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Gene expression response in target organ and whole blood varies as a function of target organ injury phenotype
Edward K Lobenhofer, J Todd Auman, Pamela E Blackshear, Gary A Boorman, Pierre R Bushel, Michael L Cunningham, Jennifer M Fostel, Kevin Gerrish, Alexandra N Heinloth, Richard D Irwin, David E Malarkey, B Alex Merrick, Stella O Sieber, Charles J Tucker, Sandra M Ward, Ralph E Wilson, Patrick Hurban, Raymond W Tennant, Richard S Paules
Genome Biol. 2008; 9(6): R100. Published online 2008 June 20. doi: 10.1186/gb-2008-9-6-r100
PMCID:
PMC2481421
Abstract Full Text PDF–1.4M Supplementary Material

Is Cited by the Following 11 Articles in this Archive:

Selecting a single model or combining multiple models for microarray-based classifier development? – A comparative analysis based on large and diverse datasets generated from the MAQC-II project
Minjun Chen, Leming Shi, Reagan Kelly, Roger Perkins, Hong Fang, Weida Tong
BMC Bioinformatics. 2011; 12(Suppl 10): S3. Published online 2011 October 18. doi: 10.1186/1471-2105-12-S10-S3
PMCID:
PMC3236846
Abstract Full Text PDF–2.8M Supplementary Material
Cross-Platform Comparison of Microarray-Based Multiple-Class Prediction
Xiaohui Fan, Li Shao, Hong Fang, Weida Tong, Yiyu Cheng
PLoS One. 2011; 6(1): e16067. Published online 2011 January 11. doi: 10.1371/journal.pone.0016067
PMCID:
PMC3019174
Abstract Full Text PDF–617K Supplementary Material
Mapping Drug Physico-Chemical Features to Pathway Activity Reveals Molecular Networks Linked to Toxicity Outcome
Philipp Antczak, Fernando Ortega, J. Kevin Chipman, Francesco Falciani
PLoS One. 2010; 5(8): e12385. Published online 2010 August 27. doi: 10.1371/journal.pone.0012385
PMCID:
PMC2929951
Abstract Full Text PDF–1.3M Supplementary Material
Genomic indicators in the blood predict drug-induced liver injury
Jianping Huang, Weiwei Shi, John Zhang, Jeff W. Chou, Richard S. Paules, Kevin Gerrish, Jianying Li, Jun Luo, Russell D. Wolfinger, Wenjun Bao, Tzu-Ming Chu, Yuri Nikolsky, Tatiana Nikolskaya, Damir Dosymbekov, Marina O. Tsyganova, Leming Shi, Xiaohui Fan, J. Christopher Corton, Minjun Chen, Yiyu Cheng, Weida Tong, Hong Fang, Pierre R. Bushel
Pharmacogenomics J. Author manuscript; available in PMC 2011 September 27.
Published in final edited form as: Pharmacogenomics J. 2010 August; 10(4): 267–277. doi: 10.1038/tpj.2010.33
PMCID:
PMC3180890
Abstract Full Text PDF–1.3M Supplementary Material
Consistency of predictive signature genes and classifiers generated using different microarray platforms
X Fan, E K Lobenhofer, M Chen, W Shi, J Huang, J Luo, J Zhang, S J Walker, T-M Chu, L Li, R Wolfinger, W Bao, R S Paules, P R Bushel, J Li, T Shi, T Nikolskaya, Y Nikolsky, H Hong, Y Deng, Y Cheng, H Fang, L Shi, W Tong
Pharmacogenomics J. 2010 August; 10(4): 247–257. Published online 2010 July 30. doi: 10.1038/tpj.2010.34
PMCID:
PMC2920073
Abstract Full Text PDF–1.0M Supplementary Material
A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data
J Luo, M Schumacher, A Scherer, D Sanoudou, D Megherbi, T Davison, T Shi, W Tong, L Shi, H Hong, C Zhao, F Elloumi, W Shi, R Thomas, S Lin, G Tillinghast, G Liu, Y Zhou, D Herman, Y Li, Y Deng, H Fang, P Bushel, M Woods, J Zhang
Pharmacogenomics J. 2010 August; 10(4): 278–291. Published online 2010 July 30. doi: 10.1038/tpj.2010.57
PMCID:
PMC2920074
Abstract Full Text PDF–895K
Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes
W Shi, M Bessarabova, D Dosymbekov, Z Dezso, T Nikolskaya, M Dudoladova, T Serebryiskaya, A Bugrim, A Guryanov, R J Brennan, R Shah, J Dopazo, M Chen, Y Deng, T Shi, G Jurman, C Furlanello, R S Thomas, J C Corton, W Tong, L Shi, Y Nikolsky
Pharmacogenomics J. 2010 August; 10(4): 310–323. Published online 2010 July 30. doi: 10.1038/tpj.2010.35
PMCID:
PMC2920075
Abstract Full Text PDF–1010K Supplementary Material
Use of transcriptomics in understanding mechanisms of drug-induced toxicity
Yuxia Cui, Richard S Paules
Pharmacogenomics. Author manuscript; available in PMC 2011 February 1.
Published in final edited form as: Pharmacogenomics. 2010 April; 11(4): 573–585. doi: 10.2217/pgs.10.37
PMCID:
PMC2884389
Abstract Full Text PDF–334K
Acetaminophen dosing of humans results in blood transcriptome and metabolome changes consistent with impaired oxidative phosphorylation
Rick D. Fannin, Mark Russo, Thomas M. O’Connell, Kevin Gerrish, Jason H. Winnike, Jeffrey Macdonald, Jack Newton, Shahid Malik, Stella O. Sieber, Joel Parker, Ruchir Shah, Tong Zhou, Paul B. Watkins, Richard S. Paules
Hepatology. Author manuscript; available in PMC 2011 January 1.
Published in final edited form as: Hepatology. 2010 January; 51(1): 227–236. doi: 10.1002/hep.23330
PMCID:
PMC2925683
Abstract Full Text PDF–1.6M Supplementary Material
Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells
Alissar Nehmé, Edward K Lobenhofer, W Daniel Stamer, Jeffrey L Edelman
BMC Med Genomics. 2009; 2: 58. Published online 2009 September 10. doi: 10.1186/1755-8794-2-58
PMCID:
PMC2749862
Abstract Full Text PDF–807K Supplementary Material
Discernment of possible mechanisms of hepatotoxicity via biological processes over-represented by co-expressed genes
Jeff W Chou, Pierre R Bushel
BMC Genomics. 2009; 10: 272. Published online 2009 June 18. doi: 10.1186/1471-2164-10-272
PMCID:
PMC2706894
Abstract Full Text PDF–1.1M Supplementary Material
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