P R Bushel

Summary

Affiliation: National Institutes of Health
Country: USA

Publications

  1. pmc The impact of classification of interest on predictive toxicogenomics
    Robnet T Kerns
    Microarray and Genome Informatics, National Institute of Environmental Health Sciences Research Triangle Park, NC, USA
    Front Genet 3:14. 2012
  2. pmc Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays
    Jun Lu
    Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, SRA International, Inc and Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 39:e86. 2011
  3. pmc Maximizing biomarker discovery by minimizing gene signatures
    Chang 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
  4. pmc Population differences in transcript-regulator expression quantitative trait loci
    Pierre R Bushel
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, United States of America
    PLoS ONE 7:e34286. 2012
  5. pmc Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype
    Edward K Lobenhofer
    Cogenics, Division of Clinical Data, Inc, Morrisville, NC 27560, USA
    Genome Biol 9:R100. 2008
  6. pmc Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
    Michael J Boedigheimer
    CDER, US FDA, Silver Spring, MD 20993, USA
    BMC Genomics 9:285. 2008
  7. pmc Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes
    Jeff W Chou
    Biostatistics Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
    BMC Genomics 10:272. 2009
  8. pmc Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants
    Lingkang Huang
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    BMC Genomics 9:288. 2008
  9. pmc Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes
    Jeff W Chou
    Microarray Group, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    BMC Bioinformatics 8:427. 2007
  10. pmc Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle
    Pierre R Bushel
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    BMC Syst Biol 3:93. 2009

Collaborators

Detail Information

Publications39

  1. pmc The impact of classification of interest on predictive toxicogenomics
    Robnet T Kerns
    Microarray and Genome Informatics, National Institute of Environmental Health Sciences Research Triangle Park, NC, USA
    Front Genet 3:14. 2012
    ....
  2. pmc Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays
    Jun Lu
    Microarray and Genome Informatics Group, National Institute of Environmental Health Sciences, SRA International, Inc and Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
    Nucleic Acids Res 39:e86. 2011
    ..We demonstrate that PVAC exhibits equal or better performance than several widely used filtering methods. Furthermore, a data-driven approach that guides the selection of the filtering threshold value is also proposed...
  3. pmc Maximizing biomarker discovery by minimizing gene signatures
    Chang 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
    ....
  4. pmc Population differences in transcript-regulator expression quantitative trait loci
    Pierre 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...
  5. pmc Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype
    Edward 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...
  6. pmc Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories
    Michael J Boedigheimer
    CDER, US FDA, Silver Spring, MD 20993, USA
    BMC Genomics 9:285. 2008
    ....
  7. pmc Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes
    Jeff 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...
  8. pmc Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants
    Lingkang Huang
    Biostatistics Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
    BMC Genomics 9:288. 2008
    ....
  9. pmc Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes
    Jeff 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...
  10. pmc Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle
    Pierre 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...
  11. ncbi request reprint Computational selection of distinct class- and subclass-specific gene expression signatures
    Pierre 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
    ....
  12. pmc Clustering of gene expression data and end-point measurements by simulated annealing
    Pierre 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...
  13. pmc Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes
    Pierre 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...
  14. ncbi request reprint MAPS: a microarray project system for gene expression experiment information and data validation
    P 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
    ....
  15. pmc 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
    ....
  16. ncbi request reprint Gene expression analysis reveals chemical-specific profiles
    Hisham 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
    ....
  17. ncbi request reprint Prediction of compound signature using high density gene expression profiling
    Hisham 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...
  18. pmc Insulin-like growth factor-1 inscribes a gene expression profile for angiogenic factors and cancer progression in breast epithelial cells
    J 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...
  19. ncbi request reprint Toward a checklist for exchange and interpretation of data from a toxicology study
    Jennifer 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...
  20. ncbi request reprint Differential toxicogenomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin in malignant and nonmalignant human airway epithelial cells
    Jeanelle 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...
  21. ncbi request reprint 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 data
    Jennifer 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)...
  22. ncbi request reprint Systematic variation normalization in microarray data to get gene expression comparison unbiased
    Jeff 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...
  23. ncbi request reprint Regulation of DNA replication fork genes by 17beta-estradiol
    Edward 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...
  24. ncbi request reprint Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation
    Alexandra 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...
  25. ncbi request reprint ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiation
    Alexandra 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...
  26. pmc Blood gene expression signatures predict exposure levels
    P 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...
  27. pmc Progress in the application of DNA microarrays
    E 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...
  28. pmc Inactivation of DNA mismatch repair by increased expression of yeast MLH1
    P 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
    ....
  29. ncbi request reprint ATM requirement in gene expression responses to ionizing radiation in human lymphoblasts and fibroblasts
    Cynthia 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...
  30. ncbi request reprint Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations
    Hisham K Hamadeh
    National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
    Toxicol Pathol 30:470-82. 2002
    ....
  31. ncbi request reprint Genomic interrogation of mechanism(s) underlying cellular responses to toxicants
    Rupesh 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...
  32. ncbi request reprint Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells
    Leslie 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...
  33. pmc Database development in toxicogenomics: issues and efforts
    William B Mattes
    Pfizer Inc, Groton, Connecticut, USA
    Environ Health Perspect 112:495-505. 2004
    ....
  34. pmc Ataxia telangiectasia-mutated dependent DNA damage checkpoint functions regulate gene expression in human fibroblasts
    Tong 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...
  35. ncbi request reprint PAGE: phase-shifted analysis of gene expression
    Elo 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...
  36. pmc Global transcriptome and deletome profiles of yeast exposed to transition metals
    Yong Hwan Jin
    Nicholas School of the Environment and Earth Sciences, Duke University, Durham, North Carolina, United States of America
    PLoS Genet 4:e1000053. 2008
    ....
  37. pmc Profiles of global gene expression in ionizing-radiation-damaged human diploid fibroblasts reveal synchronization behind the G1 checkpoint in a G0-like state of quiescence
    Tong 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
    ....
  38. pmc Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage
    Tong 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...
  39. ncbi request reprint Standardizing global gene expression analysis between laboratories and across platforms
    Theodore 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...