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Pierre Bushel, Ph.D.

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Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Ramaiahgari SC, Auerbach SS, Saddler TO, Rice JR, Dunlap PE, Sipes NS, DeVito MJ, Shah RR, Bushel PR, Merrick BA, Paules RS, Ferguson SS. The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals Using High-throughput Transcriptomics and Benchmark Concentration Modeling. Toxicol Sci. 2019 Jun 01; 169(2):553-566. PMID: 30850835.
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  2. Grimm SA, Shimbo T, Takaku M, Thomas JW, Auerbach S, Bennett BD, Bucher JR, Burkholder AB, Day F, Du Y, Duncan CG, French JE, Foley JF, Li J, Merrick BA, Tice RR, Wang T, Xu X, Bushel PR, Fargo DC, Mullikin JC, Wade PA. DNA methylation in mice is influenced by genetics as well as sex and life experience. Nat Commun. 2019 01 18; 10(1):305. PMID: 30659182.
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  3. Davis M, Knight E, Eldridge SR, Li J, Bushel PR. Transcriptomic profiles of tissues from rats treated with anticancer drug combinations. Sci Data. 2019 01 08; 6:180306. PMID: 30620345.
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  4. Bushel PR, Tong W. Editorial: Integrative Toxicogenomics: Analytical Strategies to Amalgamate Exposure Effects With Genomic Sciences. Front Genet. 2018; 9:563. PMID: 30542369.
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  5. Bushel PR, Caiment F, Wu H, O'Lone R, Day F, Calley J, Smith A, Li J. RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database. BMC Genomics. 2018 Nov 19; 19(1):825. PMID: 30453895.
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  6. Bushel PR, Paules RS, Auerbach SS. A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. Front Genet. 2018; 9:485. PMID: 30420870.
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  7. Nguyen TT, Grimm SA, Bushel PR, Li J, Li Y, Bennett BD, Lavender CA, Ward JM, Fargo DC, Anderson CW, Li L, Resnick MA, Menendez D. Revealing a human p53 universe. Nucleic Acids Res. 2018 09 19; 46(16):8153-8167. PMID: 30107566.
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  8. Duncan CG, Grimm SA, Morgan DL, Bushel PR, Bennett BD, Roberts JD, Tyson FL, Merrick BA, Wade PA. Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver. Sci Rep. 2018 Jul 04; 8(1):10138. PMID: 29973619.
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  9. Lozoya OA, Martinez-Reyes I, Wang T, Grenet D, Bushel P, Li J, Chandel N, Woychik RP, Santos JH. Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation. PLoS Biol. 2018 04; 16(4):e2005707. PMID: 29668680.
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  10. Muñoz MD, Della Vedova MC, Bushel PR, Ganini da Silva D, Mason RP, Zhai Z, Gomez Mejiba SE, Ramirez DC. The nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide dampens lipopolysaccharide-induced transcriptomic changes in macrophages. Inflamm Res. 2018 Jun; 67(6):515-530. PMID: 29589052.
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  11. Duncan CG, Kondilis-Mangum HD, Grimm SA, Bushel PR, Chrysovergis K, Roberts JD, Tyson FL, Merrick BA, Wade PA. Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. G3 (Bethesda). 2018 03 02; 8(3):805-813. PMID: 29326230.
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  12. Mav D, Shah RR, Howard BE, Auerbach SS, Bushel PR, Collins JB, Gerhold DL, Judson RS, Karmaus AL, Maull EA, Mendrick DL, Merrick BA, Sipes NS, Svoboda D, Paules RS. A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PLoS One. 2018; 13(2):e0191105. PMID: 29462216.
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  13. Funderburk KM, Auerbach SS, Bushel PR. Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53. Front Genet. 2017; 8:157. PMID: 29114260.
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  14. Osgood RS, Upham BL, Bushel PR, Velmurugan K, Xiong KN, Bauer AK. Secondhand Smoke-Prevalent Polycyclic Aromatic Hydrocarbon Binary Mixture-Induced Specific Mitogenic and Pro-inflammatory Cell Signaling Events in Lung Epithelial Cells. Toxicol Sci. 2017 05 01; 157(1):156-171. PMID: 28329830.
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  15. Bennett BD, Bushel PR. goSTAG: gene ontology subtrees to tag and annotate genes within a set. Source Code Biol Med. 2017; 12:6. PMID: 28413437.
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  16. Manrai AK, Cui Y, Bushel PR, Hall M, Karakitsios S, Mattingly CJ, Ritchie M, Schmitt C, Sarigiannis DA, Thomas DC, Wishart D, Balshaw DM, Patel CJ. Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. Annu Rev Public Health. 2017 Mar 20; 38:279-294. PMID: 28068484.
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  17. 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. 2016 08 30; 17:694. PMID: 27576563.
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  18. Kim SH, Trinh AT, Larsen MC, Mastrocola AS, Jefcoate CR, Bushel PR, Tibbetts RS. Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism. Nucleic Acids Res. 2016 Nov 16; 44(20):9667-9680. PMID: 27431323.
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  19. Ciencewicki JM, Verhein KC, Gerrish K, McCaw ZR, Li J, Bushel PR, Kleeberger SR. Effects of mannose-binding lectin on pulmonary gene expression and innate immune inflammatory response to ozone. Am J Physiol Lung Cell Mol Physiol. 2016 08 01; 311(2):L280-91. PMID: 27106289.
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  20. Li J, Bushel PR. EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data. BMC Genomics. 2016 Mar 22; 17:255. PMID: 27004791.
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  21. Bushel PR, Fannin RD, Gerrish K, Watkins PB, Paules RS. Blood gene expression profiling of an early acetaminophen response. Pharmacogenomics J. 2017 06; 17(3):230-236. PMID: 26927286.
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  22. 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. Clin Pharmacol Ther. 2016 Apr; 99(4):432-41. PMID: 26690555.
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  23. Yang J, Bennett BD, Luo S, Inoue K, Grimm SA, Schroth GP, Bushel PR, Kinyamu HK, Archer TK. LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells. Mol Cell Biol. 2015 Sep; 35(18):3225-43. PMID: 26149387.
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  24. 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. Regul Toxicol Pharmacol. 2015 Jul; 72(2):292-309. PMID: 25944780.
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  25. Davis M, Li J, Knight E, Eldridge SR, Daniels KK, Bushel PR. Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity. Front Genet. 2015; 6:14. PMID: 25729387.
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  26. Verhein KC, McCaw Z, Gladwell W, Trivedi S, Bushel PR, Kleeberger SR. Novel Roles for Notch3 and Notch4 Receptors in Gene Expression and Susceptibility to Ozone-Induced Lung Inflammation in Mice. Environ Health Perspect. 2015 Aug; 123(8):799-805. PMID: 25658374.
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  27. Hewitt SC, Winuthayanon W, Pockette B, Kerns RT, Foley JF, Flagler N, Ney E, Suksamrarn A, Piyachaturawat P, Bushel PR, Korach KS. Development of phenotypic and transcriptional biomarkers to evaluate relative activity of potentially estrogenic chemicals in ovariectomized mice. Environ Health Perspect. 2015 Apr; 123(4):344-52. PMID: 25575267.
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  28. 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, Labaj PP, Kreil DP, Megherbi D, Gaj S, Caiment F, van Delft J, Kleinjans J, Scherer A, Devanarayan V, Wang J, Yang Y, Qian HR, Lancashire LJ, Bessarabova M, Nikolsky Y, Furlanello C, Chierici M, Albanese D, Jurman G, Riccadonna S, Filosi M, Visintainer R, Zhang KK, Li J, Hsieh JH, Svoboda DL, Fuscoe JC, Deng Y, Shi L, Paules RS, Auerbach SS, Tong W. The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance. Nat Biotechnol. 2014 Sep; 32(9):926-32. PMID: 25150839.
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  29. Lowe JM, Menendez D, Bushel PR, Shatz M, Kirk EL, Troester MA, Garantziotis S, Fessler MB, Resnick MA. p53 and NF-?B coregulate proinflammatory gene responses in human macrophages. Cancer Res. 2014 Apr 15; 74(8):2182-92. PMID: 24737129.
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  30. 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 Syst Biol. 2013 Nov 04; 7:119. PMID: 24188919.
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  31. 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. Physiol Genomics. 2013 Oct 01; 45(19):907-16. PMID: 23943852.
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  32. Huang L, Zhang HH, Zeng ZB, Bushel PR. Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification. Cancer Inform. 2013; 12:143-53. PMID: 23966761.
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  33. Lu J, Bushel PR. Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. Gene. 2013 Sep 25; 527(2):616-23. PMID: 23845781.
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  34. Huda A, Bushel PR. Widespread Exonization of Transposable Elements in Human Coding Sequences is Associated with Epigenetic Regulation of Transcription. Transcr Open Access. 2013 Jun 19; 1(1). PMID: 24860841.
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  35. 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. 2013; 8(6):e63909. PMID: 23785396.
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  36. Madenspacher JH, Azzam KM, Gowdy KM, Malcolm KC, Nick JA, Dixon D, Aloor JJ, Draper DW, Guardiola JJ, Shatz M, Menendez D, Lowe J, Lu J, Bushel P, Li L, Merrick BA, Resnick MA, Fessler MB. p53 Integrates host defense and cell fate during bacterial pneumonia. J Exp Med. 2013 May 06; 210(5):891-904. PMID: 23630228.
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  37. Arana ME, Kerns RT, Wharey L, Gerrish KE, Bushel PR, Kunkel TA. Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae. DNA Repair (Amst). 2012 Dec 01; 11(12):933-41. PMID: 23079308.
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  38. Zhang L, Bushel PR, Chou J, Zhou T, Watkins PB. Identification of Identical Transcript Changes in Liver and Whole Blood during Acetaminophen Toxicity. Front Genet. 2012; 3:162. PMID: 22973295.
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  39. 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. Toxicol Pathol. 2012 Dec; 40(8):1141-59. PMID: 22688403.
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  40. 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. 2012; 7(3):e34286. PMID: 22479588.
    Citations: 4     Fields:    Translation:HumansCells
  41. Hewitt SC, Li L, Grimm SA, Chen Y, Liu L, Li Y, Bushel PR, Fargo D, Korach KS. Research resource: whole-genome estrogen receptor a binding in mouse uterine tissue revealed by ChIP-seq. Mol Endocrinol. 2012 May; 26(5):887-98. PMID: 22446102.
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  42. Kerns RT, Bushel PR. The impact of classification of interest on predictive toxicogenomics. Front Genet. 2012; 3:14. PMID: 22347226.
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  43. Corton JC, Bushel PR, Fostel J, O'Lone RB. Sources of variance in baseline gene expression in the rodent liver. Mutat Res. 2012 Aug 15; 746(2):104-12. PMID: 22230429.
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  44. Chang C, Wang J, Zhao C, Fostel J, Tong W, Bushel PR, Deng Y, Pusztai L, Symmans WF, Shi T. Maximizing biomarker discovery by minimizing gene signatures. BMC Genomics. 2011 Dec 23; 12 Suppl 5:S6. PMID: 22369133.
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  45. 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. Toxicol Pathol. 2011 Jun; 39(4):678-99. PMID: 21571946.
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  46. Lu J, Kerns RT, Peddada SD, Bushel PR. Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays. Nucleic Acids Res. 2011 Jul; 39(13):e86. PMID: 21525126.
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  47. Merrick BA, London RE, Bushel PR, Grissom SF, Paules RS. Platforms for biomarker analysis using high-throughput approaches in genomics, transcriptomics, proteomics, metabolomics, and bioinformatics. IARC Sci Publ. 2011; (163):121-42. PMID: 22997859.
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  48. Afshari CA, Hamadeh HK, Bushel PR. The evolution of bioinformatics in toxicology: advancing toxicogenomics. Toxicol Sci. 2011 Mar; 120 Suppl 1:S225-37. PMID: 21177775.
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  49. 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. 2011 Jan; 119(1):17-35. PMID: 21143523.
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  50. Luo J, Schumacher M, Scherer A, Sanoudou D, Megherbi D, Davison T, Shi T, Tong W, Shi L, Hong H, Zhao C, Elloumi F, Shi W, Thomas R, Lin S, Tillinghast G, Liu G, Zhou Y, Herman D, Li Y, Deng Y, Fang H, Bushel P, Woods M, Zhang J. A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data. Pharmacogenomics J. 2010 Aug; 10(4):278-91. PMID: 20676067.
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  51. 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, Shi L, Fan X, Corton JC, Chen M, Cheng Y, Tong W, Fang H, Bushel PR. Genomic indicators in the blood predict drug-induced liver injury. Pharmacogenomics J. 2010 Aug; 10(4):267-77. PMID: 20676066.
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  52. 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, Shi T, Nikolskaya T, Nikolsky Y, Hong H, Deng Y, Cheng Y, Fang H, Shi L, Tong W. Consistency of predictive signature genes and classifiers generated using different microarray platforms. Pharmacogenomics J. 2010 Aug; 10(4):247-57. PMID: 20676064.
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  53. 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, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010 Aug; 28(8):827-38. PMID: 20676074.
    Citations: 224     Fields:    Translation:HumansAnimals
  54. 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 Syst Biol. 2009 Sep 16; 3:93. PMID: 19758441.
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  55. Chou JW, Bushel PR. Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes. BMC Genomics. 2009 Jun 18; 10:272. PMID: 19538742.
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  56. Bushel PR, Nielsen D, Tong W. Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007). BMC Proc. 2009 Mar 10; 3 Suppl 2:S1. PMID: 19278557.
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  57. Bushel PR. Clustering of gene expression data and end-point measurements by simulated annealing. J Bioinform Comput Biol. 2009 Feb; 7(1):193-215. PMID: 19226667.
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  58. 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, Wilson RE, Hurban P, Tennant RW, Paules RS. Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype. Genome Biol. 2008; 9(6):R100. PMID: 18570634.
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  59. Huang L, Heinloth AN, Zeng ZB, Paules RS, Bushel PR. Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants. BMC Genomics. 2008 Jun 16; 9:288. PMID: 18558008.
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  60. 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, Thompson KL. Sources of variation in baseline gene expression levels from toxicogenomics study control animals across multiple laboratories. BMC Genomics. 2008 Jun 12; 9:285. PMID: 18549499.
    Citations: 23     Fields:    Translation:Animals
  61. 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 Genet. 2008 Apr 25; 4(4):e1000053. PMID: 18437200.
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  62. 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. 2007 Nov 02; 8:427. PMID: 17980031.
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  63. 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. Proc Natl Acad Sci U S A. 2007 Nov 13; 104(46):18211-6. PMID: 17984051.
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  64. 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, Chan DD, Pan Q, Gong H, Taylor J, Choi D, Rashid A, Ahmed A, Howle R, Selkirk J, Tennant R, Fostel J. CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res. 2008 Jan; 36(Database issue):D892-900. PMID: 17962311.
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  65. Zhou T, Chou J, Zhou Y, Simpson DA, Cao F, Bushel PR, Paules RS, Kaufmann WK. Ataxia telangiectasia-mutated dependent DNA damage checkpoint functions regulate gene expression in human fibroblasts. Mol Cancer Res. 2007 Aug; 5(8):813-22. PMID: 17699107.
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  66. 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. Toxicol Sci. 2007 Sep; 99(1):26-34. PMID: 17442663.
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  67. 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. 2007 Apr 15; 6(8):972-81. PMID: 17404513.
    Citations: 8     Fields:    Translation:HumansCells
  68. Bushel PR, Wolfinger RD, Gibson G. Simultaneous clustering of gene expression data with clinical chemistry and pathological evaluations reveals phenotypic prototypes. BMC Syst Biol. 2007 Feb 23; 1:15. PMID: 17408499.
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  69. Zhou T, Chou JW, Simpson DA, Zhou Y, Mullen TE, Medeiros M, Bushel PR, Paules RS, Yang X, Hurban P, Lobenhofer EK, Kaufmann WK. 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. Environ Health Perspect. 2006 Apr; 114(4):553-9. PMID: 16581545.
    Citations: 32     Fields:    Translation:HumansCells
  70. Innes CL, Heinloth AN, Flores KG, Sieber SO, Deming PB, Bushel PR, Kaufmann WK, Paules RS. ATM requirement in gene expression responses to ionizing radiation in human lymphoblasts and fibroblasts. Mol Cancer Res. 2006 Mar; 4(3):197-207. PMID: 16547157.
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  71. 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. 2006 Apr 01; 22(7):874-82. PMID: 16410321.
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  72. Leung E, Bushel PR. PAGE: phase-shifted analysis of gene expression. Bioinformatics. 2006 Feb 01; 22(3):367-8. PMID: 16322047.
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  73. 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, Frade C, Garcia A, Heinloth A, Irwin R, Madenspacher J, Merrick BA, Papoian T, Paules R, Rocca-Serra P, Sansone AS, Stevens J, Tomer K, Yang C, Waters M. 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. Toxicol Sci. 2005 Dec; 88(2):585-601. PMID: 16150882.
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  74. 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, Freedman JH, Fry RC, Harper A, Humble MC, Hurban P, Kavanagh TJ, Kaufmann WK, Kerr KF, Jing L, Lapidus JA, Lasarev MR, Li J, Li YJ, Lobenhofer EK, Lu X, Malek RL, Milton S, Nagalla SR, O'malley JP, Palmer VS, Pattee P, Paules RS, Perou CM, Phillips K, Qin LX, Qiu Y, Quigley SD, Rodland M, Rusyn I, Samson LD, Schwartz DA, Shi Y, Shin JL, Sieber SO, Slifer S, Speer MC, Spencer PS, Sproles DI, Swenberg JA, Suk WA, Sullivan RC, Tian R, Tennant RW, Todd SA, Tucker CJ, Van Houten B, Weis BK, Xuan S, Zarbl H. Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods. 2005 May; 2(5):351-6. PMID: 15846362.
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  75. Chou JW, Paules RS, Bushel PR. Systematic variation normalization in microarray data to get gene expression comparison unbiased. J Bioinform Comput Biol. 2005 Apr; 3(2):225-41. PMID: 15852502.
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  76. Hamadeh HK, Jayadev S, Gaillard ET, Huang Q, Stoll R, Blanchard K, Chou J, Tucker CJ, Collins J, Maronpot R, Bushel P, Afshari CA. Integration of clinical and gene expression endpoints to explore furan-mediated hepatotoxicity. Mutat Res. 2004 May 18; 549(1-2):169-83. PMID: 15120969.
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  77. Mattes WB, Pettit SD, Sansone SA, Bushel PR, Waters MD. Database development in toxicogenomics: issues and efforts. Environ Health Perspect. 2004 Mar; 112(4):495-505. PMID: 15033600.
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  78. Heinloth AN, Shackelford RE, Innes CL, Bennett L, Li L, Amin RP, Sieber SO, Flores KG, Bushel PR, Paules RS. ATM-dependent and -independent gene expression changes in response to oxidative stress, gamma irradiation, and UV irradiation. Radiat Res. 2003 Sep; 160(3):273-90. PMID: 12926986.
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  79. Heinloth AN, Shackelford RE, Innes CL, Bennett L, Li L, Amin RP, Sieber SO, Flores KG, Bushel PR, Paules RS. Identification of distinct and common gene expression changes after oxidative stress and gamma and ultraviolet radiation. Mol Carcinog. 2003 Jun; 37(2):65-82. PMID: 12766906.
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  80. 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. Mol Cancer Res. 2003 Feb; 1(4):300-11. PMID: 12612058.
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  81. Waters M, Boorman G, Bushel P, Cunningham M, Irwin R, Merrick A, Olden K, Paules R, Selkirk J, Stasiewicz S, Weis B, Van Houten B, Walker N, Tennant R. Systems toxicology and the Chemical Effects in Biological Systems (CEBS) knowledge base. EHP Toxicogenomics. 2003 Jan; 111(1T):15-28. PMID: 12735106.
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  82. Amin RP, Hamadeh HK, Bushel PR, Bennett L, Afshari CA, Paules RS. Genomic interrogation of mechanism(s) underlying cellular responses to toxicants. Toxicology. 2002 Dec 27; 181-182:555-63. PMID: 12505366.
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  83. 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. Toxicol Sci. 2002 Oct; 69(2):409-23. PMID: 12377990.
    Citations:    
  84. Steenbergen C, Afshari CA, Petranka JG, Collins J, Martin K, Bennett L, Haugen A, Bushel P, Murphy E. Alterations in apoptotic signaling in human idiopathic cardiomyopathic hearts in failure. Am J Physiol Heart Circ Physiol. 2003 Jan; 284(1):H268-76. PMID: 12388275.
    Citations:    
  85. Hamadeh HK, Knight BL, Haugen AC, Sieber S, Amin RP, Bushel PR, Stoll R, Blanchard K, Jayadev S, Tennant RW, Cunningham ML, Afshari CA, Paules RS. Methapyrilene toxicity: anchorage of pathologic observations to gene expression alterations. Toxicol Pathol. 2002 Jul-Aug; 30(4):470-82. PMID: 12187938.
    Citations:    
  86. Bushel PR, Hamadeh HK, Bennett L, Green J, Ableson A, Misener S, Afshari CA, Paules RS. Computational selection of distinct class- and subclass-specific gene expression signatures. J Biomed Inform. 2002 Jun; 35(3):160-70. PMID: 12669979.
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  87. Lobenhofer EK, Bennett L, Cable PL, Li L, Bushel PR, Afshari CA. Regulation of DNA replication fork genes by 17beta-estradiol. Mol Endocrinol. 2002 Jun; 16(6):1215-29. PMID: 12040010.
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  88. Hamadeh HK, Bushel PR, Jayadev S, DiSorbo O, Bennett L, Li L, Tennant R, Stoll R, Barrett JC, Paules RS, Blanchard K, Afshari CA. Prediction of compound signature using high density gene expression profiling. Toxicol Sci. 2002 Jun; 67(2):232-40. PMID: 12011482.
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  89. Hamadeh HK, Bushel PR, Jayadev S, Martin K, DiSorbo O, Sieber S, Bennett L, Tennant R, Stoll R, Barrett JC, Blanchard K, Paules RS, Afshari CA. Gene expression analysis reveals chemical-specific profiles. Toxicol Sci. 2002 Jun; 67(2):219-31. PMID: 12011481.
    Citations:    
  90. 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. 2002 May-Jun; 4(3):204-17. PMID: 11988840.
    Citations:    
  91. Hamadeh HK, Bushel P, Tucker CJ, Martin K, Paules R, Afshari CA. Detection of diluted gene expression alterations using cDNA microarrays. Biotechniques. 2002 Feb; 32(2):322, 324, 326-9. PMID: 11848409.
    Citations:    
  92. Lobenhofer EK, Bushel PR, Afshari CA, Hamadeh HK. Progress in the application of DNA microarrays. Environ Health Perspect. 2001 Sep; 109(9):881-91. PMID: 11673116.
    Citations:    
  93. Bushel PR, Hamadeh H, Bennett L, Sieber S, Martin K, Nuwaysir EF, Johnson K, Reynolds K, Paules RS, Afshari CA. MAPS: a microarray project system for gene expression experiment information and data validation. Bioinformatics. 2001 Jun; 17(6):564-5. PMID: 11395436.
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  94. Shcherbakova PV, Hall MC, Lewis MS, Bennett SE, Martin KJ, Bushel PR, Afshari CA, Kunkel TA. Inactivation of DNA mismatch repair by increased expression of yeast MLH1. Mol Cell Biol. 2001 Feb; 21(3):940-51. PMID: 11154280.
    Citations:    
  95. 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. J Comput Biol. 2001; 8(6):625-37. PMID: 11747616.
    Citations:    
  96. Hamadeh HK, Bushel P, Paules R, Afshari CA. Discovery in toxicology: mediation by gene expression array technology. J Biochem Mol Toxicol. 2001; 15(5):231-42. PMID: 11835620.
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  97. Kumar CC, Kim JH, Bushel P, Armstrong L, Catino JJ. Activation of smooth muscle alpha-actin promoter in ras-transformed cells by treatments with antimitotic agents: correlation with stimulation of SRF:SRE mediated gene transcription. J Biochem. 1995 Dec; 118(6):1285-92. PMID: 8720148.
    Citations:    
  98. Bushel P, Kim JH, Chang W, Catino JJ, Ruley HE, Kumar CC. Two serum response elements mediate transcriptional repression of human smooth muscle alpha-actin promoter in ras-transformed cells. Oncogene. 1995 Apr 06; 10(7):1361-70. PMID: 7731687.
    Citations:    
  99. Simonson MS, Walsh K, Kumar CC, Bushel P, Herman WH. Two proximal CArG elements regulate SM alpha-actin promoter, a genetic marker of activated phenotype of mesangial cells. Am J Physiol. 1995 Apr; 268(4 Pt 2):F760-9. PMID: 7733334.
    Citations:    
  100. Kim JH, Bushel PR, Kumar CC. Smooth muscle alpha-actin promoter activity is induced by serum stimulation of fibroblast cells. Biochem Biophys Res Commun. 1993 Feb 15; 190(3):1115-21. PMID: 8439311.
    Citations:    
  101. Kumar CC, Bushel P, Mohan-Peterson S, Ramirez F. Regulation of smooth muscle alpha-actin promoter in ras-transformed cells: usefulness for setting up reporter gene-based assay system for drug screening. Cancer Res. 1992 Dec 15; 52(24):6877-84. PMID: 1458476.
    Citations:    
  102. Lowndes NF, Bushel P, Mendelsohn L, Wu J, Yen MY, Allan M. A short, highly repetitive element in intron -1 of the human c-Ha-ras gene acts as a block to transcriptional readthrough by a viral promoter. Mol Cell Biol. 1990 Sep; 10(9):4990-5. PMID: 2201911.
    Citations:    
  103. Bushel P, Rego K, Mendelsohn L, Allan M. Correlation between patterns of DNase I-hypersensitive sites and upstream promoter activity of the human epsilon-globin gene at different stages of erythroid development. Mol Cell Biol. 1990 Mar; 10(3):1199-208. PMID: 2304464.
    Citations:    
  104. Wu J, Grindlay GJ, Bushel P, Mendelsohn L, Allan M. Negative regulation of the human epsilon-globin gene by transcriptional interference: role of an Alu repetitive element. Mol Cell Biol. 1990 Mar; 10(3):1209-16. PMID: 2304465.
    Citations:    
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.