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Keith Shockley, Ph.D.

Biostatistics & Computational Biology Branch

Keith R. Shockley, Ph.D.
Keith R. Shockley, Ph.D.
Staff Scientist
Tel (919) 541-3033
P.O. Box 12233
Mail Drop A3-03
Research Triangle Park, NC 27709

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Research Summary

Keith Shockley, Ph.D., is a bioinformatician for the National Toxicology Program (NTP) in the NIEHS Biostatistics and Computational Biology Branch. Shockley came to the NIEHS in 2008 from The Jackson Laboratory in Bar Harbor, Maine, where he spent four years as a postdoctoral research associate studying statistical genetics and computational biology.

He is interested in using genetic and environmental data to improve toxicity testing. He assists members of the NTP to identify genes that control biological responses to environmental exposures, analyzes and interprets biological response data from high throughput screening assays, and scrutinizes gene expression data from large scale microarray studies. He has recently become interested in using chemoinformatics approaches to support chemical nominations and biomolecular screening, and in constructing genetic models to predict human toxicity.

Shockley received his B.S. in chemical engineering from New Mexico State University in 1998, and his M.S. and Ph.D. in chemical engineering from North Carolina State University in 2000 and 2004, respectively.

Selected Publications

  1. Chen S, Hsieh JH, Huang R, Sakamuru S , Hsin LY, Xia M, Shockley KR, Auerbach S, Kanaya N, Lu H, Svoboda D, Witt KL, Merrick BA, Teng CT, Tice RR. Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library. Toxicological sciences: an official journal of the Society of Toxicology 2015 147(2):446-457.[Abstract]
  2. George-Raizen JB, Shockley KR, Trojanowski NF, Lamb AL, Raizen DM. Dynamically-expressed prion-like proteins form a cuticle in the pharynx of Caenorhabditis elegans. Biology open 2014 3(11):1139-1149.[Abstract]
  3. Huang R, Sakamuru S, Martin MT, Reif DM, Judson RS, Houck KA, Casey W, Hsieh JH, Shockley KR, Ceger P, Fostel J, Witt KL, Tong W, Rotroff DM, Zhao T, Shinn P, Simeonov A, Dix DJ, Austin CP, Kavlock RJ, Tice RR, Xia M. Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway. Scientific reports 2014 4():5664-.[Abstract]
  4. Shockley KR. Using weighted entropy to rank chemicals in quantitative high-throughput screening experiments. Journal of biomolecular screening 2014 19(3):344-353.[Abstract]
  5. Teng CT, Goodwin B, Shockley K, Xia M, Huang R, Norris J, Merrick BA, Jetten AM, Austin CP, Tice RR. Bisphenol A affects androgen receptor function via multiple mechanisms. Chemico-biological interactions 2013; 203(3): 556-564.[Abstract]
  6. Dunnick JK , Brix A, Cunny H, Vallant M , Shockley KR. Characterization of polybrominated diphenyl ether toxicity in Wistar Han rats and use of liver microarray data for predicting disease susceptibilities. Toxicologic pathology 2012 40(1):93-106.[Abstract]
  7. Shockley KR. A Three-Stage Algorithm to Make Toxicologically Relevant Activity Calls from Quantitative High Throughput Screening Data. Environmental health perspectives 2012 120(8):1107-15.[Abstract]
  8. Hoenerhoff, M.J., Pandiri, A.P., Lahousse, S.A., Hong, H.H., Ton, T.V., Masinde, T., Auerbach, S., Gerrish, K., Bushel, P.R., Shockley, K.R., Peddada, S.D. Sills, R.C. (2011). Global gene profiling of spontaneous hepatocellular carcinoma in B6C3F1 mice: similarities in the molecular landscape with human liver cancer. Toxicologic pathology, 39:678-699.[Abstract]
  9. Shockley, K. R., Lazarenko, O. P., Czernik, P. J., Rosen, C. J., Churchill, G. A. & Lecka-Czernik, B. (2009). PPAR-gamma2 nuclear receptor controls multiple regulatory pathways of osteoblast differentiation from marrow mesenchymal stem cells. Journal of Cellular Biochemistry. 106: 232-246.[Abstract]  
  10. Ackert-Bicknell, C. L., Shockley, K. R., Horton, L. G., Lecka-Czernik, B., Churchill, G. A. & Rosen, C. J. Strain specific effects of Rosiglitazone on bone mass, body composition and serum IGF-1. Endocrinol 2009; 150:1330-1340.[Abstract]  
  11. Stylianou, I. M., Affourtit, J. P., Shockley, K. R., Abdi, F. A., Sanjeev, B., Rollins, J.,Churchill, G. A., & Paigen, B. A. (2008). Applying gene expression, proteomics and SNP analysis for complex trait gene identification. Genetics. 178: 1795-1805.[Abstract]  
  12. Chou, C. J.-, Shockley, K. R., Conners, S. B., Lewis, D. L., Comfort, D. A., Adams, M. W. W. & Kelly, R. M. (2007). Impact of substrate glycoside linkage and elemental sulfur on bioenergetics of and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus. Applied and Environmental Microbiology. Applied and Environmental Microbiology. 73: 6842-6853.[Abstract]  
  13. Mackiewicz, M., Shockley, K. R., Romer, R., Galante, R., Zimmerman, J. E., Nadoo, N., Baldwin, D., Churchill, G. A. & Pack, A. I. (2007). Macromolecule biosynthesis — a key function of sleep. Physiological Genomics. Physiological Genomics. 31: 441-457.[Abstract]  
  14. Shockley, K. R., Rosen, C. J., Churchill, G. A. & Lecka-Czernik, B. (2007). PPARgamma2 regulates a molecular signature of marrow mesenchymal stem cells. PPAR Research 81219.[Abstract]  
  15. Lecka-Czernik, B., Ackert-Bicknell, C., Adamo, M. L., Marmejelos , V., Churchill, G. A., Shockley, K. R., Reid, I., Gray, A. & Rosen, C.J. (2007). Activation of peroxisome proliferator-activated receptor γ?(PPARγ) by rosiglitazone suppresses components of the insulin-like growth factor regulatory system in vitro and in vivo. Endocrinology. 148: 903-911.[Abstract]  
  16. Madding, L. S., Michel, J. K., Shockley, K. R., Conners, S. B., Epting, K. L., Johnson, M. R. & Kelly, R. M. (2007). Role of the β1 subunit in the function and stability of the 20S proteasome in the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Bacteriology. 189: 583-590.[Abstract]  
  17. Zimmerman, J. E., Rizzo, W., Shockley, K. R., Raizen, D. M., Mackiewicz, M., Churchill, G. A. & Pack, A. I. (2006). Multiple mechanisms limit the duration of wakefulness in Drosophila brain. Physiological Genomics. 27: 337-350.[Abstract]  
  18. Cui, X., Affoutit, J., Shockley, K. R., Woo, Y. & Churchill, G. A. (2006). Inheritance patterns of transcript levels in F1 hybrid mice. Genetics. 174: 627-637.[Abstract]  
  19. Li, R., WernTsaih, S., Shockley, K., Stylianou, I. M., Wergedal, J., Paigen, B. & Churchill, G. A. (2006). Structural model analysis of multiple quantitative traits. PLoS Genetics. 2: e114.[Abstract]  
  20. Shockley, K. R. & Churchill, G.A. (2006). Gene expression analysis of mouse chromosome substitution strains. Mammalian Genome. 17: 598-614.[Abstract]  
  21. Lee, H.- S., Shockley, K. R., Schut, G. J., Conners, S. B., Montero, C. I., Johnson, M. R., Chou, C.- J., Bridger, S. L., Wigner, N., Brehm, S. D., Jenney, Jr., F. E., Comfort, D. A., Kelly, R. M., & Adams, M. W. W. (2006). Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus. Journal of Bacteriology. 188: 2115-2125.[Abstract]  
  22. Johnson, M. R., Conners, S. B., Montero, C. I., Chou, C. J., Shockley, K. R. & Kelly, R. M. (2006). The Thermotoga maritima phenotype is impacted by syntrophic interaction with Methanococcus jannaschii in hyperthermophilic coculture. Applied and Environmental Microbiology. 72: 811-818.[Abstract]

Book Chapters and Review Articles

  1. Mackiewicz, M., Zimmerman, J., Shockley, K. R., Churchill, G. A. & Pack, A. I. What are microarrays teaching us about sleep? (2009). Trends in Molecular Medicine. 15: 79-87.[Abstract]  
  2. Tachdjian, S., Shockley, K. R., Conners, S. B. & Kelly, R. M. (2008). Functional genomics of stress response in extremophilic archaea. In P. Blum (ed.), Archaea: New Models for Prokaryotic Biology. Caister Academic Press, Wymondham, UK.  
  3. Adams, M. W. W., Jenney, F. E., Chou, C. —J., Hamilton-Brehm, S., Poole, F. L., Shockley, K. R., Tachdijian, S., & Kelly, R. M. (2006). Transcriptomics, proteomics and structural genomics of Pyrococcus furiosus. Archaea — physiology, molecular biology and evolution. In Garrett, R. and Klenk, R.- P. (eds.), Archaea. Blackwell Publishing Inc., Malden, Massachusetts.

Supplementary Material

  1. WES example code(2KB)

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