxa interactions in microbiome data

scientific article published in 2022

Linear mixed effects models under inequality constraints with applications

scientific article published on 21 January 2014

Longitudinal assessment of hormonal and physical alterations during normal puberty in boys. IV: Predictions of adult height by the Bayley-Pinneau, Roche-Wainer-Thissen, and Tanner-Whitehouse methods compared

scientific article

Longitudinal assessment of hormonal and physical alterations during normal puberty in boys. VI. Modeling of growth velocity, mean growth hormone (GH mean), and serum testosterone (T) concentrations

scientific article published on 01 November 2000

Male sex hormones promote vagally mediated reflex airway responsiveness to cholinergic stimulation

scientific article

Mass spectrometric determination of IgG subclass-specific glycosylation profiles in siblings discordant for myositis syndromes

scientific article

Maternal plasma folate impacts differential DNA methylation in an epigenome-wide meta-analysis of newborns

scientific article published on 10 February 2016

Maternal smoking and DNA methylation in newborns: in utero effect or epigenetic inheritance?

scientific article published on 16 April 2014

Meta-analyses on prevalence of selected Parkinson's nonmotor symptoms before and after diagnosis

scientific article

Mitochondrial damage revealed by morphometric and semiquantitative analysis of mouse pup cardiomyocytes following in utero and postnatal exposure to zidovudine and lamivudine.

scientific article

Mixed directional false discovery rate control in multiple pairwise comparisons using weighted p-values

scientific article

Mutant Brca2/p53 mice exhibit altered radiation responses in the developing mammary gland

scientific article

Neonatal genome-wide methylation patterns in relation to birth weight in the Norwegian Mother and Child Cohort

scientific article published on 20 February 2014

Normalization and microbial differential abundance strategies depend upon data characteristics

scientific article

Novel developmental analyses identify longitudinal patterns of early gut microbiota that affect infant growth

scientific article

Oncology consent forms: failure to disclose off-site treatment availability.

scientific article

Order restricted inference for multivariate binary data with application to toxicology

scientific article

Order restricted inference for oscillatory systems for detecting rhythmic signals.

scientific article published on 04 September 2016

Order-restricted inference for ordered gene expression (ORIOGEN) data under heteroscedastic variances

scientific article published on 10 April 2007

Osteonecrosis in a chemically induced rat model of human hemolytic disorders associated with thrombosis--a new model for avascular necrosis of bone.

scientific article

Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome

scientific article published on 14 February 2017

Perceptions of ethical problems with scientific journal peer review: an exploratory study

scientific article published on March 2008

Phase analysis of circadian-related genes in two tissues

scientific article

Points to consider on the statistical analysis of rodent cancer bioassay data when incorporating historical control data

scientific article

Potential for a global historical control database for proliferative rodent lesions

scientific article published on 01 August 2009

Potential sex differences in nonmotor symptoms in early drug-naive Parkinson disease

scientific article published on 29 April 2015

Preterm infants have distinct microbiomes not explained by mode of delivery, breastfeeding duration or antibiotic exposure

scientific article published on 20 April 2018

Prevalence of major depressive episodes in rural women using primary care

scientific article

Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays

scientific article

Proteomic Profiling of S-acylated Macrophage Proteins Identifies a Role for Palmitoylation in Mitochondrial Targeting of Phospholipid Scramblase 3 ⬇️

scientific article published on July 23, 2011

Reduced Disc Shedding and Phagocytosis of Photoreceptor Outer Segment Contributes to Kava Kava Extract-induced Retinal Degeneration in F344/N Rats

scientific article published on 27 May 2018

Renal Cell Carcinomas in Vinylidene Chloride-exposed Male B6C3F1 Mice Are Characterized by Oxidative Stress and TP53 Pathway Dysregulation

scientific article published on 17 December 2015

Research misconduct policies of scientific journals.

scientific article published on January 2009

Research on the premotor symptoms of Parkinson's disease: clinical and etiological implications

scientific article published on 09 August 2013

Robust Analysis of High Throughput Screening (HTS) Assay Data

scientific article

Robust nonlinear regression in applications

scientific article

Seasonal change in the gut.

scientific article

Short-term change in growth of uterine leiomyoma: tumor growth spurts

scientific article

Spontaneous mesotheliomas in F344/N rats are characterized by dysregulation of cellular growth and immune function pathways

scientific article published on 26 August 2013

Statistical inference under order restrictions in analysis of covariance using a modified restricted maximum likelihood estimator.

scientific article

Structural zeros in high-dimensional data with applications to microbiome studies

scientific article

Testing for the multivariate stochastic order among ordered experimental groups with application to dose-response studies

scientific article published on 11 October 2013

Tests for Order Restrictions in Binary Data ⬇️

scientific article published on December 1, 2001

The OECD program to validate the rat uterotrophic bioassay. Phase 2: dose-response studies.

scientific article

The fibroid growth study: determinants of therapeutic intervention.

scientific article

The hepatic endothelial carcinogen riddelliine induces endothelial apoptosis, mitosis, S phase, and p53 and hepatocytic vascular endothelial growth factor expression after short-term exposure.

scientific article published in November 2002

The linear stochastic order and directed inference for multivariate ordered distributions ⬇️

scientific article (publication date: February 2013)

The novel p53 target TNFAIP8 variant 2 is increased in cancer and offsets p53-dependent tumor suppression

scientific article published on 11 November 2016

The role of oxidative stress in indium phosphide-induced lung carcinogenesis in rats.

scientific article

Treatment of osteomyelitis in rats by injection of degradable polymer releasing gentamicin.

scientific article published on 20 July 2008

Uterine Carcinomas in Tetrabromobisphenol A-exposed Wistar Han Rats Harbor Increased Tp53 Mutations and Mimic High-grade Type I Endometrial Carcinomas in Women.

scientific article

Visualizing detailed postdoctoral employment trends using a new career outcome taxonomy.

scientific article published on 15 January 2018

isocir: An R Package for Constrained Inference using Isotonic Regression for Circular Data, with an Application to Cell Biology.

scientific article

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