Affiliation: University of North Carolina
- SAFEGUI: resampling-based tests of categorical significance in gene expression data made easyDaniel M Gatti
Department of Environmental Sciences and Engineering, Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
Bioinformatics 25:541-2. 2009..SAFEGUI incorporates both permutation and more recently proposed bootstrap algorithms that are demonstrated to be more powerful in detecting differential expression across categories of genes...
- Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathwayJean Luc C Mougeot
Department of Neurology, ALS Biomarker Laboratory James G Cannon Research Center, Carolinas Medical Center, Charlotte, NC 28203 6110, USA
BMC Med Genomics 4:74. 2011....
- Heading down the wrong pathway: on the influence of correlation within gene setsDaniel M Gatti
Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
BMC Genomics 11:574. 2010..Most popular gene set testing methods assume the independence of genes within each set, an assumption that is seriously violated, as extensive correlation between genes is a well-documented phenomenon...
- Transcriptional response of rat frontal cortex following acute in vivo exposure to the pyrethroid insecticides permethrin and deltamethrinJoshua A Harrill
Curriculum in Toxicology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
BMC Genomics 9:546. 2008..The purpose of this study was to characterize and explore changes in gene expression that occur in the rat frontal cortex, an area of CNS affected by pyrethroids, following an acute low-dose exposure...
- Discovering collectively informative descriptors from high-throughput experimentsClark D Jeffries
Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, NC, USA
BMC Bioinformatics 10:431. 2009..Combining information from these studies can increase the reliability and generalizability of results and also yield new insights that guide future research...
- Simulating association studies: a data-based resampling method for candidate regions or whole genome scansFred A Wright
Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA
Bioinformatics 23:2581-8. 2007..Improvements in study design and analytic techniques will require the simulation of datasets with realistic patterns of linkage disequilibrium and allele frequencies for typed SNPs...
- Information perspectives of the Haseman-Elston methodFred A Wright
Department of Biostatistics and Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7420, USA
Hum Hered 55:132-42. 2003..The results provide insight and analytic results that apply to general phenotype distributions and can be used to judge the effects of various data transformations and selective sampling of extreme phenotypes...
- Integrated study of copy number states and genotype calls using high-density SNP arraysWei Sun
Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
Nucleic Acids Res 37:5365-77. 2009..We evaluated genoCN by applications to 162 HapMap individuals and a brain tumor (glioblastoma) dataset and showed that our method can successfully identify both types of copy number differences and produce high-quality genotype calls...
- Significance analysis of functional categories in gene expression studies: a structured permutation approachWilliam T Barry
Department of Biostatistics, University of North Carolina at Chapel Hill, 27599 7420, USA
Bioinformatics 21:1943-9. 2005..SAFE is a two-stage, permutation-based method that can be applied to various experimental designs, accounts for the unknown correlation among genes and enables permutation-based estimation of error rates...
- Estimating odds ratios in genome scans: an approximate conditional likelihood approachArpita Ghosh
Department of Biostatistics, The University of North Carolina at Chapel Hill, NC 27599, USA
Am J Hum Genet 82:1064-74. 2008..Our approach is described in the specific context of odds ratios and logistic modeling but is more widely applicable. Application to recently published data sets demonstrates the relevance of our approach to modern genome scans...
- FastMap: fast eQTL mapping in homozygous populationsDaniel M Gatti
Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA
Bioinformatics 25:482-9. 2009..However, existing eQTL mapping software does not scale well when the number of transcripts and markers are on the order of 10(5) and 10(5)-10(6), respectively...
- Age-dependent variability in gene expression in male Fischer 344 rat retinaZhen Li
Department of Biostatistics, Carolina Environmental Bioinformatics Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
Toxicol Sci 107:281-92. 2009..Our data suggest that population stochastically induced variability should be considered in assessing sensitivity due to old age...
- Large-scale gene expression differences across brain regions and inbred strains correlate with a behavioral phenotypeJessica J Nadler
Department of Genetics, Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill 27599 7264, USA
Genetics 174:1229-36. 2006..Thus we can begin to identify expression profiles contributing to behavioral phenotypes through variation in gene expression...
- Gene expression in peripheral blood leukocytes in monozygotic twins discordant for chronic fatigue: no evidence of a biomarkerAndrea Byrnes
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
PLoS ONE 4:e5805. 2009..Chronic fatiguing illness remains a poorly understood syndrome of unknown pathogenesis. We attempted to identify biomarkers for chronic fatiguing illness using microarrays to query the transcriptome in peripheral blood leukocytes...
- Replication and narrowing of gene expression quantitative trait loci using inbred miceDaniel M Gatti
Department of Environmental Sciences and Engineering, University of North Carolina, CB 7431, Chapel Hill, NC 27599, USA
Mamm Genome 20:437-46. 2009....
- A novel two-step hierarchical quantitative structure-activity relationship modeling work flow for predicting acute toxicity of chemicals in rodentsHao Zhu
Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 7360, USA
Environ Health Perspect 117:1257-64. 2009..Accurate prediction of in vivo toxicity from in vitro testing is a challenging problem. Large public-private consortia have been formed with the goal of improving chemical safety assessment by the means of high-throughput screening...
- Quantification of population structure using correlated SNPs by shrinkage principal componentsFei Zou
Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA fzou bios unc edu
Hum Hered 70:9-22. 2010..It implicitly assumes that the markers are in linkage equilibrium, a condition that is rarely satisfied and that we plan to relax...
- Nonparametric disequilibrium mapping of functional sites using haplotypes of multiple tightly linked single-nucleotide polymorphism markersRong Cheng
Department of Psychiatry, The University of Texas Health Science Center, San Antonio, Texas 78229, USA
Genetics 164:1175-87. 2003..The sensitivity of the proposed procedure was examined on the simulated data set from the Genetic Analysis Workshop (GAW) 12. Compared with the conventional and generalized TDT methods, our procedure is more flexible and powerful...
- Confirmation of the type 2 myotonic dystrophy (CCTG)n expansion mutation in patients with proximal myotonic myopathy/proximal myotonic dystrophy of different European origins: a single shared haplotype indicates an ancestral founder effectLinda L Bachinski
Section of Cancer Genetics, Department of Molecular Genetics, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
Am J Hum Genet 73:835-48. 2003..Taken together, these data suggest a single founding mutation in DM2 patients of European origin. We estimate the age of the founding haplotype and of the DM2 (CCTG) expansion mutation to be approximately 200-540 generations...
- Assessing differential gene expression with small sample sizes in oligonucleotide arrays using a mean-variance modelJianhua Hu
Department of Biostatistics and Applied Mathematics, The University of Texas M D Anderson Cancer Center, Houston, Texas 77030 4009, USA
Biometrics 63:41-9. 2007..Our approach performs well compared to other proposed approaches in terms of the false discovery rate...
- Practical FDR-based sample size calculations in microarray experimentsJianhua Hu
Department of Biostatistics and Applied Mathematics, University of Texas M D Anderson Cancer Center, TX 77030 4009, USA
Bioinformatics 21:3264-72. 2005..With the growing use of the False Discovery Rate (FDR) in microarray analysis, an FDR-based sample size calculation is essential...
- Gene expression profiling of isogenic cells with different TP53 gene dosage reveals numerous genes that are affected by TP53 dosage and identifies CSPG2 as a direct target of p53Heejei Yoon
Human Cancer Genetics Program, Comprehensive Cancer Center, Ohio State University, 420 West 12th Avenue, Columbus 43210, USA
Proc Natl Acad Sci U S A 99:15632-7. 2002..Among them, CSPG2 is validated as being directly transactivated by p53. Our method provides a useful tool to elucidate additional mechanisms by which p53 exerts its functions...
- Pooled analysis of loss of heterozygosity in breast cancer: a genome scan provides comparative evidence for multiple tumor suppressors and identifies novel candidate regionsBrian J Miller
College of Medicine and Public Health, The Ohio State University, Columbus, OH, USA
Am J Hum Genet 73:748-67. 2003..Our approach provides a comparative framework for further investigation of regions exhibiting LOH and identifies broad genomic regions for which there exist few data...
- A founding locus within the RET proto-oncogene may account for a large proportion of apparently sporadic Hirschsprung disease and a subset of cases of sporadic medullary thyroid carcinomaSalud Borrego
Unidad de Genética Medica y Diagnóstico Prenatal, Hospitales Universitarios Virgen del Rocio, Sevilla, Spain
Am J Hum Genet 72:88-100. 2003..We postulate that this founding locus is germane to both isolated HSCR and MTC but also that different mutations in this locus would predispose to one or the other...
- Genetic modifiers of lung disease in cystic fibrosisMitchell L Drumm
Department of Pediatrics, Case Western Reserve University, Cleveland, USA
N Engl J Med 353:1443-53. 2005..Polymorphisms in genes other than the cystic fibrosis transmembrane conductance regulator (CFTR) gene may modify the severity of pulmonary disease in patients with cystic fibrosis...
- Inferring the location of tumor suppressor genes by modeling frequency of allelic lossAndrew Sterrett
Colorado Prevention Center, 789 Sherman Street, Suite 200, Denver, Colorado 80203, USA
Biometrics 63:33-40. 2007..We describe an extension of the allelotype model to handle FAL data, using a hidden Markov model or a normal approximation to compute the likelihood. The FAL model is illustrated using data from a study of colorectal cancer...
- Amnionless, essential for mouse gastrulation, is mutated in recessive hereditary megaloblastic anemiaStephan M Tanner
Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
Nat Genet 33:426-9. 2003..When the 5' end of AMN is truncated by mutations, translation is initiated from alternative downstream start codons...
- Comment on a simple and improved correction for population stratificationSeunggeun Lee
Am J Hum Genet 82:524-6; author reply 526-8. 2008
- Theoretical and experimental comparisons of gene expression indexes for oligonucleotide arraysWilliam J Lemon
Division of Human Cancer Genetics, The Ohio State University, Columbus, Ohio, USA
Bioinformatics 18:1470-6. 2002..Recently, a gene expression index has been proposed that explicitly models probe effects, and provides improved fits of hybridization intensity for arrays containing perfect match (PM) and mismatch (MM) probe pairs...
- INFERENCE AND ROBUST METHODS FOR LINKAGE MAPPINGFred Wright; Fiscal Year: 2002..The robustness and wide applicability of the methods proposed will be examined using a combination of simulation and analysis of existing linkage datasets. ..