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Time-dependent cellular and transcriptional changes in the osteoblast lineage associated with sclerostin antibody treatment in ovariectomized rats.

Taylor S, Ominsky MS, Hu R, Pacheco E, He YD, Brown DL, Aguirre JI, Wronski TJ, Buntich S, Afshari CA, Pyrah I, Nioi P, Boyce RW.

Bone. 2016 Mar;84:148-59. doi: 10.1016/j.bone.2015.12.013. Epub 2015 Dec 22.


Utilization of human nuclear receptors as an early counter screen for off-target activity: a case study with a compendium of 615 known drugs.

Fan F, Hu R, Munzli A, Chen Y, Dunn RT 2nd, Weikl K, Strauch S, Schwandner R, Afshari CA, Hamadeh H, Nioi P.

Toxicol Sci. 2015 Jun;145(2):283-95. doi: 10.1093/toxsci/kfv052. Epub 2015 Mar 9.


Retinal Toxicity Induced by a Novel β-secretase Inhibitor in the Sprague-Dawley Rat.

Fielden MR, Werner J, Jamison JA, Coppi A, Hickman D, Dunn RT 2nd, Trueblood E, Zhou L, Afshari CA, Lightfoot-Dunn R.

Toxicol Pathol. 2015 Jun;43(4):581-92. doi: 10.1177/0192623314553804. Epub 2014 Oct 31.


A systematic assessment of mitochondrial function identified novel signatures for drug-induced mitochondrial disruption in cells.

Li N, Oquendo E, Capaldi RA, Robinson JP, He YD, Hamadeh HK, Afshari CA, Lightfoot-Dunn R, Narayanan PK.

Toxicol Sci. 2014 Nov;142(1):261-73. doi: 10.1093/toxsci/kfu176. Epub 2014 Aug 27.


Common handling procedures conducted in preclinical safety studies result in minimal hepatic gene expression changes in Sprague-Dawley rats.

He YD, Karbowski CM, Werner J, Everds N, Di Palma C, Chen Y, Higgins-Garn M, Tran S, Afshari CA, Hamadeh HK.

PLoS One. 2014 Feb 14;9(2):e88750. doi: 10.1371/journal.pone.0088750. eCollection 2014.


A multifactorial approach to hepatobiliary transporter assessment enables improved therapeutic compound development.

Morgan RE, van Staden CJ, Chen Y, Kalyanaraman N, Kalanzi J, Dunn RT 2nd, Afshari CA, Hamadeh HK.

Toxicol Sci. 2013 Nov;136(1):216-41. doi: 10.1093/toxsci/kft176. Epub 2013 Aug 16.


A novel statistical algorithm for gene expression analysis helps differentiate pregnane X receptor-dependent and independent mechanisms of toxicity.

Mongan MA, Dunn RT, Vonderfecht S, Everds N, Chen G, Su C, Higgins-Garn M, Chen Y, Afshari CA, Williamson TL, Carlock L, Dipalma C, Moss S, Bussiere J, Qualls C, He YD, Hamadeh HK.

PLoS One. 2010 Dec 21;5(12):e15595. doi: 10.1371/journal.pone.0015595.


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.


Interference with bile salt export pump function is a susceptibility factor for human liver injury in drug development.

Morgan RE, Trauner M, van Staden CJ, Lee PH, Ramachandran B, Eschenberg M, Afshari CA, Qualls CW Jr, Lightfoot-Dunn R, Hamadeh HK.

Toxicol Sci. 2010 Dec;118(2):485-500. doi: 10.1093/toxsci/kfq269. Epub 2010 Sep 9.


Application of genomics for identification of systemic toxicity triggers associated with VEGF-R inhibitors.

Hamadeh HK, Todd M, Healy L, Meyer JT, Kwok AM, Higgins M, Afshari CA.

Chem Res Toxicol. 2010 Jun 21;23(6):1025-33. doi: 10.1021/tx1000333.


Forum Series: the "Vision" for Toxicity Testing in the 21st Century: promises and conundrums.

Holsapple MP, Afshari CA, Lehman-McKeeman LD.

Toxicol Sci. 2009 Feb;107(2):307-8. doi: 10.1093/toxsci/kfn258. Epub 2008 Dec 9. No abstract available.


Insight into redox-regulated gene networks in vascular cells.

Johnson CD, Balagurunathan Y, Dougherty ER, Afshari CA, He Q, Ramos KS.

Bioinformation. 2007 Apr 10;1(10):379-83.


Use of a mixed tissue RNA design for performance assessments on multiple microarray formats.

Thompson KL, Rosenzweig BA, Pine PS, Retief J, Turpaz Y, Afshari CA, Hamadeh HK, Damore MA, Boedigheimer M, Blomme E, Ciurlionis R, Waring JF, Fuscoe JC, Paules R, Tucker CJ, Fare T, Coffey EM, He Y, Collins PJ, Jarnagin K, Fujimoto S, Ganter B, Kiser G, Kaysser-Kranich T, Sina J, Sistare FD.

Nucleic Acids Res. 2005 Dec 23;33(22):e187.


Adaptation of estrogen-regulated genes in long-term estradiol deprived MCF-7 breast cancer cells.

Santen RJ, Lobenhofer EK, Afshari CA, Bao Y, Song RX.

Breast Cancer Res Treat. 2005 Dec;94(3):213-23.


Estrogen-induced changes in IGF-I, Myb family and MAP kinase pathway genes in human uterine leiomyoma and normal uterine smooth muscle cell lines.

Swartz CD, Afshari CA, Yu L, Hall KE, Dixon D.

Mol Hum Reprod. 2005 Jun;11(6):441-50. Epub 2005 May 6.


Prediction of nephrotoxicant action and identification of candidate toxicity-related biomarkers.

Thukral SK, Nordone PJ, Hu R, Sullivan L, Galambos E, Fitzpatrick VD, Healy L, Bass MB, Cosenza ME, Afshari CA.

Toxicol Pathol. 2005;33(3):343-55.


Integrating phenotypic and expression profiles to map arsenic-response networks.

Haugen AC, Kelley R, Collins JB, Tucker CJ, Deng C, Afshari CA, Brown JM, Ideker T, Van Houten B.

Genome Biol. 2004;5(12):R95. Epub 2004 Nov 29.


Exploration of low-dose estrogen effects: identification of No Observed Transcriptional Effect Level (NOTEL).

Lobenhofer EK, Cui X, Bennett L, Cable PL, Merrick BA, Churchill GA, Afshari CA.

Toxicol Pathol. 2004 Jul-Aug;32(4):482-92.


Integration of clinical and gene expression endpoints to explore furan-mediated hepatotoxicity.

Hamadeh HK, Jayadev S, Gaillard ET, Huang Q, Stoll R, Blanchard K, Chou J, Tucker CJ, Collins J, Maronpot R, Bushel P, Afshari CA.

Mutat Res. 2004 May 18;549(1-2):169-83.


Short-chain fatty acids enhance nuclear receptor activity through mitogen-activated protein kinase activation and histone deacetylase inhibition.

Jansen MS, Nagel SC, Miranda PJ, Lobenhofer EK, Afshari CA, McDonnell DP.

Proc Natl Acad Sci U S A. 2004 May 4;101(18):7199-204. Epub 2004 Apr 21.

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