Research Topics
| Grier P PageSummaryAffiliation: University of Alabama at Birmingham Country: USA Publications
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Detail Information
Publications
A design and statistical perspective on microarray gene expression studies in nutrition: the need for playful creativity and scientific hard-mindednessGrier P Page
Department of Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294 0022, USA
Nutrition 19:997-1000. 2003....
Transcriptional reprogramming of gene expression in bovine somatic cell chromatin transfer embryosNelida Rodriguez-Osorio
Department of Animal and Dairy Sciences, Mississippi State University, Starkville, MS, USA
BMC Genomics 10:190. 2009..Identifying the "cumulative errors" could reveal the epigenetic reprogramming blocks in animal cloning...- Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertilityJean M Feugang
Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS 39762, USA
BMC Genomics 10:176. 2009..We performed a comprehensive genome wide analysis of single nucleotide polymorphisms (SNP) for bull fertility followed by a second-stage replication in additional bulls for a restricted set of markers... - The PowerAtlas: a power and sample size atlas for microarray experimental design and researchGrier P Page
Department of Biostatistics, University of Alabama, Birmingham, AL, USA
BMC Bioinformatics 7:84. 2006..In addition, investigators frequently do not have pilot data to estimate the sample sizes required for microarray studies... - HDBStat!: a platform-independent software suite for statistical analysis of high dimensional biology dataPrinal Trivedi
Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
BMC Bioinformatics 6:86. 2005..HDBStat! provides statisticians and biologists a flexible and easy-to-use interface to analyze complex microarray data using a variety of methods for data preprocessing, quality control analysis and hypothesis testing... - A proposed metric for assessing the measurement quality of individual microarraysKyoungmi Kim
Department of Biostatistics, University of Alabama, Birmingham, Alabama, USA
BMC Bioinformatics 7:35. 2006..In some cases this may be manifested as systematic spatial variation on the surface of microarray in which expression measurements within an individual array may vary as a function of geographic position on the array surface... - Optimal allocation of replicates for measurement evaluation studiesStanislav O Zakharkin
Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL 35294-0022, USA
Genomics Proteomics Bioinformatics 4:196-202. 2006..Therefore, it is recommended to use two technical replicates for each biological replicate if the goal is to evaluate the reproducibility of measurements... - Microarray data analysis: from disarray to consolidation and consensusDavid B Allison
Section on Statistical Genetics, Department of Biostatistics, Ryals Public Health Building, 1665 University Avenue, University of Alabama at Birmingham, Alabama 35294 0022, USA
Nat Rev Genet 7:55-65. 2006..Many are special cases of more general models, and points of consensus are emerging about the general approaches that warrant use and elaboration... - Sources of variation in Affymetrix microarray experimentsStanislav O Zakharkin
University of Alabama, Birmingham, Alabama, USA
BMC Bioinformatics 6:214. 2005..The objectives of this study were: (1) to estimate relative magnitudes of different sources of variation and (2) to evaluate agreement between biological and technical replicates... - Microarray analysisGrier P Page
Department of Biostatistics, University of Alabama at Birmingham, Hoover, AL, USA
Methods Mol Biol 404:409-30. 2007..These steps include a clearly stated biological question, experimental design, careful experimental conduct, complete statistical analysis, validation/verification of results, and dissemination of the data... - CressExpress: a tool for large-scale mining of expression data from ArabidopsisVinodh Srinivasasainagendra
Section on Statistical Genetics, Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294, USA
Plant Physiol 147:1004-16. 2008..The tool is available at http://www.cressexpress.org... - Human breast fibroblasts inhibit growth of the MCF10AT xenograft model of proliferative breast diseaseAndrea Sadlonova
Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
Am J Pathol 170:1064-76. 2007..These findings imply that NAFs can inhibit the growth of normal and hyperplastic epi-thelium but are less able to regulate the more transformed epithelial cells that arise during carcino-genesis... - Identification of molecular distinctions between normal breast-associated fibroblasts and breast cancer-associated fibroblastsAndrea Sadlonova
Department of Pathology, Wallace Tumor Institute, University of Alabama at Birmingham, Room 420, Birmingham, AL 35294, USA
Cancer Microenviron 2:9-21. 2009..Furthermore, these early passage fibroblast cultures can be representative of gene expression in stromal fibroblasts in vivo... - Applications of Bayesian statistical methods in microarray data analysisDongyan Yang
Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Am J Pharmacogenomics 4:53-62. 2004..Bayesian methods will undoubtedly become more common in the future because of their great utility in microarray analysis... 
Single nucleotide polymorphisms affect both cis- and trans-eQTLsLang Chen
Department of Biostatistics, Section on Statistical Genetics, School of Public Health, University of Alabama at Birmingham, AL 35209, USA
Genomics 93:501-8. 2009..These results indicate that SNPs do affect both probe set summaries and eQTLs (both cis and trans), thus SNP-containing probes should be filtered out to improve the performance of eQTL mapping...- The effect of insulin on expression of genes and biochemical pathways in human skeletal muscleXuxia Wu
Department of Nutrition Sciences, University of Alabama at Birmingham, 1675 University Boulevard, Birmingham, AL 35294 3360, USA
Endocrine 31:5-17. 2007..The role of NGFI-B (NR4A1) as a new potential mediator of insulin action highlights the need for greater understanding of nuclear transcription factors in insulin action... - Transcriptional coordination of the metabolic network in ArabidopsisHairong Wei
Department of Biostatistics, University of Alabama, Birmingham, Alabama 35294, USA
Plant Physiol 142:762-74. 2006..These methods and results will aid in the prioritization of candidates for genetic analysis of metabolism in plants and contribute to the improvement of functional annotation of the Arabidopsis genome... - 2D difference gel electrophoresis of prepubertal and pubertal rat mammary gland proteomesHelen Kim
Departments of Pharmacology and Toxicology, the UAB Center for Nutrient Gene Interaction, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
J Proteome Res 7:4638-50. 2008..This is a first report of mammary gland proteome differences at these important breast cancer-relevant time-points... - Breast fibroblasts modulate epithelial cell proliferation in three-dimensional in vitro co-cultureAndrea Sadlonova
Department of Pathology, The University of Alabama at Birmingham, Alabama, USA
Breast Cancer Res 7:R46-59. 2005..To this end, the effect of CAF and normal breast-associated fibroblasts (NAF) on the growth of epithelial cells representative of pre-neoplastic breast disease was assessed... - The association between the rs2234693 and rs9340799 estrogen receptor alpha gene polymorphisms and risk factors for cardiovascular disease: a reviewKrista Casazza
Department of Nutrition, University of Alabama at Birmingham, AL, USA
Biol Res Nurs 12:84-97. 2010.... - Novel tumor necrosis factor alpha-regulated genes in rheumatoid arthritisHuang-Ge Zhang
The University of Alabama at Birmingham, and the Birmingham Department of Veterans Affairs Medical Center, Birmingham, AL 35294-0007, USA
Arthritis Rheum 50:420-31. 2004.... - Hedgehog signaling and response to cyclopamine differ in epithelial and stromal cells in benign breast and breast cancerShibani Mukherjee
Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
Cancer Biol Ther 5:674-83. 2006..Determination as to whether the increase in GLI1 and SHH expression in breast cancer indicates a significant increase in hedgehog signaling will require further evaluation... - Differential gene expression modulated by the cytoplasmic domain of Fc gamma RIa (CD64) alpha-chainHongwei Qin
Department of Medicine, University of Alabama at Birmingham, 1900 University Boulevard, Birmingham, AL 35294 0006, USA
J Immunol 173:6211-9. 2004.... - Employment of microarray analysis to characterize biologic differences associated with tropism-modified adenoviral vectors: utilization of non-native cellular entry pathwaysAndrea L Volk
Division of Human Gene Therapy and The Gene Therapy Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
Cancer Gene Ther 12:162-74. 2005..This analysis represents a unique application of microarray to study vector-related issues. Furthermore, these studies demonstrate the utility of microarray for characterizing the biologic sequelae of host-vector interaction... - COGA phenotypes and linkages on chromosome 2Howard W Wiener
Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
BMC Genet 6:S125. 2005..A region on chromosome 2 at 250 cM was found to be linked to both of these derived phenotypes. Further examination of the SNPs in this region identified several haplotypes strongly associated with these derived phenotypes... - Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data II: Analysis Beyond Single GeneIssa Coulibaly
Department of Biostatistics, University of Alabama at Birmingham, 1665 University Blvd Ste 327, Birmingham, AL 35294 0022, USA
Int J Plant Genomics 2008:893941. 2008..The overall goal of this review is to provide researchers with tools and information to facilitate the interpretation of microarray data... - Correlation of microRNA levels during hypoxia with predicted target mRNAs through genome-wide microarray analysisJennifer S Guimbellot
Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, AL 35294, USA
BMC Med Genomics 2:15. 2009..The methods described here for comparative analysis of cellular miRNA and mRNA will be useful for understanding genome wide regulatory responsiveness and refining miRNA predictive algorithms... - Cross-Chip Probe Matching Tool: A Web-Based Tool for Linking Microarray Probes within and across Plant SpeciesRuchi Ghanekar
Department of Electrical and Computer Engineering, UAB School of Engineering, University of Alabama at Birmingham, 1530 Third Avenue South, Birmingham, AL 35294 4461, USA
Int J Plant Genomics 2008:451327. 2008.... - Bioinformatic tools for inferring functional information from plant microarray data: tools for the first stepsGrier P Page
Department of Biostatistics, University of Alabama at Birmingham, 1665 University Blvd Ste 327, Birmingham, AL 35294 0022, USA
Int J Plant Genomics 2008:147563. 2008.... - Proteomics and mass spectrometry in nutrition researchHelen Kim
Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
Nutrition 20:155-65. 2004 - S-adenosylmethionine prevents chronic alcohol-induced mitochondrial dysfunction in the rat liverShannon M Bailey
Department of Environmental Health Sciences, School of Public Health, University of Alabama, Birmingham, AL 35294, USA
Am J Physiol Gastrointest Liver Physiol 291:G857-67. 2006..These findings reveal new molecular targets through which SAM may work to alleviate one critical component of alcohol-induced liver injury: mitochondria dysfunction... - Adipose tissue energy metabolism: altered gene expression profile of mice subjected to long-term caloric restrictionYoshikazu Higami
Wisconsin Primate Research Center, Madison, Wisconsin, USA
FASEB J 18:415-7. 2004..Our data provide new insights on the metabolic state associated with aging retardation by LCR... - Identification of genes required for cellulose synthesis by regression analysis of public microarray data setsStaffan Persson
Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 102:8633-8. 2005..Thus, the general approach developed here is useful for identification of elements of multicomponent processes... - Evaluating statistical methods using plasmode data sets in the age of massive public databases: an illustration using false discovery ratesGary L Gadbury
Department of Statistics, Kansas State University, Manhattan, Kansas, United States of America
PLoS Genet 4:e1000098. 2008..We use the procedure to compare estimates for the proportion of true null hypotheses, the false discovery rate (FDR), and a local version of FDR obtained from 15 different statistical methods... - alpha- and gamma-Tocopherol prevent age-related transcriptional alterations in the heart and brain of miceSang Kyu Park
Department of Genetics and Medical Genetics, University of Wisconsin, Madison, WI 53706, USA
J Nutr 138:1010-8. 2008..These results demonstrate that middle age-onset dietary supplementation with alphaT and gammaT can partially prevent age-associated transcriptional changes and that these effects are tissue and tocopherol specific... - Reproducible clusters from microarray research: whither?Nikhil R Garge
Medical College of Georgia, 1120 15th Street, Ca4100, Augusta, GA 30912, USA, Email
BMC Bioinformatics 6:S10. 2005..We used this approach to determine the performance of commonly used clustering algorithms and the degree of replicability achieved using several microarray datasets... - DCDC2 is associated with reading disability and modulates neuronal development in the brainHaiying Meng
Department of Pediatrics, Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT 06520, USA
Proc Natl Acad Sci U S A 102:17053-8. 2005..The statistical and functional studies are complementary and are consistent with the latest clinical imaging data for RD. Thus, we propose that DCDC2 is a candidate gene for RD... - Results of a genomewide linkage scan: support for chromosomes 9 and 11 loci increasing risk for cigarette smokingJoel Gelernter
Department of Psychiatry, Yale University School of Medicine, VA Psychiatry 116A2, 950 Campbell Avenue, West Haven, CT 06516, USA
Am J Med Genet B Neuropsychiatr Genet 128:94-101. 2004..Interestingly, one of our most promising linkage regions, includes a region previously identified as linked to PD... - Mitochondrial DNA (mtDNA) haplotypes reveal maternal population genetic affinities of Sea Island Gullah-speaking African AmericansDavid C McLean
Division of Endocrinology, Diabetes, and Medical Genetics, Department of Medicine, Sea Island Families Project and Project Sugar, Medical University of South Carolina, Charleston, SC 20425, USA
Am J Phys Anthropol 127:427-38. 2005.... - The Collaborative Cross, a community resource for the genetic analysis of complex traitsGary A Churchill
The Jackson Laboratory, 600 Main Street Bar Harbor, Maine 04609, USA
Nat Genet 36:1133-7. 2004..The Collaborative Cross will provide a common reference panel specifically designed for the integrative analysis of complex systems and will change the way we approach human health and disease... - Empirical Bayes estimation of gene-specific effects in micro-array researchJode W Edwards
United States Department of Agriculture, Agricultural Research Service, Department of Agronomy, Iowa State University, Ames, IA 50014, USA
Funct Integr Genomics 5:32-9. 2005..e., increase in precision, associated with EB estimators in this analysis. The method described here is available in software that is available at http://www.soph.uab.edu/ssg.asp?id=1087... - Inhaled NO accelerates restoration of liver function in adults following orthotopic liver transplantationJohn D Lang
Department of Anesthesiology, University of Washington School of Medicine, Seattle, Washington 98108 1597, USA
J Clin Invest 117:2583-91. 2007..In summary, this study supports the clinical use of iNO as an extrapulmonary therapeutic to improve organ function following transplantation...