Research Topics
Genomes and Genes | P R BushelSummaryAffiliation: National Institutes of Health Country: USA Publications
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Detail Information
Publications
Maximizing biomarker discovery by minimizing gene signaturesChang Chang
The Center for Bioinformatics and Institute of Biomedical Sciences, School of Life Science, East China Normal University, 500 Dongchuan Road, Shanghai 200241, China
BMC Genomics 12:S6. 2011....- Population differences in transcript-regulator expression quantitative trait lociPierre R Bushel
Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
PLoS ONE 7:e34286. 2012..The potential pleiotropic effect of the Foxp3 TReQTLs was gleaned from integrating mRNA-Seq data and SNP-set enrichment into the analysis... - Gene expression response in target organ and whole blood varies as a function of target organ injury phenotypeEdward K Lobenhofer
Cogenics, Division of Clinical Data, Inc, Morrisville, NC 27560, USA
Genome Biol 9:R100. 2008..The results of the study demonstrate the classification of histopathological differences, likely reflecting differences in mechanisms of cell-specific toxicity, using either liver tissue or blood transcriptomic data... - Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratoriesMichael J Boedigheimer
CDER, US FDA, Silver Spring, MD 20993, USA
BMC Genomics 9:285. 2008.... - Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genesJeff W Chou
Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
BMC Genomics 10:272. 2009..However, there are no straightforward ways of using co-expressed genes anchored to a phenotype or constrained by the experimental design for discerning mechanisms of a biological response... - Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicantsLingkang Huang
Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
BMC Genomics 9:288. 2008.... - Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processesJeff W Chou
Microarray Group, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
BMC Bioinformatics 8:427. 2007..The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions... - 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... - Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypesPierre R Bushel
National Center for Toxicogenomics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
BMC Syst Biol 1:15. 2007..The inability of clustering algorithms to incorporate biological data in the grouping process can limit proper interpretation of the data and its underlying biology... 
MAPS: a microarray project system for gene expression experiment information and data validationP R Bushel
Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, Research Triangle Park, NC 27709, USA
Bioinformatics 17:564-5. 2001....- Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)Pierre R Bushel
Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
BMC Proc 3:S1. 2009.... - Computational selection of distinct class- and subclass-specific gene expression signaturesPierre R Bushel
National Institute of Environmental Health Sciences, P O Box 12233, Research Triangle Park, NC 27709, USA
J Biomed Inform 35:160-70. 2002.... - Clustering of gene expression data and end-point measurements by simulated annealingPierre R Bushel
Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
J Bioinform Comput Biol 7:193-215. 2009..Map kinase signaling and linoleic acid metabolism were significant biological processes influenced by the exposures of acetaminophen that manifested centrilobular necrosis... - Gene expression analysis reveals chemical-specific profilesHisham K Hamadeh
National Institute of Environmental Health Sciences, P.O. Box 12233, MD2-04, Research Triangle Park, NC 27709, USA
Toxicol Sci 67:219-31. 2002.... - Prediction of compound signature using high density gene expression profilingHisham K Hamadeh
National Institute of Environmental Health Sciences, P.O. Box 12233, MD2-04, Research Triangle Park, NC 27709, USA
Toxicol Sci 67:232-40. 2002..This validates our initial hypothesis and lends credibility to the concept that the further development of a gene expression database for chemical effects will greatly enhance the hazard identification processes... - Insulin-like growth factor-1 inscribes a gene expression profile for angiogenic factors and cancer progression in breast epithelial cellsJ S Oh
Laboratory of Molecular Carcinogenesis, Hormones and Cancer Group, National Institute of Environmental Health Sciences NIEHS, Research Triangle Park, NC, USA
Neoplasia 4:204-17. 2002..In summary, IGF-1 inscribes a gene expression profile relevant to cancer progression, and this study provides insight into the mechanism(s) whereby some of these changes occur... - Chemical effects in biological systems--data dictionary (CEBS-DD): a compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and 'omics dataJennifer Fostel
LIMT Lockheed Martin Information Technology LMIT, Research Triangle Park, NC 27709, USA
Toxicol Sci 88:585-601. 2005..To illustrate the utility of the CEBS-DD, we present an example of integrating data from two proteomics and transcriptomics studies of the response to acute acetaminophen toxicity (A. N. Heinloth et al., 2004, Toxicol. Sci. 80, 193-202)... - Systematic variation normalization in microarray data to get gene expression comparison unbiasedJeff W Chou
National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
J Bioinform Comput Biol 3:225-41. 2005..Biologically meaningful comparisons of gene expression patterns between control and test channels or among multiple arrays are therefore unbiased using normalized but not unnormalized datasets... - ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiationAlexandra N Heinloth
Growth Control and Cancer Group, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Radiat Res 160:273-90. 2003..ATM-dependent and ATM-independent components were detected within these patterns, as were novel indications of involvement of ATM in regulation of transcription factors such as SP1, AP1 and MTF1... - Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiationAlexandra N Heinloth
Growth Control and Cancer Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
Mol Carcinog 37:65-82. 2003..In addition, cell cultures from different individuals displayed significant differences in their gene expression responses to DNA damage... - Differential toxicogenomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin in malignant and nonmalignant human airway epithelial cellsJeanelle M Martinez
National Institute of Environmental Health Sciences, Rall Building 101, 111 Alexander Drive, Research Triangle Park, NC 27709, USA
Toxicol Sci 69:409-23. 2002..In addition, TCDD altered specific immunomodulatory genes in the HPL1A cells. These data show that TCDD alters multiple integrated networks of signaling pathways associated with pulmonary disease, particularly that of lung cancer... - Regulation of DNA replication fork genes by 17beta-estradiolEdward K Lobenhofer
Gene Regulation Group, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Mol Endocrinol 16:1215-29. 2002..The coexpression of DNA replication fork genes by estrogen without the support of serum growth factors indicates an important estrogen regulatory component of the molecular mechanism driving estrogen-induced mitogenesis... - Toward a checklist for exchange and interpretation of data from a toxicology studyJennifer M Fostel
NIEHS, LMIT ITSS Contract, Research Triangle Park, North Carolina 27709 2233, USA
Toxicol Sci 99:26-34. 2007..It is anticipated that once a toxicology checklist is accepted and put into use, then toxicology databases can be configured to require and output these fields, making it straightforward to annotate data for interpretation by others... - Blood gene expression signatures predict exposure levelsP R Bushel
Biostatistics Branch, Environmental Stress and Cancer Group, Environmental Toxicology Program, Microarray Group, Cancer Biology Group, National Institute of Environmental Health Sciences, P O Box 12233, Research Triangle Park, NC 27709
Proc Natl Acad Sci U S A 104:18211-6. 2007..It also supports the potential use of genomic markers in the blood as surrogates for clinical markers of potential acute liver damage... - Progress in the application of DNA microarraysE K Lobenhofer
Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Environ Health Perspect 109:881-91. 2001..For this reason, the focus of this review will be not on the technology itself but on the application of microarrays as a research tool and the future challenges of the field... - Inactivation of DNA mismatch repair by increased expression of yeast MLH1P V Shcherbakova
Laboratories of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Mol Cell Biol 21:940-51. 2001.... - Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterationsHisham K Hamadeh
National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
Toxicol Pathol 30:470-82. 2002.... - Genomic interrogation of mechanism(s) underlying cellular responses to toxicantsRupesh P Amin
National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Mail Drop F1-05, Research Triangle Park, NC 27709, USA
Toxicology 181:555-63. 2002..Ultimately, the expectation is that novel approaches for predicting xenobiotic toxicity in humans will emerge from such information... - ATM requirement in gene expression responses to ionizing radiation in human lymphoblasts and fibroblastsCynthia L Innes
Growth Control and Cancer Group, National Institute of Environmental Health Sciences, PO Box 12233, MD D2-03, Research Triangle Park, NC 27709, USA
Mol Cancer Res 4:197-207. 2006..Interestingly, after 5 Gy IR, lymphoblasts displayed ATM-independent responses not seen in the fibroblasts at this dose, which likely reflect signaling through ATM-related kinases, e.g., ATR, in the absence of ATM function... - Ataxia telangiectasia-mutated dependent DNA damage checkpoint functions regulate gene expression in human fibroblastsTong Zhou
Department of Pathology and Laboratory Medicine, Center for Environmental Health and Susceptibility, CB 7295, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599 7295, USA
Mol Cancer Res 5:813-22. 2007..The reduced change in DNA damage response genes and the attenuated repression of cell cycle-regulated genes may account for the defects in cell cycle checkpoint function in AT cells... - Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cellsLeslie C Hodges
Department of Carcinogenesis, UT M.D. Anderson Cancer Center, Smithville, TX 78957, USA
Mol Cancer Res 1:300-11. 2003..However, cyclin D1 was a key estrogen-induced gene not expressed in response to tamoxifen or raloxifene but constitutively expressed in tamoxifen-resistant cells... - Database development in toxicogenomics: issues and effortsWilliam B Mattes
Pfizer Inc, Groton, Connecticut, USA
Environ Health Perspect 112:495-505. 2004.... - PAGE: phase-shifted analysis of gene expressionElo Leung
Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, Manassas, VA 20110, USA
Bioinformatics 22:367-8. 2006..The patterns and genes within q-Clusters are visualized in trend plots and compared to determine biological relevance from the gene annotations... - Global transcriptome and deletome profiles of yeast exposed to transition metalsYong Hwan Jin
Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina, United States of America
PLoS Genet 4:e1000053. 2008.... - Profiles of global gene expression in ionizing-radiation-damaged human diploid fibroblasts reveal synchronization behind the G1 checkpoint in a G0-like state of quiescenceTong Zhou
Department of Pathology and Laboratory Medicine, Center for Environmental Health and Susceptibility, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
Environ Health Perspect 114:553-9. 2006.... - Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damageTong Zhou
Department of Pathology and Laboratory Medicine, Center for Environmental Health and Susceptibility, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
Cell Cycle 6:972-81. 2007..Changes in expression of these genes after IR treatment derived from both direct transcriptional regulation and cell cycle synchronization... - Standardizing global gene expression analysis between laboratories and across platformsTheodore Bammler
Nat Methods 2:351-6. 2005..These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used...