Pierre R. Bushel, Ph.D. - Publications

North Carolina State University, Raleigh, NC 
Evolutionary Genomics

36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Smith A, Calley J, Mathur S, Qian HR, Wu H, Farmen M, Caiment F, Bushel PR, Li J, Fisher C, Kirby P, Koenig E, Hall DG, Watson DE. The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog. Bmc Genomics. 17: 694. PMID 27576563 DOI: 10.1186/s12864-016-2956-z  0.64
2016 Bushel PR, Fannin RD, Gerrish K, Watkins PB, Paules RS. Blood gene expression profiling of an early acetaminophen response. The Pharmacogenomics Journal. PMID 26927286 DOI: 10.1038/tpj.2016.8  0.64
2015 Fannin RD, Gerrish K, Sieber SO, Bushel PR, Watkins PB, Paules RS. Blood transcript immune signatures distinguish a subset of people with elevated serum ALT from others given acetaminophen. Clinical Pharmacology and Therapeutics. PMID 26690555 DOI: 10.1002/cpt.328  0.64
2015 Bourdon-Lacombe JA, Moffat ID, Deveau M, Husain M, Auerbach S, Krewski D, Thomas RS, Bushel PR, Williams A, Yauk CL. Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals. Regulatory Toxicology and Pharmacology : Rtp. 72: 292-309. PMID 25944780 DOI: 10.1016/j.yrtph.2015.04.010  0.64
2014 Wang C, Gong B, Bushel PR, Thierry-Mieg J, Thierry-Mieg D, Xu J, Fang H, Hong H, Shen J, Su Z, Meehan J, Li X, Yang L, Li H, ?abaj PP, et al. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nature Biotechnology. 32: 926-32. PMID 25150839 DOI: 10.1038/nbt.3001  0.64
2014 . A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nature Biotechnology. 32: 903-14. PMID 25150838 DOI: 10.1038/nbt.2957  0.64
2014 Lowe JM, Menendez D, Bushel PR, Shatz M, Kirk EL, Troester MA, Garantziotis S, Fessler MB, Resnick MA. p53 and NF-κB coregulate proinflammatory gene responses in human macrophages. Cancer Research. 74: 2182-92. PMID 24737129 DOI: 10.1158/0008-5472.CAN-13-1070  0.64
2013 Williams-DeVane CR, Reif DM, Hubal EC, Bushel PR, Hudgens EE, Gallagher JE, Edwards SW. Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes. Bmc Systems Biology. 7: 119. PMID 24188919 DOI: 10.1186/1752-0509-7-119  0.64
2013 Zhang L, Simpson DA, Innes CL, Chou J, Bushel PR, Paules RS, Kaufmann WK, Zhou T. Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals. Physiological Genomics. 45: 907-16. PMID 23943852 DOI: 10.1152/physiolgenomics.00064.2013  0.64
2013 Davis BJ, Risinger JI, Chandramouli GV, Bushel PR, Baird DD, Peddada SD. 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). Plos One. 8: e63909. PMID 23785396 DOI: 10.1371/journal.pone.0063909  0.64
2012 Pandiri AR, Sills RC, Ziglioli V, Ton TV, Hong HH, Lahousse SA, Gerrish KE, Auerbach SS, Shockley KR, Bushel PR, Peddada SD, Hoenerhoff MJ. Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancer. Toxicologic Pathology. 40: 1141-59. PMID 22688403 DOI: 10.1177/0192623312447543  0.64
2012 Bushel PR, McGovern R, Liu L, Hofmann O, Huda A, Lu J, Hide W, Lin X. Population differences in transcript-regulator expression quantitative trait loci. Plos One. 7: e34286. PMID 22479588 DOI: 10.1371/journal.pone.0034286  0.64
2012 Corton JC, Bushel PR, Fostel J, O'Lone RB. Sources of variance in baseline gene expression in the rodent liver. Mutation Research. 746: 104-12. PMID 22230429 DOI: 10.1016/j.mrgentox.2011.12.017  0.64
2011 Hoenerhoff MJ, Pandiri AR, Lahousse SA, Hong HH, Ton TV, Masinde T, Auerbach SS, Gerrish K, Bushel PR, Shockley KR, Peddada SD, Sills RC. Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer. Toxicologic Pathology. 39: 678-99. PMID 21571946 DOI: 10.1177/0192623311407213  0.64
2011 Lu J, Kerns RT, Peddada SD, Bushel PR. Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays. Nucleic Acids Research. 39: e86. PMID 21525126 DOI: 10.1093/nar/gkr241  0.64
2011 Eggesbø M, Moen B, Peddada S, Baird D, Rugtveit J, Midtvedt T, Bushel PR, Sekelja M, Rudi K. Development of gut microbiota in infants not exposed to medical interventions. Apmis : Acta Pathologica, Microbiologica, Et Immunologica Scandinavica. 119: 17-35. PMID 21143523 DOI: 10.1111/j.1600-0463.2010.02688.x  0.64
2010 Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, ... ... Bushel PR, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 28: 827-38. PMID 20676074 DOI: 10.1038/nbt.1665  0.64
2010 Huang J, Shi W, Zhang J, Chou JW, Paules RS, Gerrish K, Li J, Luo J, Wolfinger RD, Bao W, Chu TM, Nikolsky Y, Nikolskaya T, Dosymbekov D, Tsyganova MO, ... ... Bushel PR, et al. Genomic indicators in the blood predict drug-induced liver injury. The Pharmacogenomics Journal. 10: 267-77. PMID 20676066 DOI: 10.1038/tpj.2010.33  0.64
2010 Fan X, Lobenhofer EK, Chen M, Shi W, Huang J, Luo J, Zhang J, Walker SJ, Chu TM, Li L, Wolfinger R, Bao W, Paules RS, Bushel PR, Li J, et al. Consistency of predictive signature genes and classifiers generated using different microarray platforms. The Pharmacogenomics Journal. 10: 247-57. PMID 20676064 DOI: 10.1038/tpj.2010.34  0.64
2009 Bushel PR, Heard NA, Gutman R, Liu L, Peddada SD, Pyne S. Dissecting the fission yeast regulatory network reveals phase-specific control elements of its cell cycle. Bmc Systems Biology. 3: 93. PMID 19758441 DOI: 10.1186/1752-0509-3-93  0.64
2008 Lobenhofer EK, Auman JT, Blackshear PE, Boorman GA, Bushel PR, Cunningham ML, Fostel JM, Gerrish K, Heinloth AN, Irwin RD, Malarkey DE, Merrick BA, Sieber SO, Tucker CJ, Ward SM, et al. Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype. Genome Biology. 9: R100. PMID 18570634 DOI: 10.1186/gb-2008-9-6-r100  0.64
2008 Boedigheimer MJ, Wolfinger RD, Bass MB, Bushel PR, Chou JW, Cooper M, Corton JC, Fostel J, Hester S, Lee JS, Liu F, Liu J, Qian HR, Quackenbush J, Pettit S, et al. Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories. Bmc Genomics. 9: 285. PMID 18549499 DOI: 10.1186/1471-2164-9-285  0.64
2008 Jin YH, Dunlap PE, McBride SJ, Al-Refai H, Bushel PR, Freedman JH. Global transcriptome and deletome profiles of yeast exposed to transition metals. Plos Genetics. 4: e1000053. PMID 18437200 DOI: 10.1371/journal.pgen.1000053  0.64
2008 Waters M, Stasiewicz S, Merrick BA, Tomer K, Bushel P, Paules R, Stegman N, Nehls G, Yost KJ, Johnson CH, Gustafson SF, Xirasagar S, Xiao N, Huang CC, Boyer P, et al. CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Research. 36: D892-900. PMID 17962311 DOI: 10.1093/nar/gkm755  0.64
2007 Bushel PR, Heinloth AN, Li J, Huang L, Chou JW, Boorman GA, Malarkey DE, Houle CD, Ward SM, Wilson RE, Fannin RD, Russo MW, Watkins PB, Tennant RW, Paules RS. Blood gene expression signatures predict exposure levels. Proceedings of the National Academy of Sciences of the United States of America. 104: 18211-6. PMID 17984051 DOI: 10.1073/pnas.0706987104  0.64
2007 Chou JW, Zhou T, Kaufmann WK, Paules RS, Bushel PR. Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes. Bmc Bioinformatics. 8: 427. PMID 17980031 DOI: 10.1186/1471-2105-8-427  0.64
2007 Fostel JM, Burgoon L, Zwickl C, Lord P, Corton JC, Bushel PR, Cunningham M, Fan L, Edwards SW, Hester S, Stevens J, Tong W, Waters M, Yang C, Tennant R. Toward a checklist for exchange and interpretation of data from a toxicology study. Toxicological Sciences : An Official Journal of the Society of Toxicology. 99: 26-34. PMID 17442663 DOI: 10.1093/toxsci/kfm090  0.64
2007 Bushel PR, Wolfinger RD, Gibson G. Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes. Bmc Systems Biology. 1: 15. PMID 17408499 DOI: 10.1186/1752-0509-1-15  0.64
2007 Zhou T, Chou J, Mullen TE, Elkon R, Zhou Y, Simpson DA, Bushel PR, Paules RS, Lobenhofer EK, Hurban P, Kaufmann WK. Identification of primary transcriptional regulation of cell cycle-regulated genes upon DNA damage. Cell Cycle (Georgetown, Tex.). 6: 972-81. PMID 17404513  0.64
2006 Xirasagar S, Gustafson SF, Huang CC, Pan Q, Fostel J, Boyer P, Merrick BA, Tomer KB, Chan DD, Yost KJ, Choi D, Xiao N, Stasiewicz S, Bushel P, Waters MD. Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application. Bioinformatics (Oxford, England). 22: 874-82. PMID 16410321 DOI: 10.1093/bioinformatics/btk045  0.64
2005 Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A, Bao W, Richard A, Tong W, Bushel PR, Brown R, Bruno M, Cunningham ML, Dix D, Eastin W, et al. 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. Toxicological Sciences : An Official Journal of the Society of Toxicology. 88: 585-601. PMID 16150882 DOI: 10.1093/toxsci/kfi315  0.64
2005 Bammler T, Beyer RP, Bhattacharya S, Boorman GA, Boyles A, Bradford BU, Bumgarner RE, Bushel PR, Chaturvedi K, Choi D, Cunningham ML, Deng S, Dressman HK, Fannin RD, Farin FM, et al. Standardizing global gene expression analysis between laboratories and across platforms. Nature Methods. 2: 351-6. PMID 15846362 DOI: 10.1038/nmeth754  0.64
2003 Hodges LC, Cook JD, Lobenhofer EK, Li L, Bennett L, Bushel PR, Aldaz CM, Afshari CA, Walker CL. Tamoxifen functions as a molecular agonist inducing cell cycle-associated genes in breast cancer cells. Molecular Cancer Research : McR. 1: 300-11. PMID 12612058  0.64
2002 Martinez JM, Afshari CA, Bushel PR, Masuda A, Takahashi T, Walker NJ. Differential toxicogenomic responses to 2,3,7,8-tetrachlorodibenzo-p-dioxin in malignant and nonmalignant human airway epithelial cells. Toxicological Sciences : An Official Journal of the Society of Toxicology. 69: 409-23. PMID 12377990 DOI: 10.1093/toxsci/69.2.409  0.64
2002 Oh JS, Kucab JE, Bushel PR, Martin K, Bennett L, Collins J, DiAugustine RP, Barrett JC, Afshari CA, Dunn SE. Insulin-like growth factor-1 inscribes a gene expression profile for angiogenic factors and cancer progression in breast epithelial cells. Neoplasia (New York, N.Y.). 4: 204-17. PMID 11988840 DOI: 10.1038/sj/neo/7900229  0.64
2001 Wolfinger RD, Gibson G, Wolfinger ED, Bennett L, Hamadeh H, Bushel P, Afshari C, Paules RS. Assessing gene significance from cDNA microarray expression data via mixed models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 8: 625-37. PMID 11747616 DOI: 10.1089/106652701753307520  0.64
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