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Items: 1 to 50 of 110

1.

Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics.

Balik-Meisner MR, Mav D, Phadke DP, Everett LJ, Shah RR, Tal T, Shepard PJ, Merrick BA, Paules RS.

Zebrafish. 2019 Aug;16(4):331-347. doi: 10.1089/zeb.2018.1720. Epub 2019 Jun 12.

2.

Arsenite malignantly transforms human prostate epithelial cells in vitro by gene amplification of mutated KRAS.

Merrick BA, Phadke DP, Bostrom MA, Shah RR, Wright GM, Wang X, Gordon O, Pelch KE, Auerbach SS, Paules RS, DeVito MJ, Waalkes MP, Tokar EJ.

PLoS One. 2019 Apr 22;14(4):e0215504. doi: 10.1371/journal.pone.0215504. eCollection 2019.

3.

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
4.

Detection and Prioritization of Developmentally Neurotoxic and/or Neurotoxic Compounds Using Zebrafish.

Quevedo C, Behl M, Ryan K, Paules RS, Alday A, Muriana A, Alzualde A.

Toxicol Sci. 2019 Mar 1;168(1):225-240. doi: 10.1093/toxsci/kfy291.

PMID:
30521027
5.

Screening for Developmental Neurotoxicity at the National Toxicology Program: The Future Is Here.

Behl M, Ryan K, Hsieh JH, Parham F, Shapiro AJ, Collins BJ, Sipes NS, Birnbaum LS, Bucher JR, Foster PMD, Walker NJ, Paules RS, Tice RR.

Toxicol Sci. 2019 Jan 1;167(1):6-14. doi: 10.1093/toxsci/kfy278. Erratum in: Toxicol Sci. 2019 Apr 1;168(2):644.

PMID:
30496580
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.

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow.

Phillips JR, Svoboda DL, Tandon A, Patel S, Sedykh A, Mav D, Kuo B, Yauk CL, Yang L, Thomas RS, Gift JS, Davis JA, Olszyk L, Merrick BA, Paules RS, Parham F, Saddler T, Shah RR, Auerbach SS.

Bioinformatics. 2019 May 15;35(10):1780-1782. doi: 10.1093/bioinformatics/bty878.

8.

Toxicity profiling of flame retardants in zebrafish embryos using a battery of assays for developmental toxicity, neurotoxicity, cardiotoxicity and hepatotoxicity toward human relevance.

Alzualde A, Behl M, Sipes NS, Hsieh JH, Alday A, Tice RR, Paules RS, Muriana A, Quevedo C.

Neurotoxicol Teratol. 2018 Nov - Dec;70:40-50. doi: 10.1016/j.ntt.2018.10.002. Epub 2018 Oct 9.

9.

Comprehensive Analyses and Prioritization of Tox21 10K Chemicals Affecting Mitochondrial Function by in-Depth Mechanistic Studies.

Xia M, Huang R, Shi Q, Boyd WA, Zhao J, Sun N, Rice JR, Dunlap PE, Hackstadt AJ, Bridge MF, Smith MV, Dai S, Zheng W, Chu PH, Gerhold D, Witt KL, DeVito M, Freedman JH, Austin CP, Houck KA, Thomas RS, Paules RS, Tice RR, Simeonov A.

Environ Health Perspect. 2018 Jul 26;126(7):077010. doi: 10.1289/EHP2589. eCollection 2018 Jul.

10.

The US Federal Tox21 Program: A strategic and operational plan for continued leadership.

Thomas RS, Paules RS, Simeonov A, Fitzpatrick SC, Crofton KM, Casey WM, Mendrick DL.

ALTEX. 2018;35(2):163-168. doi: 10.14573/altex.1803011. Epub 2018 Mar 8.

11.

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.

12.

Three-Dimensional (3D) HepaRG Spheroid Model With Physiologically Relevant Xenobiotic Metabolism Competence and Hepatocyte Functionality for Liver Toxicity Screening.

Ramaiahgari SC, Waidyanatha S, Dixon D, DeVito MJ, Paules RS, Ferguson SS.

Toxicol Sci. 2017 Nov 1;160(1):189-190. doi: 10.1093/toxsci/kfx194. No abstract available.

PMID:
29077947
13.

Correction: Real-time cell toxicity profiling of Tox21 10K compounds reveals cytotoxicity dependent toxicity pathway linkage.

Hsieh JH, Huang R, Lin JA, Sedykh A, Zhao J, Tice RR, Paules RS, Xia M, Auerbach SS.

PLoS One. 2017 Jul 7;12(7):e0181291. doi: 10.1371/journal.pone.0181291. eCollection 2017.

14.

From the Cover: Three-Dimensional (3D) HepaRG Spheroid Model With Physiologically Relevant Xenobiotic Metabolism Competence and Hepatocyte Functionality for Liver Toxicity Screening.

Ramaiahgari SC, Waidyanatha S, Dixon D, DeVito MJ, Paules RS, Ferguson SS.

Toxicol Sci. 2017 Sep 1;159(1):124-136. doi: 10.1093/toxsci/kfx122. Erratum in: Toxicol Sci. 2017 Nov 1;160(1):189-190.

15.

Real-time cell toxicity profiling of Tox21 10K compounds reveals cytotoxicity dependent toxicity pathway linkage.

Hsieh JH, Huang R, Lin JA, Sedykh A, Zhao J, Tice RR, Paules RS, Xia M, Auerbach SS.

PLoS One. 2017 May 22;12(5):e0177902. doi: 10.1371/journal.pone.0177902. eCollection 2017. Erratum in: PLoS One. 2017 Jul 7;12 (7):e0181291.

16.

Identifying environmental chemicals as agonists of the androgen receptor by using a quantitative high-throughput screening platform.

Lynch C, Sakamuru S, Huang R, Stavreva DA, Varticovski L, Hager GL, Judson RS, Houck KA, Kleinstreuer NC, Casey W, Paules RS, Simeonov A, Xia M.

Toxicology. 2017 Jun 15;385:48-58. doi: 10.1016/j.tox.2017.05.001. Epub 2017 May 4.

17.

A type I IFN-dependent DNA damage response regulates the genetic program and inflammasome activation in macrophages.

Morales AJ, Carrero JA, Hung PJ, Tubbs AT, Andrews JM, Edelson BT, Calderon B, Innes CL, Paules RS, Payton JE, Sleckman BP.

Elife. 2017 Mar 31;6. pii: e24655. doi: 10.7554/eLife.24655.

18.

Comment on "On the Utility of ToxCast™ and ToxPi as Methods for Identifying New Obesogens".

Houck KA, Judson RS, Knudsen TB, Martin MT, Richard AM, Crofton KM, Simeonov A, Paules RS, Bucher JR, Thomas RS.

Environ Health Perspect. 2017 Jan 1;125(1):A8-A11. doi: 10.1289/EHP881. No abstract available.

19.

Molecular effects of 1-naphthyl-methylcarbamate and solar radiation exposures on human melanocytes.

Ferrucio B, Tiago M, Fannin RD, Liu L, Gerrish K, Maria-Engler SS, Paules RS, Barros SBM.

Toxicol In Vitro. 2017 Feb;38:67-76. doi: 10.1016/j.tiv.2016.11.005. Epub 2016 Nov 6.

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.
23.

Depletion of ATR selectively sensitizes ATM-deficient human mammary epithelial cells to ionizing radiation and DNA-damaging agents.

Cui Y, Palii SS, Innes CL, Paules RS.

Cell Cycle. 2014;13(22):3541-50. doi: 10.4161/15384101.2014.960729.

24.

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.

25.

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.

26.

Genome-wide small RNA sequencing and gene expression analysis reveals a microRNA profile of cancer susceptibility in ATM-deficient human mammary epithelial cells.

Hesse JE, Liu L, Innes CL, Cui Y, Palii SS, Paules RS.

PLoS One. 2013 May 31;8(5):e64779. doi: 10.1371/journal.pone.0064779. Print 2013.

27.

DNA damage activates a complex transcriptional response in murine lymphocytes that includes both physiological and cancer-predisposition programs.

Innes CL, Hesse JE, Palii SS, Helmink BA, Holub AJ, Sleckman BP, Paules RS.

BMC Genomics. 2013 Mar 12;14:163. doi: 10.1186/1471-2164-14-163.

28.

Dissecting cellular responses to irradiation via targeted disruptions of the ATM-CHK1-PP2A circuit.

Palii SS, Cui Y, Innes CL, Paules RS.

Cell Cycle. 2013 Apr 1;12(7):1105-18. doi: 10.4161/cc.24127. Epub 2013 Mar 5.

29.

A prognostic signature of G(2) checkpoint function in melanoma cell lines.

Omolo B, Carson C, Chu H, Zhou Y, Simpson DA, Hesse JE, Paules RS, Nyhan KC, Ibrahim JG, Kaufmann WK.

Cell Cycle. 2013 Apr 1;12(7):1071-82. doi: 10.4161/cc.24067. Epub 2013 Mar 1.

30.

Perturbation of microRNAs in rat heart during chronic doxorubicin treatment.

Vacchi-Suzzi C, Bauer Y, Berridge BR, Bongiovanni S, Gerrish K, Hamadeh HK, Letzkus M, Lyon J, Moggs J, Paules RS, Pognan F, Staedtler F, Vidgeon-Hart MP, Grenet O, Couttet P.

PLoS One. 2012;7(7):e40395. doi: 10.1371/journal.pone.0040395. Epub 2012 Jul 31.

31.

Genomic-derived markers for early detection of calcineurin inhibitor immunosuppressant-mediated nephrotoxicity.

Cui Y, Huang Q, Auman JT, Knight B, Jin X, Blanchard KT, Chou J, Jayadev S, Paules RS.

Toxicol Sci. 2011 Nov;124(1):23-34. doi: 10.1093/toxsci/kfr217. Epub 2011 Aug 24.

32.

Gene expression profiles from discordant monozygotic twins suggest that molecular pathways are shared among multiple systemic autoimmune diseases.

O'Hanlon TP, Rider LG, Gan L, Fannin R, Paules RS, Umbach DM, Weinberg CR, Shah RR, Mav D, Gourley MF, Miller FW.

Arthritis Res Ther. 2011 Apr 26;13(2):R69. doi: 10.1186/ar3330.

33.

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
34.

Moving forward in human cancer risk assessment.

Paules RS, Aubrecht J, Corvi R, Garthoff B, Kleinjans JC.

Environ Health Perspect. 2011 Jun;119(6):739-43. doi: 10.1289/ehp.1002735. Epub 2010 Dec 13.

35.

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.

36.

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.

37.

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.

38.

Revised genetic requirements for the decatenation G2 checkpoint: the role of ATM.

Bower JJ, Zhou Y, Zhou T, Simpson DA, Arlander SJ, Paules RS, Cordeiro-Stone M, Kaufmann WK.

Cell Cycle. 2010 Apr 15;9(8):1617-28. Epub 2010 Apr 15.

39.

Use of transcriptomics in understanding mechanisms of drug-induced toxicity.

Cui Y, Paules RS.

Pharmacogenomics. 2010 Apr;11(4):573-85. doi: 10.2217/pgs.10.37. Review.

40.

Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival.

Fu D, Brophy JA, Chan CT, Atmore KA, Begley U, Paules RS, Dedon PC, Begley TJ, Samson LD.

Mol Cell Biol. 2010 May;30(10):2449-59. doi: 10.1128/MCB.01604-09. Epub 2010 Mar 22.

41.

Acetaminophen dosing of humans results in blood transcriptome and metabolome changes consistent with impaired oxidative phosphorylation.

Fannin RD, Russo M, O'Connell TM, Gerrish K, Winnike JH, Macdonald J, Newton J, Malik S, Sieber SO, Parker J, Shah R, Zhou T, Watkins PB, Paules RS.

Hepatology. 2010 Jan;51(1):227-36. doi: 10.1002/hep.23330.

42.

Parallelogram approach using rat-human in vitro and rat in vivo toxicogenomics predicts acetaminophen-induced hepatotoxicity in humans.

Kienhuis AS, van de Poll MC, Wortelboer H, van Herwijnen M, Gottschalk R, Dejong CH, Boorsma A, Paules RS, Kleinjans JC, Stierum RH, van Delft JH.

Toxicol Sci. 2009 Feb;107(2):544-52. doi: 10.1093/toxsci/kfn237. Epub 2008 Nov 12.

PMID:
19008212
43.

DNA double-strand breaks activate a multi-functional genetic program in developing lymphocytes.

Bredemeyer AL, Helmink BA, Innes CL, Calderon B, McGinnis LM, Mahowald GK, Gapud EJ, Walker LM, Collins JB, Weaver BK, Mandik-Nayak L, Schreiber RD, Allen PM, May MJ, Paules RS, Bassing CH, Sleckman BP.

Nature. 2008 Dec 11;456(7223):819-23. doi: 10.1038/nature07392. Epub 2008 Oct 12.

44.

Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype.

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.

Genome Biol. 2008;9(6):R100. doi: 10.1186/gb-2008-9-6-r100. Epub 2008 Jun 20.

45.

Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants.

Huang L, Heinloth AN, Zeng ZB, Paules RS, Bushel PR.

BMC Genomics. 2008 Jun 16;9:288. doi: 10.1186/1471-2164-9-288.

46.

DNA protein kinase-dependent G2 checkpoint revealed following knockdown of ataxia-telangiectasia mutated in human mammary epithelial cells.

Arlander SJ, Greene BT, Innes CL, Paules RS.

Cancer Res. 2008 Jan 1;68(1):89-97. doi: 10.1158/0008-5472.CAN-07-0675.

47.

Blood gene expression signatures predict exposure levels.

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.

Proc Natl Acad Sci U S A. 2007 Nov 13;104(46):18211-6. Epub 2007 Nov 2.

48.
49.

Ataxia telangiectasia-mutated dependent DNA damage checkpoint functions regulate gene expression in human fibroblasts.

Zhou T, Chou J, Zhou Y, Simpson DA, Cao F, Bushel PR, Paules RS, Kaufmann WK.

Mol Cancer Res. 2007 Aug;5(8):813-22.

50.

Heat map visualization of high-density clinical chemistry data.

Auman JT, Boorman GA, Wilson RE, Travlos GS, Paules RS.

Physiol Genomics. 2007 Oct 22;31(2):352-6. Epub 2007 Jul 24.

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