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Items: 1 to 50 of 86

1.

The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals Using High-throughput Transcriptomics and Benchmark Concentration Modeling.

Ramaiahgari SC, Auerbach SS, Saddler TO, Rice JR, Dunlap PE, Sipes NS, DeVito MJ, Shah RR, Bushel PR, Merrick BA, Paules RS, Ferguson SS.

Toxicol Sci. 2019 Jun 1;169(2):553-566. doi: 10.1093/toxsci/kfz065.

PMID:
30850835
2.

DNA methylation in mice is influenced by genetics as well as sex and life experience.

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; NISC Comparative Sequencing Program, Bushel PR, Fargo DC, Mullikin JC, Wade PA.

Nat Commun. 2019 Jan 18;10(1):305. doi: 10.1038/s41467-018-08067-z.

3.

Transcriptomic profiles of tissues from rats treated with anticancer drug combinations.

Davis M, Knight E, Eldridge SR, Li J, Bushel PR.

Sci Data. 2019 Jan 8;6:180306. doi: 10.1038/sdata.2018.306.

4.

Editorial: Integrative Toxicogenomics: Analytical Strategies to Amalgamate Exposure Effects With Genomic Sciences.

Bushel PR, Tong W.

Front Genet. 2018 Nov 27;9:563. doi: 10.3389/fgene.2018.00563. eCollection 2018. No abstract available.

5.

RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database.

Bushel PR, Caiment F, Wu H, O'Lone R, Day F, Calley J, Smith A, Li J.

BMC Genomics. 2018 Nov 19;19(1):825. doi: 10.1186/s12864-018-5220-x.

6.

A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples.

Bushel PR, Paules RS, Auerbach SS.

Front Genet. 2018 Oct 30;9:485. doi: 10.3389/fgene.2018.00485. eCollection 2018.

7.

Revealing a human p53 universe.

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.

Nucleic Acids Res. 2018 Sep 19;46(16):8153-8167. doi: 10.1093/nar/gky720.

8.

Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver.

Duncan CG, Grimm SA, Morgan DL, Bushel PR, Bennett BD; NISC Comparative Sequencing Program, Roberts JD, Tyson FL, Merrick BA, Wade PA.

Sci Rep. 2018 Jul 4;8(1):10138. doi: 10.1038/s41598-018-28356-3.

9.

The nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide dampens lipopolysaccharide-induced transcriptomic changes in macrophages.

Muñoz MD, Della Vedova MC, Bushel PR, Ganini da Silva D, Mason RP, Zhai Z, Gomez Mejiba SE, Ramirez DC.

Inflamm Res. 2018 Jun;67(6):515-530. doi: 10.1007/s00011-018-1141-z. Epub 2018 Mar 27.

PMID:
29589052
10.

A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics.

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.

PLoS One. 2018 Feb 20;13(2):e0191105. doi: 10.1371/journal.pone.0191105. eCollection 2018.

11.

Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells.

Duncan CG, Kondilis-Mangum HD, Grimm SA, Bushel PR, Chrysovergis K, Roberts JD, Tyson FL, Merrick BA, Wade PA.

G3 (Bethesda). 2018 Mar 2;8(3):805-813. doi: 10.1534/g3.117.300446.

12.
13.

goSTAG: gene ontology subtrees to tag and annotate genes within a set.

Bennett BD, Bushel PR.

Source Code Biol Med. 2017 Apr 13;12:6. doi: 10.1186/s13029-017-0066-1. eCollection 2017.

14.

Secondhand Smoke-Prevalent Polycyclic Aromatic Hydrocarbon Binary Mixture-Induced Specific Mitogenic and Pro-inflammatory Cell Signaling Events in Lung Epithelial Cells.

Osgood RS, Upham BL, Bushel PR, Velmurugan K, Xiong KN, Bauer AK.

Toxicol Sci. 2017 May 1;157(1):156-171. doi: 10.1093/toxsci/kfx027.

15.

Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health.

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.

Annu Rev Public Health. 2017 Mar 20;38:279-294. doi: 10.1146/annurev-publhealth-082516-012737. Epub 2016 Dec 23. Review.

16.

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.

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.

BMC Genomics. 2016 Aug 30;17:694. doi: 10.1186/s12864-016-2956-z.

17.

Tunable regulation of CREB DNA binding activity couples genotoxic stress response and metabolism.

Kim SH, Trinh AT, Larsen MC, Mastrocola AS, Jefcoate CR, Bushel PR, Tibbetts RS.

Nucleic Acids Res. 2016 Nov 16;44(20):9667-9680. Epub 2016 Jul 18.

18.

Effects of mannose-binding lectin on pulmonary gene expression and innate immune inflammatory response to ozone.

Ciencewicki JM, Verhein KC, Gerrish K, McCaw ZR, Li J, Bushel PR, Kleeberger SR.

Am J Physiol Lung Cell Mol Physiol. 2016 Aug 1;311(2):L280-91. doi: 10.1152/ajplung.00205.2015. Epub 2016 Apr 22.

19.

EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data.

Li J, Bushel PR.

BMC Genomics. 2016 Mar 22;17:255. doi: 10.1186/s12864-016-2584-7.

20.

Blood gene expression profiling of an early acetaminophen response.

Bushel PR, Fannin RD, Gerrish K, Watkins PB, Paules RS.

Pharmacogenomics J. 2017 Jun;17(3):230-236. doi: 10.1038/tpj.2016.8. Epub 2016 Mar 1.

21.

Blood transcript immune signatures distinguish a subset of people with elevated serum ALT from others given acetaminophen.

Fannin RD, Gerrish K, Sieber SO, Bushel PR, Watkins PB, Paules RS.

Clin Pharmacol Ther. 2016 Apr;99(4):432-41. doi: 10.1002/cpt.328. Epub 2016 Feb 22.

22.

LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells.

Yang J, Bennett BD, Luo S, Inoue K, Grimm SA, Schroth GP, Bushel PR, Kinyamu HK, Archer TK.

Mol Cell Biol. 2015 Sep;35(18):3225-43. doi: 10.1128/MCB.00426-15. Epub 2015 Jul 6.

23.

Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals.

Bourdon-Lacombe JA, Moffat ID, Deveau M, Husain M, Auerbach S, Krewski D, Thomas RS, Bushel PR, Williams A, Yauk CL.

Regul Toxicol Pharmacol. 2015 Jul;72(2):292-309. doi: 10.1016/j.yrtph.2015.04.010. Epub 2015 May 2.

PMID:
25944780
24.

Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity.

Davis M, Li J, Knight E, Eldridge SR, Daniels KK, Bushel PR.

Front Genet. 2015 Feb 12;6:14. doi: 10.3389/fgene.2015.00014. eCollection 2015.

25.

Novel Roles for Notch3 and Notch4 Receptors in Gene Expression and Susceptibility to Ozone-Induced Lung Inflammation in Mice.

Verhein KC, McCaw Z, Gladwell W, Trivedi S, Bushel PR, Kleeberger SR.

Environ Health Perspect. 2015 Aug;123(8):799-805. doi: 10.1289/ehp.1408852. Epub 2015 Feb 6.

26.

Development of phenotypic and transcriptional biomarkers to evaluate relative activity of potentially estrogenic chemicals in ovariectomized mice.

Hewitt SC, Winuthayanon W, Pockette B, Kerns RT, Foley JF, Flagler N, Ney E, Suksamrarn A, Piyachaturawat P, Bushel PR, Korach KS.

Environ Health Perspect. 2015 Apr;123(4):344-52. doi: 10.1289/ehp.1307935. Epub 2015 Jan 9.

27.

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance.

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, Łabaj 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.

Nat Biotechnol. 2014 Sep;32(9):926-32. doi: 10.1038/nbt.3001. Epub 2014 Aug 24.

29.

p53 and NF-κB coregulate proinflammatory gene responses in human macrophages.

Lowe JM, Menendez D, Bushel PR, Shatz M, Kirk EL, Troester MA, Garantziotis S, Fessler MB, Resnick MA.

Cancer Res. 2014 Apr 15;74(8):2182-92. doi: 10.1158/0008-5472.CAN-13-1070.

30.

Decision tree-based method for integrating gene expression, demographic, and clinical data to determine disease endotypes.

Williams-DeVane CR, Reif DM, Hubal EC, Bushel PR, Hudgens EE, Gallagher JE, Edwards SW.

BMC Syst Biol. 2013 Nov 4;7:119. doi: 10.1186/1752-0509-7-119.

31.

Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification.

Huang L, Zhang HH, Zeng ZB, Bushel PR.

Cancer Inform. 2013 Aug 4;12:143-53. doi: 10.4137/CIN.S10212. eCollection 2013.

32.

Gene expression signatures but not cell cycle checkpoint functions distinguish AT carriers from normal individuals.

Zhang L, Simpson DA, Innes CL, Chou J, Bushel PR, Paules RS, Kaufmann WK, Zhou T.

Physiol Genomics. 2013 Oct 1;45(19):907-16. doi: 10.1152/physiolgenomics.00064.2013. Epub 2013 Aug 13.

33.

Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling.

Lu J, Bushel PR.

Gene. 2013 Sep 25;527(2):616-23. doi: 10.1016/j.gene.2013.06.052. Epub 2013 Jul 9.

34.

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).

Davis BJ, Risinger JI, Chandramouli GV, Bushel PR, Baird DD, Peddada SD.

PLoS One. 2013 Jun 13;8(6):e63909. doi: 10.1371/journal.pone.0063909. Print 2013.

35.

Transcriptional responses to loss of RNase H2 in Saccharomyces cerevisiae.

Arana ME, Kerns RT, Wharey L, Gerrish KE, Bushel PR, Kunkel TA.

DNA Repair (Amst). 2012 Dec 1;11(12):933-41. doi: 10.1016/j.dnarep.2012.09.006. Epub 2012 Oct 15.

36.

Identification of Identical Transcript Changes in Liver and Whole Blood during Acetaminophen Toxicity.

Zhang L, Bushel PR, Chou J, Zhou T, Watkins PB.

Front Genet. 2012 Sep 4;3:162. doi: 10.3389/fgene.2012.00162. eCollection 2012.

37.

Differential transcriptomic analysis of spontaneous lung tumors in B6C3F1 mice: comparison to human non-small cell lung cancer.

Pandiri AR, Sills RC, Ziglioli V, Ton TV, Hong HH, Lahousse SA, Gerrish KE, Auerbach SS, Shockley KR, Bushel PR, Peddada SD, Hoenerhoff MJ.

Toxicol Pathol. 2012 Dec;40(8):1141-59. doi: 10.1177/0192623312447543. Epub 2012 Jun 11.

38.

Population differences in transcript-regulator expression quantitative trait loci.

Bushel PR, McGovern R, Liu L, Hofmann O, Huda A, Lu J, Hide W, Lin X.

PLoS One. 2012;7(3):e34286. doi: 10.1371/journal.pone.0034286. Epub 2012 Mar 27.

39.

Research resource: whole-genome estrogen receptor α binding in mouse uterine tissue revealed by ChIP-seq.

Hewitt SC, Li L, Grimm SA, Chen Y, Liu L, Li Y, Bushel PR, Fargo D, Korach KS.

Mol Endocrinol. 2012 May;26(5):887-98. doi: 10.1210/me.2011-1311. Epub 2012 Mar 22.

40.

Maximizing biomarker discovery by minimizing gene signatures.

Chang C, Wang J, Zhao C, Fostel J, Tong W, Bushel PR, Deng Y, Pusztai L, Symmans WF, Shi T.

BMC Genomics. 2011 Dec 23;12 Suppl 5:S6. doi: 10.1186/1471-2164-12-S5-S6. Epub 2011 Dec 23.

41.

The impact of classification of interest on predictive toxicogenomics.

Kerns RT, Bushel PR.

Front Genet. 2012 Feb 7;3:14. doi: 10.3389/fgene.2012.00014. eCollection 2012.

42.

Sources of variance in baseline gene expression in the rodent liver.

Corton JC, Bushel PR, Fostel J, O'Lone RB.

Mutat Res. 2012 Aug 15;746(2):104-12. doi: 10.1016/j.mrgentox.2011.12.017. Epub 2012 Jan 5. Review.

43.

Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer.

Hoenerhoff MJ, Pandiri AR, Lahousse SA, Hong HH, Ton TV, Masinde T, Auerbach SS, Gerrish K, Bushel PR, Shockley KR, Peddada SD, Sills RC.

Toxicol Pathol. 2011 Jun;39(4):678-99. doi: 10.1177/0192623311407213. Epub 2011 May 13.

44.

Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays.

Lu J, Kerns RT, Peddada SD, Bushel PR.

Nucleic Acids Res. 2011 Jul;39(13):e86. doi: 10.1093/nar/gkr241. Epub 2011 Apr 27.

45.

Platforms for biomarker analysis using high-throughput approaches in genomics, transcriptomics, proteomics, metabolomics, and bioinformatics.

Merrick BA, London RE, Bushel PR, Grissom SF, Paules RS.

IARC Sci Publ. 2011;(163):121-42. Review.

PMID:
22997859
46.

The evolution of bioinformatics in toxicology: advancing toxicogenomics.

Afshari CA, Hamadeh HK, Bushel PR.

Toxicol Sci. 2011 Mar;120 Suppl 1:S225-37. doi: 10.1093/toxsci/kfq373. Epub 2010 Dec 22. Review.

47.

Development of gut microbiota in infants not exposed to medical interventions.

Eggesbø M, Moen B, Peddada S, Baird D, Rugtveit J, Midtvedt T, Bushel PR, Sekelja M, Rudi K.

APMIS. 2011 Jan;119(1):17-35. doi: 10.1111/j.1600-0463.2010.02688.x. Epub 2010 Oct 25.

48.

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, 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; MAQC Consortium.

Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30.

49.

Genomic indicators in the blood predict drug-induced liver injury.

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.

Pharmacogenomics J. 2010 Aug;10(4):267-77. doi: 10.1038/tpj.2010.33.

50.

Consistency of predictive signature genes and classifiers generated using different microarray platforms.

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.

Pharmacogenomics J. 2010 Aug;10(4):247-57. doi: 10.1038/tpj.2010.34.

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