National Academies Press: OpenBook
« Previous: 12 Conclusions and Recommendations
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 213
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 214
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 215
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 216
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 217
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 218
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 219
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 220
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 221
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 222
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 223
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 224
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 225
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 226
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 227
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 228
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 229
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 230
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 231
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 232
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 233
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 234
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 235
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 236
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 237
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 238
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 239
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 240
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 241
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 242
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 243
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 244
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 245
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 246
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 247
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 248
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 249
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 250
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 251
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 252
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 253
Suggested Citation:"References." National Research Council. 2007. Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment. Washington, DC: The National Academies Press. doi: 10.17226/12037.
×
Page 254

Below is the uncorrected machine-read text of this chapter, intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text of each book. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.

References Aebersold, R., and M. Mann. 2003. Mass spectrometry-based proteomics. Nature 422(6928):198-207. Ahn, N.S., H. Hu, J.S. Park, J.S. Park, J.S. Kim, S. An, G. Kong, O.I. Aruoma, Y.S. Lee, and K.S. Kang. 2005. Molecular mechanisms of the 2,3,7,8-tetrachlorodibenzo-p- dioxin-induced inverted U-shaped dose responsiveness in anchorage independent growth and cell proliferation of human breast epithelial cells with stem cell charac- teristics. Mutat. Res. 579(1-2):189-199. AHS (Agricultural Health Study). 2006. Agricultural Health Study [online]. Available: http://www.aghealth.org/ [accessed Aug. 24, 2006]. Akutsu, T., S. Miyano, and S. Kuhara. 2000. Algorithms for identifying Boolean net- works and related biological networks based on matrix multiplication and finger- print function. J. Comput. Biol. 7(3-4):331-343. Alban, A., S.O. David, L. Bjorkesten, C. Andersson, E. Sloge, S. Lewis, and I. Currie. 2003. A novel experimental design for comparative two-dimensional gel analysis: Two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3(1):36-44. Alexander, J., R. Reistad, S. Hegstad, H. Frandsen, K. Ingebrigtsen, J.E. Paulsen, and G. Becher. 2002. Biomarkers of exposure to heterocyclic amines: Approaches to im- prove the exposure assessment. Food Chem. Toxicol. 40(8):1131-1137. Allen, A.L. 1997. Genetic privacy: Emerging concepts and values. Pp. 31-59 in Genetic Secrets: Protecting Privacy and Confidentiality in the Genetic Era, M.A. Rothstein, ed. New Haven: Yale University Press. Allen, E.E., J.S. Fetrow, L.W. Daniel, S.J. Thomas, and D.J. John. 2006. Algebraic de- pendency models of protein signal transduction networks from time-series data. J. Theor. Biol. 238(2):317-330. Ames, R.G., S.K. Brown, D.C. Mengle, E. Kahn, J.W. Stratton, and R.J. Jackson. 1989. Cholinesterase activity depression among California agricultural pesticide applica- tors. Am. J. Ind. Med. 15(2):143-150. Amin, R.P., A.E. Vickers, F. Sistare, K.L. Thompson, R.J. Roman, M. Lawton, J. Kramer, H.K. Hamadeh, J. Collins, S. Grissom, L. Bennett, C.J. Tucker, S. Wild, C. Kind, V. Oreffo, J.W. Davis II, S. Curtiss, J.M. Naciff, M. Cunningham, R. Tennant, J. Stevens, B. Car, T.A. Bertram, and C.A. Afshari. 2004. Identification of putative gene based markers of renal toxicity. Environ. Health Perspect. 112(4):465-479. 213

214 Applications of Toxicogenomic Technologies Anazawa, Y., H. Nakagawa, M. Furihara, S. Ashida, K. Tamura, H. Yoshioka, T. Shuin, T. Fujioka, T. Katagiri, and Y. Nakamura. 2005. PCOTH, a novel gene overex- pressed in prostate cancers, promotes prostate cancer cell growth through phos- phorylation of oncoprotein TAF-Ibeta/SET. Cancer Res. 65(11):4578-4586. Andersen, M.E., H.J. Clewell III, M.L. Gargas, F.A. Smith, and R.H. Reitz. 1987. Physiologically based pharmacokinetics and the risk assessment process for me- thylene chloride. Toxicol. Appl. Pharmacol. 87(2):185-205. Anderson, N.L., and N.G. Anderson. 2002. The human plasma proteome: History, char- acter, and diagnostic prospects. Mol. Cell Proteomics 1(11):845-867. Anderson, N.L., N.G. Anderson, L.R. Haines, D.B. Hardie, R.W. Olafson, and T.W. Pearson. 2004. Mass spectrometric quantitation of peptides and proteins using Sta- ble Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA). J. Pro- teome Res. 3(2):235-244. Ando, Y., and Y. Hayashizaki. 2006. Restriction landmark genomic scanning. Nat. Pro- toc. 1(6):2774-2783. Andrew, A.S., A.J. Warren, A. Barchowsky, K.A. Temple, L. Klei, N.V. Soucy, K.A. O'Hara, and J.W. Hamilton. 2003. Genomic and proteomic profiling of responses to toxic metals in human lung cells. Environ. Health Perspect. 111(6):825-835. Andrews, L.B. 2005. Harnessing the benefits of biobanks. J. Law Med. Ethics 33(1):22- 30. Antoniadis, A., S. Lambert-Lacroix, and F. Leblanc. 2003. Effective dimension reduction methods for tumor classification using gene expression data. Bioinformatics 19(5):563-570. Anway, M.D., A.S. Cupp, M. Uzumcu, and M.K. Skinner. 2005. Epigenetic transgenera- tional actions of endocrine disruptors and male fertility. Science 308(5727):1466- 1469. Arbour, N.C., E. Lorenz, B.C. Schutte, J. Zabner, J.N. Kline, M. Jones, K. Frees, J.L. Watt, and D.A. Schwartz. 2000. TLR4 mutations are associated with endotoxin hyporesponsiveness in humans. Nat. Genet. 25(2):187-191. Ausness, R.C. 2002. Will more aggressive marketing practices lead to greater tort liabil- ity for prescription drug manufacturers? Wake Forest Law Rev. 37(1):97-139. Azmi, J., J.L. Griffin, H. Antti, R.F. Shore, E. Johansson, J.K. Nicholson, and E. Holmes. 2002. Metabolic trajectory characterisation of xenobiotic-induced hepatotoxic le- sions using statistical batch processing of NMR data. Analyst 127(2):271-276. Bae, D.S., W.H. Hanneman, R.S. Yang, and J.A. Campain. 2002. Characterization of gene expression changes associated with MNNG, arsenic, or metal mixture treat- ment in human keratinocytes: Application of cDNA microarray technology. Envi- ron. Health Perspect. 110(Suppl. 6):931-941. Baggerly, K.A., K.R. Coombes, K.R. Hess, D.N. Stivers, L.V. Abruzzo, and W. Zhang. 2001. Identifying differentially expressed genes in cDNA microarray experiments. J. Comput. Biol. 8(6):639-659. Baggerly, K.A., J.S. Morris, and K.R. Coombes. 2004. Reproducibility of SELDI-TOF protein patterns in serum: Comparing datasets from different experiments. Bioin- formatics 20(5):777-785. Baggerly, K.A., J.S. Morris, S.R. Edmonson, and K.R. Coombes. 2005. Signal in noise: Evaluating reported reproducibility of serum proteomic tests for ovarian cancer. J. Natl. Cancer Inst. 97(4):307-309. Bailey, W.J., and R. Ulrich. 2004. Molecular profiling approaches for identifying novel biomarkers. Expert. Opin. Drug Saf. 3(2):137-151.

References 215 Baker, V.A., H.M. Harries, J.F. Waring, C.M. Duggan, H.A. Ni, R.A. Jolly, L.W. Yoon, A.T. De Souza, J.E. Schmid, R.H. Brown, R.G. Ulrich, and J.C. Rockett. 2004. Clofibrate-induced gene expression changes in rat liver: A cross-laboratory analy- sis using membrane cDNA arrays. Environ. Health Perspect. 112(4):428-438. Ball, C.A, G. Sherlock, H. Parkinson, P. Rocca-Sera, C. Brooksbank, H.C. Causton, D. Cavalieri, T. Gaasterland, P. Hingamp, F. Holstege, M. Ringwald, P. Spellman, C.J. Stoeckert, Jr., J.E. Stewart, R. Taylor, A. Brazma, and J. Quackenbush. 2002a. Standards for microarray data [letter]. Science 298(5593):539. Ball, C.A., G. Sherlock, H. Parkinson, P. Rocca-Sera, C. Brooksbank, H.C. Causton, D. Cavalieri, T. Gaasterland, P. Hingamp, F. Holstege, M. Ringwald, P. Spellman, C.J. Stoeckert, Jr., J.E. Stewart, R. Taylor, A. Brazma, and J. Quackenbush. 2002b. The underlying principles of scientific publication [review]. Bioinformatics 18(11):1409. Ball, C.A., A. Brazma, H.C. Causton, S. Chervitz, R. Edgar, P. Hingamp, J.C. Matese, H. Parkinson, J. Quackenbush, M. Ringwald, S.A. Sansone, G. Sherlock, P. Spellman, C. Stoeckert, Y. Tateno, R. Taylor, J. White, and N. Winegarden. (MGED Soci- ety). 2004a. Standards for microarray data: An open letter. Environ. Health Per- spect. 112(12):A666-A667. Ball, C.A., A. Brazma, H. Causton, S. Chervitz, R. Edgar, P. Hingamp, J.C. Matese, C. Icahn, H. Parkinson, J. Quackenbush, M. Ringwald, S.A. Sansone, G. Sherlock, P. Spellman, C. Stoeckert, Y. Tateno, R. Taylor, J. White, and N. Winegarden. (MGED Society). 2004b. An open letter on microarray data from the MGED Soci- ety. Microbiology 150(Pt 11):3522-3524. Bammler, T., R.P. Beyer, S. Bhattacharya, G.A. Boorman, A. Boyles, B.U. Bradford, R.E. Bumgarner, P.R. Bushel, K. Chaturvedi, D. Choi, M.L. Cunningham, S. Deng, H.K. Dressman, R.D. Fannin, F.M. Farin, J.H. Freedman, R.C. Fry, A. Harper, M.C. Humble, P. Hurban, T.J. Kavanagh, W.K. Kaufmann, K.F. Kerr, L. Jing, J.A. Lapidus, M.R. Lasarev, J. Li, Y.J. Li, E.K. Lobenhofer, X. Lu, R.L. Malek, S. Milton, S.R. Nagalla, J.P. O'Malley, V.S. Palmer, P. Pattee, R.S. Paules, C.M. Perou, K. Phillips, L.X. Qin, Y. Qiu, S.D. Quigley, M. Rodland, I. Rusyn, L.D. Samson, D.A. Schwartz, Y. Shi, J.L. Shin, S.O. Sieber, S. Slifer, M.C. Speer, P.S. Spencer, D.I. Sproles, J.A. Swenberg, W.A. Suk, R.C. Sullivan, R. Tian, R.W. Tennant, S.A. Todd, C.J. Tucker, B. Van Houten, B.K. Weis, S. Xuan, and H. Zarbl. 2005. Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods 2(5):351-356. Bandara, L.R., M.D. Kelly, E.A. Lock, and S. Kennedy. 2003. A correlation between a proteomic evaluation and conventional measurements in the assessment of renal proximal tubular toxicity. Toxicol. Sci. 73(1):195-206. Baram, M. 2001. Genetic testing for susceptibility to disease from exposure to toxic chemicals: Implications for public and worker health policies. Jurimetrics 41(2):165-176. Barczak, A., M.W. Rodriguez, K. Hanspers, L.L. Koth, T.C. Tai, B.M. Bolstad, T.P. Speed, and D.J. Erle. 2003. Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res. 13(7):1775-1785. Battuello, K., R. Fenske, C. Furlong, M. Austin, and W. Burke. 2002. CEEH ILSI Core Case Study 1: Genetic Variation in PON1 and Pesticide Sensitivity: Implications for Workplace Screening. March 13, 2002 [online]. Available: http://depts. washington.edu/ceeh/issues/PON.pdf [accessed March 6, 2006].

216 Applications of Toxicogenomic Technologies BDW Group (Biomarkers Definitions Working Group). 2001. Biomarkers and surrogate endpoints: Preferred definitions and conceptual framework. Clin. Pharmacol. Ther. 69(3):89-95. Beckwith-Hall, B.M., J.K. Nicholson, A.W. Nicholls, P.J. Foxall, J.C. Lindon, S.C. Connor, M. Abdi, J. Connelly, and E. Holmes. 1998. Nuclear magnetic resonance spectroscopic and principal components analysis investigations into biochemical effects of three model hepatotoxins. Chem. Res. Toxicol. 11(4):260-272. Begley, T.J., and L.D. Samson. 2004. Network responses to DNA damaging agents. DNA Repair (Amst). 3(8-9):1123-1132. Begley, T.J., A.S. Rosenbach, T. Ideker, and L.D. Samson. 2002. Damage recovery pathways in Saccharomyces cerevisiae revealed by genomic phenotyping and in- teractome mapping. Mol. Cancer Res. 1(2):103-112. Begley, T.J., A.S. Rosenbach, T. Ideker, and L.D. Samson. 2004. Hot spots for modulat- ing toxicity identified by genomic phenotyping and localization mapping. Mol. Cell. 16(1):117-125. Bellamy, R., C. Ruwende, T. Corrah, K.P. McAdam, H.C. Whittle, and A.V. Hill. 1998. Variations in the NRAMP1 gene and susceptibility to tuberculosis in West Afri- cans. N. Engl. J. Med. 338(10):640-644. Bellamy, R., N. Beyers, K.P. McAdam, C. Ruwende, R. Gie, P. Samaai, D. Bester, M. Meyer, T. Corrah, M. Collin, D.R. Camidge, D. Wilkinson, E. Hoal-Van Helden, H.C. Whittle, W. Amos, P. van Helden, and A.V. Hill. 2000. Genetic susceptibility to tuberculosis in Africans: A genome-wide scan. Proc. Natl. Acad. Sci. USA 97(14):8005-8009. Berra, E., A. Ginouves, and J. Pouyssegur. 2006. The hypoxia-inducible-factor hydroxy- lases bring fresh air into hypoxia signalling. EMBO Rep. 7(1):41-45. Bibikova, M., Z. Lin, L. Zhou, E. Chudin, E.W. Garcia, B. Wu, D. Doucet, N.J. Thomas, Y. Wang, E. Vollmer, T. Goldmann, C. Seifart, W. Jiang, D.L. Barker, M.S. Chee, J. Floros, and J.B. Fan. 2006. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16(3):383-393. Birnbaum, L.S., and S.E. Fenton. 2003. Cancer and developmental exposure to endocrine disruptors. Environ. Health Perspect. 111(4):389-394. Bjornsson, H.T., M.D. Fallin, and A.P. Feinberg. 2004. An integrated epigenetic and genetic approach to common human disease. Trends Genet. 20(8):350-358. Blackwell, J.M., C.H. Barton, J.K. White, S. Searle, A.M. Baker, H. Williams, and M.A. Shaw. 1995. Genomic organization and sequence of the human NRAMP gene: Identification and mapping of a promoter region polymorphism. Mol. Med. 1(2):194-205. Blondell, J. 1999. Review of Poison Control Center Data for Residential Exposures to Organophosphate Pesticides, 1993-1996. Memorandum to Dennis Utterback, Team Leader, Organophosphate Residential Team, from Jerome Blondell, Health Statistician, Chemistry and Exposure Branch 2 Health Effects Division, Office of Prevention, Pesticides and Toxic Substances, U.S. Environmental Protection Agency, Washington, DC. February 11, 1999 [online]. Available: http://www.epa. gov/pesticides/op/disulfoton/ppcdata.pdf [accessed May 8, 2007]. Bloom, G., I.V. Yang, D. Boulware, K.Y. Kwong, D. Coppola, S. Eschrich, J. Quackenbush, and T.J. Yeatman. 2004. Multi-platform, multi-site, microarray- based human tumor classification. Am. J. Pathol. 164(1):9-16. Boess, F., M. Kamber, S. Romer, R. Gasser, D. Muller, S. Albertini, and L. Suter. 2003. Gene expression in two hepatic cell lines, cultured primary hepatocytes, and liver

References 217 slices compared to the in vivo liver gene expression in rats: Possible implications for toxicogenomics use of in vitro systems. Toxicol. Sci. 73(2):386-402. Bogaerts, J., F. Cardoso, M. Buyse, S. Braga, S. Loi, J.A. Harrison, J. Bines, S. Mook, N. Decker, P. Ravdin, P. Therasse, E. Rutgers, L.J. van 't Veer, and M. Piccart. 2006. Gene signature evaluation as a prognostic tool: Challenges in the design of the MINDACT trial. Nat. Clin. Pract. Oncol. 3(10):540-551. Bollard, M.E., J. Xu, W. Purcell, J.L. Griffin, C. Quirk, E. Holmes, and J.K. Nicholson. 2002. Metabolic profiling of the effects of D-galactosamine in liver spheroids us- ing (1)H NMR and MAS-NMR spectroscopy. Chem. Res. Toxicol. 15(11):1351- 1359. Bollard, M.E., H.C. Keun, O. Beckonert, T.M. Ebbels, H. Antti, A.W. Nicholls, J.P. Shockcor, G.H. Cantor, G. Stevens, J.C. Lindon, E. Holmes, and J.K. Nicholson. 2005. Comparative metabonomics of differential hydrazine toxicity in the rat and mouse. Toxicol. Appl. Pharmacol. 204(2):135-151. Bombail, V., J.G. Moggs, and G. Orphanides. 2004. Perturbation of epigenetic status by toxicants. Toxicol. Lett. 149(1-3):51-58. Bookman, E.B., A.A. Langehorne, J.H. Eckfeldt, K.C. Glass, G.P. Jarvik, M. Klag, G. Koski, A. Motulsky, B. Wilfond, T.A. Manolio, R.R. Fabsitz, and R.V. Luepker. 2006. Reporting genetic results in research studies: Summary and recommenda- tions of an NHLBI working group. Am. J. Med. Genet. A 140(10): 1033-1040. Boulesteix, A.L., G. Tutz, and K. Strimmer. 2003. A CART-based approach to discover emerging patterns in microarray data. Bioinformatics 19(18):2465-2472. Boverhof, D.R., K.C. Fertuck, L.D. Burgoon, J.E. Eckel, C. Gennings, and T.R. Zacharewski. 2004. Temporal- and dose-dependent hepatic gene expression changes in immature ovariectomized mice following exposure to ethynyl estradiol. Carcinogenesis. 25(7):1277-1291. Boverhof, D.R., L.D. Burgoon, C. Tashiro, B. Chittim, J.R. Harkema, D.B. Jump, and T.R. Zacharewski. 2005. Temporal and dose-dependent hepatic gene expression patterns in mice provide new insights into TCDD-Mediated hepatotoxicity. Toxi- col. Sci. 85(2):1048-1063. Bradshaw, R.A. 2005a. DRAFT Proposed Publication Guidelines for the Analysis and Documentation of Peptide and Protein Identifications. July 14, 2005 [online]. Available: http://www.mcponline.org/misc/ParisReport.shtml [accessed Nov. 8, 2005]. Bradshaw, R.A. 2005b. Revised draft guidelines for proteomic data publication. Mol.Cell Proteomics. 4(9):1223-1225. Branca, A.F., and A. Peck. 2004. Toxicogenomics: A Brenchmark Assessment of Current Practices and Future Expectations. Cambridge Healthtech Advisors, Cambridge, MA. Brazma, A., P. Hingamp, J. Quackenbush, G. Sherlock, P. Spellman, C. Stoeckert, J. Aach, W. Ansorge, C.A. Ball, H.C. Causton, T. Gaasterland, P. Glenisson, F.C. Holstege, I.F. Kim, V. Markowitz, J.C. Matese, H. Parkinson, A. Robinson, U. Sarkans, S. Schulze-Kremer, J. Stewart, R. Taylor, J. Vilo, and M. Vingron. 2001. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat. Genet. 29(4):365-371. Brazma, A., H. Parkinson, U. Sarkans, M. Shojatalab, J. Vilo, N. Abeygunawardena, E. Holloway, M. Kapushesky, P. Kemmeren, G.G. Lara, A. Oezcimen, P. Rocca- Serra, and S.A. Sansone. 2003. ArrayExpress: A public repository for microarray gene expression data at the EBI. Nucleic Acids Res. 31(1):68-71.

218 Applications of Toxicogenomic Technologies Breyer, S.G. 1995. Breaking the Vicious Cycle: Toward Effective Risk Regulation. Cam- bridge, MA: Harvard University Press. Brown, M.P., W.N. Grundy, D. Lin, N. Cristianini, C.W. Sugnet, T.S. Furey, M. Ares, Jr., and D. Haussler. 2000. Knowledge-based analysis of microarray gene expres- sion data by using support vector machines. Proc. Natl. Acad. Sci. USA 97(1):262- 267. Brown, S.C., G. Kruppa, and J.L. Dasseux. 2005. Metabolomics applications of FT-ICR mass spectrometry. Mass Spectrom. Rev. 24(2):223-231. Budinsky, R.A. 2005. A summary of the 2005 winter toxicology forum session on dioxin toxic equivalency factors. Workshop report. Regul. Toxicol. Pharmacol. 43(3): 324-326. Burke, W., L. Acheson, J. Botkin, K. Bridges, A. Davis, J. Evans, J. Frias, J. Hanson, N. Kahn, R. Kahn, D. Lanier, L.E. Pinsky, N. Press, M.A. Lloyd-Puryear, E. Rich, N. Stevens, E. Thomson, S. Wartman, and M. Wilson. 2002. Genetics in primary care: A USA faculty development initiative. Community Genet. 5(2):138-146. Bus, J.S., R.A. Canady, T.K. Collier, W. Owens, S.D. Pettit, N.L. Scholz, and A.C. Street. 2007. The extension of molecular and computational information to risk as- sessment and regulatory decision making. Pp. 151-177 in Genomic Approaches for Cross-Species Extrapolation in Toxicology, W.H. Benson, and R.T. Di Guiulio, eds. Pensacola, FL: SETAC Press. Butcher, E.C. 2005. Can cell systems biology rescue drug discovery? Nat. Rev. Drug Discov. 4(6):461-467. Butte, A.J., and I.S. Kohane. 1999. Unsupervised knowledge discovery in medical data- bases using relevance networks. Proc. AMIA Symp. (1999):711-715. Buyse, M., S. Loi, L. van't Veer, G. Viale, M. Delorenzi, A.M. Glas, M.S. d'Assignies, J. Bergh, R. Lidereau, P. Ellis, A. Harris, J. Bogaerts, P. Therasse, A. Floore, M. Amakrane, F. Piette, E. Rutgers, C. Sotiriou, F. Cardoso, and M.J. Piccart. 2006. Validation and clinical utility of a 70-gene prognostic signature for women with node-negative breast cancer. J. Natl. Cancer Inst. 98(17):1183-1192. Carruth, R.S., and B.D. Goldstein. 2001. Relative risk greater than two in proof of causa- tion in toxic tort litigation. Jurimetrics 41(2):195-210. Carter, M.G., T. Hamatani, A.A. Sharov, C.E. Carmack, Y. Qian, K. Aiba, N.T. Ko, D.B. Dudekula, P.M. Brzoska, S.S. Hwang, and M.S. Ko. 2003. In situ-synthesized novel microarray optimized for mouse stem cell and early developmental expres- sion profiling. Genome Res. 13(5):1011-1021. Castoldi, M, S. Schmidt, V. Benes, M. Noerholm, A.E. Kulozik, M.W. Hentze, and M.U. Muckenthaler. 2006. A sensitive array for microRNA expression profiling (mi- Chip) based on locked nucleic acids (LNA). RNA 12(5):913-920. CEBS (Chemical Effects in Biological Systems). 2007. Chemical Effects in Biological Systems. National Institute of Environmental Health Sciences, U.S. National Institutes of Health [online]. Available: http://cebs.niehs.nih.gov/cebs-browser/ cebsHome.do [accessed May 30, 2007]. Chadwick, R.F. 2004. The right not to know: A challenge for accurate self-assessment. Philos. Psychiatry Psychology 11(4):299-301. Chan, E.Y. 2005. Advances in sequencing technology. Mutat Res. 573(1-2):13-40. Chan, E.Y., N.M. Goncalves, R.A. Haeusler, A.J. Hatch, J.W. Larson, A.M. Maletta, G.R. Yantz, E.D. Carstea, M. Fuchs, G.G. Wong, S.R. Gullans, and R. Gilmanshin. 2004. DNA mapping using microfluidic stretching and single- molecule detection of fluorescent site-specific tags. Genome Res. 14(6):1137- 1146.

References 219 Chaurand, P., M. Stoeckli, and R.M. Caprioli. 1999. Direct profiling of proteins in bio- logical tissue sections by MALDI mass spectrometry. Anal. Chem. 71(23):5263- 5270. Chellappan, S.P. 2001. HOG on the promoter: Regulation of the osmotic stress response. Sci. STKE (93):PE1 Cheung, S.T., X. Chen, X.Y. Guan, S.Y. Wong, L.S. Tai, I.O. Ng, S. So, and S.T. Fan. 2002. Identify metastasis-associated genes in hepatocellular carcinoma through clonality delineation for multinodular tumor. Cancer Res. 62(16):4711-4721. Cheung, V.G., L.K. Conlin, T.M. Weber, M. Arcaro, K.Y. Jen, M. Morley, and R.S. Spielman. 2003. Natural variation in human gene expression assessed in lym- phoblastoid cells. Nat Genet. 33(3):422-425. Christiani, D.C., R.R. Sharp, G.W. Collman, and W.A. Suk. 2001. Applying genomic technologies in environmental health research: Challenges and opportunities. J. Occup. Environ. Med. 43(6):526-533. Chu, T.M., S. Deng, R. Wolfinger, R.S. Paules, and H.K. Hamadeh. 2004. Cross-site comparison of gene expression data reveals high similarity. Environ. Health Per- spect. 112(4):449-455. Churchill, G.A. 2002. Fundamentals of experimental design for cDNA microarrays. Nat. Genet. 32(Suppl.):490-495. Churchill, G.A., D.C. Airey, H. Allayee, J.M. Angel, A.D. Attie, J. Beatty, W.D. Beavis, J.K. Belknap, B. Bennett, W. Berrettini, A. Bleich, M. Bogue, K.W. Broman, K.J. Buck, E. Buckler, M. Burmeister, E.J. Chesler, J.M. Cheverud, S. Clapcote, M.N. Cook, R.D. Cox, J.C. Crabbe, W.E. Crusio, A. Darvasi, C.F. Deschepper, R.W. Doerge, C.R. Farber, J. Forejt, D. Gaile, S.J. Garlow, H. Geiger, H. Gershenfeld, T. Gordon, J. Gu, W. Gu, G. de Haan, N.L. Hayes, C. Heller, H. Himmelbauer, R. Hitzemann, K. Hunter, H.C. Hsu, F.A. Iraqi, B. Ivandic, H.J. Jacob, R.C. Jansen, K.J. Jepsen, D.K. Johnson, T.E. Johnson, G. Kempermann, C. Kendziorski, M. Kotb, R.F. Kooy, B. Llamas, F. Lammert, J.M. Lassalle, P.R. Lowenstein, L. Lu, A. Lusis, K.F. Manly, R. Marcucio, D. Matthews, J.F. Medrano, D.R. Miller, G. Mittleman, B.A. Mock, J.S. Mogil, X. Montagutelli, G. Morahan, D.G. Morris, R. Mott, J.H. Nadeau, H. Nagase, R.S. Nowakowski, B.F. O'Hara, A.V. Osadchuk, G.P. Page, B. Paigen, K. Paigen, A.A. Palmer, H.J. Pan, L. Peltonen-Palotie, J. Peirce, D. Pomp, M. Pravenec, D.R. Prows, Z. Qi, R.H. Reeves, J. Roder, G.D. Rosen, E.E. Schadt, L.C. Schalkwyk, Z. Seltzer, K. Shimomura, S. Shou, M.J. Sillanpaa, L.D. Siracusa, H.W. Snoeck, J.L. Spearow, K. Svenson, L.M. Tarantino, D. Threadgill, L.A. Toth, W. Valdar, F.P. de Villena, C. Warden, S. Whatley, R.W. Williams, T. Wiltshire, N. Yi, D. Zhang, M. Zhang, F. Zou, Complex Trait Consortium. 2004. The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat. Genet. 36(11):1133-1137. Ciesielski, S., D.P. Loomis, S.R. Mims, and A. Auer. 1994. Pesticide exposures, choli- nesterase depression, and symptoms among North Carolina migrant farmworkers. Am. J. Public Health 84(3):446-451. Clayton, E.W. 2003. Ethical, legal, and social implications of genomic medicine. N. Engl. J. Med. 349(6):562-569. Clayton, E.W. 2005. Informed consent and biobanks. J. Law Med. Ethics 33(1):15-21. Clifford, R.J., M.N. Edmonson, C. Nguyen, and K.H. Buetow. 2004. Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformat- ics 20(7):1006-1014.

220 Applications of Toxicogenomic Technologies Coen, M., E.M. Lenz, J.K. Nicholson, I.D. Wilson, F. Pognan, and J.C. Lindon. 2003. An integrated metabonomic investigation of acetaminophen toxicity in the mouse us- ing NMR spectroscopy. Chem. Res. Toxicol. 16(3):295-303. Coen, M., S.U. Ruepp, J.C. Lindon, J.K. Nicholson, F. Pognan, E.M. Lenz, and I.D. Wilson. 2004. Integrated application of transcriptomics and metabonomics yields new insight into the toxicity due to paracetamol in the mouse. J. Pharm. Biomed. Anal. 35(1):93-105. Cohen, S.D., N.R. Pumford, E.A. Khairallah, K. Boekelheide, L.R. Pohl, H.R. Amouzadeh, and J.A. Hinson. 1997. Selective protein covalent binding and target organ toxicity. Toxicol. Appl. Pharmacol. 143(1):1-12. Colburn, W.A. 2003. Biomarkers in drug discovery and development: From target identi- fication through drug marketing. J. Clin. Pharmacol. 43(4):329-341. Cole, T.B., B.J. Walter, D.M. Shih, A.D. Tward, A.J. Lusis, C. Timchalk, R.J. Richter, L.G. Costa, and C.E. Furlong. 2005. Toxicity of chlorpyrifos and chlorpyrifos oxon in a transgenic mouse model of the human paraoxonase (PON1) Q192R polymorphism. Pharmacogenet. Genomics. 15(8):589-598. Conrads, T.P., B.L. Hood, H.J. Issaq, and T.D. Veenstra. 2004. Proteomic patterns as a diagnostic tool for early-stage cancer: A review of its progress to a clinically rele- vant tool. Mol. Diagn. 8(2):77-85. Cook, D.N., S. Wang, Y. Wang, G.P. Howles, G.S. Whitehead, K.G. Berman, T.D. Church, B.C. Frank, R.M. Gaspard, Y. Yu, J. Quackenbush, and D.A. Schwartz. 2004. Genetic regulation of endotoxin-induced airway disease. Genomics 83(6):961-969. Coon, J. J., B. Ueberheide, J.E. Syka, D.D. Dryhurst, J. Ausio, J. Shabanowitz, and D.F. Hunt. 2005. Protein identification using sequential ion/ion reactions and tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A 102(27):9463-9468. Corvi, R., H.J. Ahr, S. Albertini, D.H. Blakey, L. Clerici, S. Coecke, G.R. Douglas, L. Gribaldo, J.P. Groten, B. Haase, K. Hamernik, T. Hartung, T. Inoue, I. Indans, D. Maurici, G. Orphanides, D. Rembges, S.A. Sansone, J.R. Snape, E. Toda, W. Tong, J.H. van Delft, B. Weis, and L.M. Schechtman. 2006. Validation of Toxico- genomics-Based Test Systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use. Environ. Health Perspect. 114(3):420-429. Cosma, G.N., P. Toniolo, D. Currie, B.S. Pasternack, and S.J. Garte. 1992. Expression of the CYP1A1 gene in peripheral lymphocytes as a marker of exposure to creosote in railroad workers. Cancer Epidemiol. Biomarkers Prev. 1(2):137-142. Craig, R., and R.C. Beavis. 2004. TANDEM: Matching proteins with tandem mass spec- tra. Bioinformatics 20(9):1466-1467. Craig, R., J.P. Cortens, and R.C. Beavis. 2004. Open source system for analyzing, vali- dating, and storing protein identification data. J. Proteome Res. 3(6):1234-1242. Cranor, C.F. 1997. Eggshell skulls and loss of hair from fright: Some moral and legal principles that protect susceptible subpopulations. Environ. Toxicol. Pharmacol. 4(3-4):239-245. Crespi, C.L., and V.P. Miller. 1999. The use of heterologously expressed drug metaboliz- ing enzymes--state of the art and prospects for the future. Pharmacol. Ther. 84(2):121-131. Crespi, C.L., B.W. Penman, D.T. Steimel, T. Smith, C.S. Yang, and T.R. Sutter. 1997. Development of a human lymphoblastoid cell line constitutively expressing human CYP1B1 cDNA: Substrate specificity with model substrates and promutagens. Mutagenesis 12(2):83-89.

References 221 Cronin, M., K. Ghosh, F. Sistare, J. Quackenbush, V. Vilker, and C. O'Connell. 2004. Universal RNA reference materials for gene expression. Clin. Chem. 50(8):1464- 1471. Cupp, A.S., M. Uzumcu, H. Suzuki, K. Dirks, B. Phillips, and M.K. Skinner. 2003. Effect of transient embryonic in vivo exposure to the endocrine disruptor methoxychlor on embryonic and postnatal testis development. J. Androl. 24(5):736-745. Daston, G.P. 2004. Developmental toxicity evaluation of butylparaben in Sprague- Dawley rats. Birth Defects Res. B Dev. Reprod. Toxicol 71(4):296-302. Daston, G.P., and J.M. Naciff. 2005. Gene expression changes related to growth and differentiation in the fetal and juvenile reproductive system of the female rat: Evaluation of microarray results. Reprod. Toxicol. 19(3):381-394. Datta, A., A. Choudhary, M.L. Bittner, and E.R. Dougherty. 2004. External control in Markovian genetic regulatory networks: The imperfect information case. Bioin- formatics 20(6):924-930. De Sanctis, G.T., and J.M. Drazen. 1997. Genetics of native airway responsiveness in mice. Am. J. Respir. Crit. Care Med. 156(4 Pt 2):S82-S88. Deschênes, M., and C. Sallée. 2005. Accountability in population biobanking: Comparative approaches. J. Law Med. Ethics 33(1):40-53. Desiere, F., E.W. Deutsch, A.I. Nesvizhskii, P. Mallick, N.L. King, J.K. Eng, A. Aderem, R. Boyle, E. Brunner, S. Donohoe, N. Fausto, E. Hafen, L. Hood, M.G. Katze, K.A. Kennedy, F. Kregenow, H. Lee, B. Lin, D. Martin, J.A. Ranish, D.J. Rawlings, L.E. Samelson, Y. Shiio, J.D. Watts, B. Wollscheid, M.E. Wright, W. Yan, L. Yang, E.C. Yi, H. Zhang, and R. Aebersold. 2005. Integration with the human genome of peptide sequences obtained by high-throughput mass spec- trometry. Genome Biol. 6(1):R9. Desiere, F., E.W. Deutsch, N.L. King, A.I. Nesvizhskii, P. Mallick, J. Eng, S. Chen, J. Eddes, S.N. Loevenich, and R. Aebersold. 2006. The PeptideAtlas project. Nucleic Acids Res. 34:D655-D658. de Wildt, R.M., C.R. Mundy, B.D. Gorick, and I.M. Tomlinson. 2000. Antibody arrays for high-throughput screening of antibody-antigen interactions. Nat. Biotechnol. 18(9):989-994. DHHS (U.S. Department of Health and Human Services). 1997. Issues to Consider in the Research Use of Stored Data or Tissues. Office for Protection from Research Risks, U.S. Department of Health and Human Services [online]. Available: www.hhs.gov/ohrp/humansubjects/guidance/reposit.htm [accessed Nov. 10, 2005]. DHHS (U.S. Department of Health and Human Services). 2004. Guidance on Research Involving Coded Private Information or Biological Specimens. Office for Human Research Protections, U.S. Department of Health and Human Services [online]. Available: http://www.hhs.gov/ohrp/humansubjects/guidance/cdebiol.pdf [ac- cessed Nov. 10, 2005]. DHHS (U.S. Department of Health and Human Services). 2006. Medical Privacy – Na- tional Standards to Protect the Privacy of Personal Health Information. Office for Civil Rights – HIPAA, U.S. Department of Health and Human Services, Washing- ton, DC [online]. Available: http://www.hhs.gov/ocr/hipaa/ [accessed Aug. 24, 2006]. Diamandis, E.P. 2004. Analysis of serum proteomic patterns for early cancer diagnosis: Drawing attention to potential problems. J. Natl. Cancer Inst. 96(5):353-356. Dickinson, D.A., G.R. Warnes, G. Quievryn, J. Messer, A. Zhitkovich, E. Rubitski, and J. Aubrecht. 2004. Differentiation of DNA reactive and non-reactive genotoxic mechanisms using gene expression profile analysis. Mutat. Res. 549(1-2):29-41.

222 Applications of Toxicogenomic Technologies Dobbin, K.K., and R.M. Simon. 2005. Sample size determination in microarray experi- ments for class comparison and prognostic classification. Biostat. 6(1):27-38. Dobbin, K.K., D.G. Beer, M. Meyerson, T.J. Yeatman, W.L. Gerald, J.W. Jacobson, B. Conley, K.H. Buetow, M. Heiskanen, R.M. Simon, J.D. Minna, L. Girard, D.E. Misek, J.M. Taylor, S. Hanash, K. Naoki, D.N. Hayes, C. Ladd-Acosta, S.A. Enkemann, A. Viale, and T.J. Giordano. 2005. Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays. Clin. Cancer Res. 11(2 Pt. 1):565-572. Doll, R., and R. Wakeford. 1997. Risk of childhood cancer from fetal irradiation. Br. J. Radiol. 70:130-139. Doniger, S.W., N. Salomonis, K.D. Dahlquist, K. Vranizan, S.C. Lawlor, and B.R. Conklin. 2003. MAPPFinder: Using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data. Genome Biol. 4(1):R7. Dorne, J.L., K. Walton, W. Slob, and A.G. Renwick. 2002. Human variability in poly- morphic CYP2D6 metabolism: Is the kinetic default uncertainty factor adequate? Food Chem. Toxicol. 40(11):1633-1656. Dorne, J.L., K. Walton, and A.G. Renwick. 2005. Human variability in xenobiotic me- tabolism and pathway-related uncertainty factors for chemical risk assessment: A review. Food Chem. Toxicol. 43(2):203-216. Dudoit, S., R.C. Gentleman, and J. Quackenbush. 2003. Open source software for the analysis of microarray data. Biotechniques (Suppl.):45-51. EDF (Environmental Defense Fund). 1997. Toxic Ignorance: The Continuing Absence of Basic Health Testing for Top-Selling Chemicals in the United States. New York: Environmental Defense Fund. Edgar, R., M. Domrachev, and A.E. Lash. 2002. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 30(1):207- 210. Ehrenberg, L., F. Granath, and M. Tornqvist. 1996. Macromolecule adducts as bio- markers of exposure to environmental mutagens in human populations. Environ. Health Perspect. 104(Suppl. 3):423-428. Eiseman, E., and S.B. Haga. 1999. Handbook of Human Tissue Sources: A National Re- source of Human Tissue Samples. Santa Monica, CA: RAND. Eisen, M.B., P.T. Spellman, P.O. Brown, and D. Botstein. 1998. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95(25):14863-14868. Elias, J.E., W. Haas, B.K. Faherty, and S.P. Gygi. 2005. Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Meth- ods 2(9):667-675. Ellinger-Ziegelbauer, H., B. Stuart, B. Wahle, W. Bomann, and H.J. Ahr. 2004. Charac- teristic expression profiles induced by genotoxic carcinogens in rat liver. Toxicol. Sci. 77(1):19-34. Ellis, M., N. Davis, A. Coop, M. Liu, L. Schumaker, R.Y. Lee, R. Srikanchana, C.G. Russell, B. Singh, W.R. Miller, V. Stearns, M. Pennanen, T. Tsangaris, A. Gallagher, A. Liu, A. Zwart, D.F. Hayes, M.E. Lippman, Y. Wang, and R. Clarke. 2002. Development and validation of a method for using breast core needle biop- sies for gene expression microarray analyses. Clin. Cancer Res. 8(5):1155-1166. El-Masri, H.A., D.A. Bell, and C.J. Portier. 1999. Effects of glutathione transferase theta polymorphism on the risk estimates of dichloromethane to humans. Toxicol. Appl. Pharmacol. 158(3):221-230.

References 223 Eng, J.K., A.L. McCormack, and J.R.Yates III. 1994. An approach to correlate tandem mass spectra data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 5(11):976-989. EPA (U.S. Environmental Protection Agency). 1986. Guidelines for Carcinogen Risk Assessment. EPA/630/R-00/004. Risk Assessment Forum, U.S. Environmental Protection Agency, Washington, DC. EPA (U.S. Environmental Protection Agency). 2002. Interim Genomics Policy (June 25, 2002). Science Policy Council, U.S. Environmental Protection Agency [online]. Available: http://www.epa.gov/osa/spc/genomics.htm [accessed Nov. 14, 2005]. EPA (U.S. Environmental Protection Agency). 2003. Exposure and Human Health Reas- sessment of 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) and Related Com- pounds. NAS Review Draft. National Center for Environmental Assessment, Of- fice of Research and Development, U.S. Environmental Protection Agency, Washington, DC. December 2003 [online]. Available: http://www.epa.gov/ncea/ pdfs/dioxin/nas-review/ [accessed Aug. 29, 2006]. EPA (U.S. Environmental Protection Agency). 2004. Potential Implications of Genomics for Regulatory and Risk Assessment Applications at EPA. EPA 100/B-04/002. Genomics Task Force Workgroup, Science Policy Council, U.S. Environmental Protection Agency, Washington, DC. December 2004 [online]. Available: http://www.epa.gov/osa/pdfs/EPA-Genomics-White-Paper.pdf [accessed Nov. 28, 2005]. EPA (U.S. Environmental Protection Agency). 2006a. The HPV Voluntary Challenge Chemical List. U.S. Environmental Protection Agency [online]. Available: http://www.epa.gov/chemrtk/pubs/update/hpvchmlt.htm [accessed May 1, 2007]. EPA (U.S. Environmental Protection Agency). 2006b. TSCA Regulations. Civil En- forcement, U.S. Environmental Protection Agency [online]. Available: http:// www.epa.gov/compliance/civil/tsca/tscaenfstatreq.html#regs [accessed May 1, 2007]. Famili, I., R. Mahadevan, and B.O. Palsson. 2005. k-Cone analysis: Determining all can- didate values for kinetic parameters on a network scale. Biophys. J. 88(3):1616- 1625. Farber, D.A. 1987. Toxic causation. Minn. L. Rev. 71:1219-1261. FDA (Food and Drug Administration). 2005a. Guidance for Industry: Pharmacogenomic Data Submissions. U.S. Department of Health and Human Services, Food and Drug Administration, Center for Drug Evaluation and Research, Center for Biolog- ics Evaluation and Research, Center for Devices and Radiological Health. March 2005 [online]. Available: http://www.fda.gov/cber/gdlns/pharmdtasub.htm [ac- cessed Feb. 3, 2006]. FDA (Food and Drug Administration). 2005b. Drug-Diagnostic Co-Development Con- cept Paper. U.S. Department of Health and Human Services, Food and Drug Ad- ministration. April 2005 [online]. Available: http://www.fda.gov/cder/genomics/ pharmacoconceptfn.pdf [accessed Feb. 10, 2006]. Fella, K., M. Gluckmann, J. Hellmann, M. Karas, P.J. Kramer, and M. Kroger. 2005. Use of two-dimensional gel electrophoresis in predictive toxicology: Identification of potential early protein biomarkers in chemically induced hepatocarcinogenesis. Proteomics 5(7):1914-1927. Fenyo, D. 2000. Identifying the proteome: Software tools. Curr. Opin. Biotechnol. 1(4):391-395.

224 Applications of Toxicogenomic Technologies Fielden, M.R., B.P. Eynon, G. Natsoulis, K. Jarnagin, D. Banas, and K.L. Kolaja. 2005. A gene expression signature that predicts the future onset of drug-induced renal tubular toxicity. Toxicol. Pathol. 33(6):675-683. Finkel, T., and N.J. Holbrook. 2000. Oxidants, oxidative stress and the biology of ageing. Nature 408(6809):239-247. Fletcher, N., D. Wahlstrom, R. Lundberg, C.B. Nilsson, K.C. Nilsson, K. Stockling, H. Hellmold, and H. Hakansson. 2005. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) alters the mRNA expression of critical genes associated with cholesterol metabo- lism, bile acid biosynthesis, and bile transport in rat liver: A microarray study. Toxicol. Appl. Pharmacol. 207(1):1-24. Fodor, S.P., R.P. Rava, X.C. Huang, A.C. Pease, C.P. Holmes, and C.L. Adams. 1993. Multiplexed biochemical assays with biological chips. Nature 364(6437):555-556. Fontenot, A.P., and L.A. Maier. 2005. Genetic susceptibility and immune-mediated de- struction in beryllium-induced disease. Trends Immunol. 26(10):543-549. Forand, P.E., S.J. Kunselman, J.M. Drazen, E. Israel, A. Pillari, T.J. Armstrong, and T.B. Britton. 2001. Genetic analysis in the Asthma Clinical Research Network. Control. Clin. Trials 22(Suppl. 6):S196-S206. Fornace Jr., A.J., I. Alamo Jr., and M.C. Hollander. 1988. DNA damage-inducible tran- scripts in mammalian cells. Proc. Natl. Acad. Sci. USA 85(23):8800-8804. Forrest, M.S., Q. Lan, A.E. Hubbard, L. Zhang, R. Vermeulen, X. Zhao, G. Li, Y.Y. Wu, M. Shen, S. Yin, S.J. Chanock, N. Rothman, and M.T. Smith. 2005. Discovery of novel biomarkers by microarray analysis of peripheral blood mononuclear cell gene expression in benzene-exposed workers. Environ. Health Perspect. 113(6):801-807. Fortier, A., G. Min-Oo, J. Forbes, S. Lam-Yuk-Tseung, and P. Gros. 2005. Single gene effects in mouse models of host: Pathogen interactions. J. Leukoc. Biol. 77(6):868- 877. Foster, M.W., and R.R. Sharp. 2002. Race, ethnicity, and genomics: Social classifications as proxies of biological heterogeneity. Genome Res. 12(6):844-850. Fountoulakis, M., P. Berndt, U.A. Boelsterli, F. Crameri, M. Winter, S. Albertini, and L. Suter. 2000. Two-dimensional database of mouse liver proteins: Changes in he- patic protein levels following treatment with acetaminophen or its nontoxic regioi- somer 3-acetamidophenol. Electrophoresis 21(11):2148-2161. Frank, R., and R. Hargreaves. 2003. Clinical biomarkers in drug discovery and develop- ment. Nat. Rev. Drug Discov. 2(7):566-580. Friedman, N., M. Linial, I. Nachman, and D. Pe'er. 2000. Using Bayesian networks to analyze expression data. J. Comput. Biol. 7(3-4):601-620. Frueh, F.W., K.C. Hayashibara, P.O. Brown, and J.P. Whitlock Jr. 2001. Use of cDNA microarrays to analyze dioxin-induced changes in human liver gene expression. Toxicol. Lett. 122(3):189-203. Furlong, C.E., T.B. Cole, G.P. Jarvik, C. Pettan-Brewer, G.K. Geiss, R.J. Richter, D.M. Shih, A.D. Tward, A.J. Lusis, and L.G. Costa. 2005a. Role of paraoxonase (PON1) status in pesticide sensitivity: Genetic and temporal determinants. Neurotoxicology 26(4):651-659. Furlong, C.E., T.B. Cole, B.J. Walter, D.M. Shih, A. Tward, A.J. Lusis, C. Timchalk, R.J. Richter, and L.G. Costa. 2005b. Paraoxonase 1 (PON1) status and risk of insecti- cide exposure. J. Biochem. Mol. Toxicol. 19(3):182-183. Gallagher, K., W.H. Benson, M. Brody, A. Fairbrother, J. Hasan, R. Klaper, D. Lattier, S. Lundquist, N. McCarroll, G. Miller, J. Preston, P. Sayre, J. Seed, B. Smith, A. Street, R. Troast, V. Vu, L. Reiter, W. Farland, and K. Dearfield. 2006. Genomics:

References 225 Applications, challenges, and opportunities for the U.S. Environmental Protection Agency. Hum. Ecol. Risk Assess. 12(3):572-590. Gant, T.W., P.R. Baus, B. Clothier, J. Riley, R. Davies, D.J. Judah, R.E. Edwards, E. George, P. Greaves, and A.G. Smith. 2003. Gene expression profiles associated with inflammation, fibrosis, and cholestasis in mouse liver after griseofulvin. EHP Toxicogenomics 111(1T):37-43. Gao, J., G.J. Opiteck, M.S. Friedrichs, A.R. Dongre, and S.A. Hefta. 2003. Changes in the protein expression of yeast as a function of carbon source. J. Proteome Res. 2(6):643-649. Garner, J.M. et al. 2000. Medical monitoring: The evolution of a cause of action. Envi- ron. Law Rep. 30(1):10,024-10,033. Garosi, P., C. De Filippo, M. van Erk, P. Rocca-Serra, S.A. Sansone, and R. Elliott. 2005. Defining best practice for microarray analyses in nutrigenomic studies. Br. J. Nutr. 93(4):425-432. Garrod, S., E. Humpher, S.C. Connor, J.C. Connelly, M. Spraul, J.K. Nicholson, and E. Holmes. 2001. High-resolution (1)H NMR and magic angle spinning NMR spec- troscopic investigation of the biochemical effects of 2-bromoethanamine in intact renal and hepatic tissue. Magn. Reson. Med. 45(5):781-790. Ge, Y., B.G. Lawhorn, M. ElNaggar, E. Strauss, J.H. Park, T.P. Begley, and F.W. McLafferty. 2002. Top down characterization of larger proteins (45 kDa) by elec- tron capture dissociation mass spectrometry. J. Am. Chem. Soc. 124(4):672-678. Geller, G., J.R. Botkin, M.J. Green, N. Press, B.B. Biesecker, B. Wilfond, G. Grana, M.B. Daly, K. Schneider, and M.J. Kahn. 1997. Genetic testing for susceptibility to adult-onset cancer. The process and content of informed consent. JAMA 277(18):1467-1474. Gene Logic, Inc. 2005. ToxExpress Program. Gene Logic, Inc. [online]. Available: http://www.genelogic.com/docs/pdfs/toxExpressProductSheet.pdf [accessed Nov. 8, 2005]. Gerber, S.A., J. Rush, O. Stemman, M.W. Kirschner, and S. P. Gygi. 2003. Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc. Natl. Acad. Sci. U.S.A 100(12):6940-6945. Giaever, G., A.M. Chu, L. Ni, C. Connelly, L. Riles, S. Veronneau, S. Dow, A. Lucau- Danila, K. Anderson, B. Andre, A.P. Arkin, A. Astromoff, M. El-Bakkoury, R. Bangham, R. Benito, S. Brachat, S. Campanaro, M. Curtiss, K. Davis, A. Deutschbauer, K.D. Entian, P. Flaherty, F. Foury, D.J. Garfinkel, M. Gerstein, D. Gotte, U. Guldener, J.H. Hegemann, S. Hempel, Z. Herman, D.F. Jaramillo, D.E. Kelly, S.L. Kelly, P. Kotter, D. LaBonte, D.C. Lamb, N. Lan, H. Liang, H. Liao, L. Liu, C. Luo, M. Lussier, R. Mao, P. Menard, S.L. Ooi, J.L. Revuelta, C.J. Roberts, M. Rose, P. Ross-Macdonald, B. Scherens, G. Schimmack, B. Shafer, D.D. Shoemaker, S. Sookhai-Mahadeo, R.K. Storms, J.N. Strathern, G. Valle, M. Voet, G. Volckaert, C.Y. Wang, T.R. Ward, J. Wilhelmy, E.A. Winzeler, Y. Yang, G. Yen, E. Youngman, K. Yu, H. Bussey, J.D. Boeke, M. Snyder, P. Philippsen, R.W. Davis, and M. Johnston. 2002. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418(6896):387-391. Ginsburg, G.S., and M. Angrist. 2006. The future may be closer than you think: A re- sponse from the Personalized Medicine Coalition to the Royal Society’s report on personalized medicine. Personalized Medicine 3(2):119-123. Golub, T.R., D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek, J.P. Mesirov, H. Coller, M.L. Loh, J.R. Downing, M.A. Caligiuri, C.D. Bloomfield, and E.S.

226 Applications of Toxicogenomic Technologies Lander. 1999. Molecular classification of cancer: Class discovery and class predic- tion by gene expression monitoring. Science 286(5439):531-537. Grabher, C., and A.T. Look. 2006. Fishing for cancer models. Nat. Biotechnol. 24(1):45- 46. Gray, J.P., T.L. Leas, E. Obert, D. Brown, G.C. Clark, and J.P. Vanden Heuvel. 2003. Evidence of aryl hydrocarbon receptor ligands in Presque Isle Bay of Lake Erie. Aquat. Toxicol. 64(3):343-358. Green, M.J., S.K. Peterson, M.W. Baker, G.R. Harper, L.C. Friedman, W.S. Rubinstein, and D.T. Mauger. 2004. Effect of a computer-based decision aid on knowledge, perceptions, and intentions about genetic testing for breast cancer susceptibility: A randomized controlled trial. JAMA 292(4):442-452. Greenberg, D.S. 2001. Science, Money, and Politics: Political Triumph and Ethical Ero- sion. Chicago: University of Chicago Press. Griffin, J.L. 2004. Metabolic profiles to define the genome: Can we hear the phenotypes? Philos. Trans. R Soc. Lond. B Biol. Sci. 359(1446):857-871. Griffin, J.L., S.A. Bonney, C. Mann, A.M. Hebbachi, G.F. Gibbons, J.K. Nicholson, C.C. Shoulders, and J. Scott. 2004. An integrated reverse functional genomic and meta- bolic approach to understanding orotic acid-induced fatty liver. Physiol. Genomics 17(2):140-149. Griffin, R.J., S. Dunwoody, and K. Neuwirth. 1999. Proposed model of the relationship of risk information seeking and processing to the development of preventive be- haviors. Environ. Res. 80(2 Pt 2):S230-S245. Grodsky, J.A. 2005. Genetics and environmental law: Redefining public health. Calif. Law Rev. 93(1):171-270. Gunderson, K.L., F.J. Steemers, G. Lee, L.G. Mendoza, and M.S. Chee. 2005. A ge- nome-wide scalable SNP genotyping assay using microarray technology. Nat. Genet. 37(5):549-554. Guo, Y., L.L. Breeden, H. Zarbl, B.D. Preston, and D.L. Eaton. 2005. Expression of a human cytochrome p450 in yeast permits analysis of pathways for response to and repair of aflatoxin-induced DNA damage. Mol. Cell Biol. 25(14):5823-5833. Guo, Y., L.L. Breeden, W. Fan, L.P. Zhao, D.L. Eaton, and H. Zarbl. 2006. Analysis of cellular responses to aflatoxin B(1) in yeast expressing human cytochrome P450 1A2 using cDNA microarrays. Mutat. Res. 593(1-2):121-142. Gut, I.G. 2004. DNA analysis by MALDI-TOF mass spectrometry. Hum. Mutat. 23(5):437-441. Gygi, S.P., B. Rist, S.A. Gerber, F. Turecek, M.H. Gelb, and R. Aebersold. 1999. Quanti- tative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17(10):994-999. Gygi, S.P., G.L. Corthals, Y. Zhang, Y. Rochon, and R. Aebersold. 2000. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97(17):9390-9395. Haber, L.T., A. Maier, P.R. Gentry, H.J. Clewell, and M.L. Dourson. 2002. Genetic polymorphisms in assessing interindividual variability in delivered dose. Regul. Toxicol. Pharmacol. 35(2 Pt.1):177-197. Hadley, D.W., J.F. Jenkins, E. Dimond, M. de Carvalho, I. Kirsch, and C.G. Palmer. 2004. Colon cancer screening practices after genetic counseling and testing for he- reditary nonpolyposis colorectal cancer. J. Clin. Oncol. 22(1):39-44. Hamadeh, H.K., P.R. Bushel, S. Jayadev, K. Martin, O. DiSorbo, S. Sieber, L. Bennett, R. Tennant, R. Stoll, J.C. Barrett, K. Blanchard, R.S. Paules, and C.A. Afshari.

References 227 2002a. Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci. 67(2):219-231. Hamadeh, H.K., P.R. Bushel, S. Jayadev, O. DiSorbo, L. Bennett, L. Li, R. Tennant, R. Stoll, J.C. Barrett, R.S. Paules, K. Blanchard, and C.A. Afshari. 2002b. Prediction of compound signature using high density gene expression profiling. Toxicol. Sci. 67(2):232-240. Hamadeh, H.K., S. Jayadev, E.T. Gaillard, Q. Huang, R. Stoll, K. Blanchard, J. Chou, C.J. Tucker, J. Collins, R. Maronpot, P. Bushel, and C.A. Afshari. 2004. Integra- tion of clinical and gene expression endpoints to explore furan-mediated hepato- toxicity. Mutat. Res. 549(1-2):169-183. Hanahan, D., and R.A. Weinberg. 2000. The hallmarks of cancer. Cell 100(1):57-70. Hannon, G.J., and J.J. Rossi. 2004. Unlocking the potential of the human genome with RNA interference. Nature 431(7006):371-378. Hansen, B.T., J.A. Jones, D.E. Mason, and D.C. Liebler. 2001. SALSA: A pattern recog- nition algorithm to detect electrophile-adducted peptides by automated evaluation of CID spectra in LC-MS-MS analyses. Anal. Chem. 73(8):1676-1683. Hansen, B.T., S.W. Davey, A.J. Ham, and D.C. Liebler. 2005. P-Mod: An algorithm and software to map modifications to peptide sequences using tandem MS data. J. Pro- teome Res. 4(2):358-368. Harada, M. 1978. Congenital Minamata disease: Intrauterine methylmercury poisoning. Teratology 18(2):285-258. Hard, M.L., M. Abdolell, B.H. Robinson, and G. Koren. 2005. Gene-expression analysis after alcohol exposure in the developing mouse. J. Lab. Clin. Med. 145(1):47-54. Hardiman, G. 2004. Microarray platforms--comparisons and contrasts. Pharmacogenom- ics 5(5):487-502. Hashimoto, R.F., S. Kim, I. Shmulevich, W. Zhang, M.L. Bittner, and E.R. Dougherty. 2004. Growing genetic regulatory networks from seed genes. Bioinformatics 20(8):1241-1247. Haugen, A.C., R. Kelley, J.B. Collins, C.J. Tucker, C. Deng, C.A. Afshari, J.M. Brown, T. Ideker, and B. Van Houten. 2004. Integrating phenotypic and expression pro- files to map arsenic-response networks. Genome Biol. 5(12):R95. Hayashi, H., G. Nagae, S. Tsutsumi, K. Kaneshiro, T. Kozaki, A. Kaneda, H. Sugisaki, and H. Aburatani. 2007. High-resolution mapping of DNA methylation in human genome using oligonucleotide tiling array. Hum. Genet. 120(5):701-711. Heijne, W.H., R.H. Stierum, M. Slijper, P.J. van Bladeren, and B. van Ommen. 2003. Toxicogenomics of bromobenzene hepatotoxicity: A combined transcriptomics and proteomics approach. Biochem. Pharmacol. 65(5):857-875. Heinloth, A.N., R.D. Irwin, G.A. Boorman, P. Nettesheim, R.D. Fannin, S.O. Sieber, M.L. Snell, C.J. Tucker, L. Li, G.S. Travlos, G. Vansant, P.E. Blackshear, R.W. Tennant, M.L. Cunningham, and R.S. Paules. 2004. Gene expression profiling of rat livers reveals indicators of potential adverse effects. Toxicol. Sci. 80(1):193- 202 Heinloth, A.N., G.A. Boorman, J.F. Foley, N.D. Flagler, and R.S. Paules. 2007. Gene expression analysis offers unique advantages to histopathology in liver biopsy evaluations. Toxicol. Pathol. 35(2):276-283. Herrero, J., A. Valencia, and J. Dopazo. 2001. A hierarchical unsupervised growing neu- ral network for clustering gene expression patterns. Bioinformatics 17(2):126-136. Hinds, D.A., L.L. Stuve, G.B. Nilsen, E. Halperin, E. Eskin, D.G. Ballinger, K.A. Frazer, and D.R. Cox. 2005. Whole-genome patterns of common DNA variation in three human populations. Science 307(5712):1072-1079.

228 Applications of Toxicogenomic Technologies Hirschhorn, J.N., K. Lohmueller, E. Byrne, and K. Hirschhorn. 2002. A comprehensive review of genetic association studies. Genet. Med. 4(2):45-61. Hoffmann, R., T. Seidl, and M. Dugas. 2002. Profound effect of normalization on detec- tion of differentially expressed genes in oligonucleotide microarray data analysis. Genome Biol. 3(7):RESEARCH0033. Hogstrand, C., S. Balesaria, and C.N. Glover. 2002. Application of genomics and pro- teomics for study of the integrated response to zinc exposure in a non-model fish species, the rainbow trout. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 133(4):523-535. Holladay, S.D., and R.J. Smialowicz. 2000. Development of the murine and human im- mune system: Differential effects of immunotoxicants depend on time of exposure. Environ Health Perspect. 108(Suppl. 3):463-473. Holmes, E., A.W. Nicholls, J.C. Lindon, S. Ramos, M. Spraul, P. Neidig, S.C. Connor, J. Connelly, S.J. Damment, J. Haselden, and J.K. Nicholson. 1998. Development of a model for classification of toxin-induced lesions using 1H NMR spectroscopy of urine combined with pattern recognition. NMR Biomed. 11(4-5):235-244. Holtzman, N.A. 1996. Medical and ethical issues in genetic screening: An academic view. Environ. Health Perspect. 104(Suppl. 5):987-990. Homola, J. 2003. Present and future of surface plasmon resonance biosensors. Anal. Bio- anal. Chem. 377(3):528-539. Hopwood, P., A. Howell, F. Lalloo, and G. Evans. 2003. Do women understand the odds? Risk perceptions and recall of risk information in women with a family his- tory of breast cancer. Community Genet. 6(4):214-223. Hosack, D.A., G. Dennis, Jr, B.T. Sherman, H.C. Lane, and R.A. Lempicki. 2003. Identi- fying biological themes within lists of genes with EASE. Genome Biol. 4(10):R70. Hu, Q., R.J. Noll, H. Li, A. Makarov, M. Hardman, and C.R. Graham. 2005. The Orbi- trap: A new mass spectrometer. J. Mass Spectrom. 40(4):430-443. Hughes, T.R., M. Mao, A.R. Jones, J. Burchard, M.J. Marton, K.W. Shannon, S.M. Lefkowitz, M. Ziman, J.M. Schelter, M.R. Meyer, S. Kobayashi, C. Davis, H. Dai, Y.D. He, S.B. Stephaniants, G. Cavet, W.L. Walker, A. West, E. Coffey, D.D. Shoemaker, R. Stoughton, A.P. Blanchard, S.H. Friend, and P.S. Linsley. 2001. Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat. Biotechnol. 19(4):342-347. HUGO (Human Genome Organisation). 1997. Statement on Patenting Issues Related to Early Release of Raw Sequence Data. HUGO Intellectual Property Committee. May 1997 [online]. Available: http://www.hugo-international.org/committee_ ip.htm [accessed Aug. 30, 2006]. HUGO (Human Genome Organisation). 2000. Statement on Benefit-Sharing. HUGO Ethics Committee. April 9, 2000 [online]. Available: http://www.hugo-interna tional.org/Statement_on_Benefit_Sharing.htm [accessed Aug. 30, 2006]. IARC (International Agency for Research on Cancer). 1987. P. 58 in IARC Monographs on the Evaluation of Carcinogenic Risks to Humans, Supplement 7. Overall Evaluations of Carcinogenicity: An Updating of IARC Monographs Volumes 1- 42. Lyon: International Agency for Research on Cancer. Iconix Pharmaceuticals. 2005. Bridging Genomics and Chemistry. Products. Applications [online]. Available: http://www.iconixpharm.com/products/products_applications. html [accessed Nov 8, 2005]. Iida, M., C.H. Anna, J. Hartis, M. Bruno, B. Wetmore, J.R. Dubin, S. Sieber, L. Bennett, M.L. Cunningham, R.S. Paules, K.B. Tomer, C.D. Houle, A.B. Merrick, R.C. Sills, and T.R. Devereux. 2003. Changes in global gene and protein expression

References 229 during early mouse liver carcinogenesis induced by non-genotoxic model carcino- gens oxazepam and Wyeth-14,643. Carcinogenesis 24(4):757-770. ILSI HESI. 2006. International Life Sciences Institute- Health and Environmental Sci- ences Institute [online]. Available: http://www.hesiglobal.org/ [accessed Jan. 12, 2006]. Imoto, S., S. Kim, T. Goto, S. Miyano, S. Aburatani, K. Tashiro, and S. Kuhara. 2003. Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network. J. Bioinform. Comput. Biol. 1(2):231-252. Infante-Rivard, C. 2004. Drinking water contaminants, gene polymorphisms, and fetal growth. Environ. Health Perspect. 112(11):1213-1216. IOM (Institute of Medicine). 1996. Fetal Alcohol Syndrome: Diagnosis, Epidemiology, Prevention, and Treatment, K. Stratton, S. Howe, and F. Battaglia, eds. Washing- ton, DC: National Academy Press. IOM (Institute of Medicine). 2004. Health Literacy: A Prescription to End Confusion. Washington, DC: The National Academies Press. Iorio, M.V., M. Ferracin, C.G. Liu, A. Veronese, R. Spizzo, S. Sabbioni, E. Magri, M. Pedriali, M. Fabbri, M. Campiglio, S. Menard, J.P. Palazzo, A. Rosenberg, P. Musiani, S. Volinia, I. Nenci, G.A. Calin, P. Querzoli, M. Negrini, and C.M. Croce. 2005. MicroRNA gene expression deregulation in human breast cancer. Cancer Res. 65(16):7065-7070. Irizarry, R.A., D. Warren, F. Spencer, I.F. Kim, S. Biswal, B.C. Frank, E. Gabrielson, J.G. Garcia, J. Geoghegan, G. Germino, C. Griffin, S.C. Hilmer, E. Hoffman, A.E. Jedlicka, E. Kawasaki, F. Martinez-Murillo, L. Morsberger, H. Lee, D. Petersen, J. Quackenbush, A. Scott, M. Wilson, Y. Yang, S.Q. Ye, and W. Yu. 2005. Multiple- laboratory comparison of microarray platforms. Nat. Methods 2(5):345-350. Ishimura, R., S. Ohsako, T. Kawakami, M. Sakaue, Y. Aoki, and C. Tohyama. 2002. Altered protein profile and possible hypoxia in the placenta of 2,3,7,8- tetrachlorodibenzo-p-dioxin-exposed rats. Toxicol. Appl. Pharmacol. 185(3):197- 206. Jaenisch, R., and A. Bird. 2003. Epigenetic regulation of gene expression: How the ge- nome integrates intrinsic and environmental signals. Nat. Genet. 33(Suppl.):245- 254. Janger, E.J. 2005. Genetic information, privacy and insolvency. J. Law Med. Ethics 33(1):79-88. Janzi, M., J. Odling, Q. Pan-Hammarstrom, M. Sundberg, J. Lundeberg, M. Uhlen, L. Hammarstrom, and P. Nilsson. 2005. Serum microarrays for large scale screening of protein levels. Mol. Cell. Proteomics 4(12):1942-1947. Jarvinen, A.K., S. Hautaniemi, H. Edgren, P. Auvinen, J. Saarela, O.P. Kallioniemi, and O. Monni. 2004. Are data from different gene expression microarray platforms comparable? Genomics 83(6):1164-1168. Jelinsky, S.A., and L.D. Samson. 1999. Global response of Saccharomyces cerevisiae to an alkylating agent. Proc. Natl. Acad. Sci. USA 96(4):1486-1491. Jelinsky, S.A., P. Estep, G.M. Church, and L.D. Samson. 2000. Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol. Cell Biol. 20(21):8157- 8167. Jessen, B.A., J.S. Mullins, A. De Peyster, and G.J. Stevens. 2003. Assessment of hepato- cytes and liver slices as in vitro test systems to predict in vivo gene expression. Toxicol. Sci. 75(1):208-222.

230 Applications of Toxicogenomic Technologies Johnson, C.D., Y. Balagurunathan, K.P. Lu, M. Tadesse, M.H. Falahatpisheh, R.J. Carroll, E.R. Dougherty, C.A. Afshari, and K.S. Ramos. 2003. Genomic profiles and predictive biological networks in oxidant-induced atherogenesis. Physiol. Ge- nomics 13(3):263-275. Johnson, C.D., Y. Balagurunathan, M.G. Tadesse, M.H. Falahatpisheh, M. Brun, M.K. Walker, E.R. Dougherty, K.S. Ramos. 2004. Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor. Environ. Health Perspect. 112(4):403-412. Johnson, D.E., and G.H. Wolfgang. 2000. Predicting human safety: Screening and com- putational approaches. Drug Discov. Today 5(10):445-454. Jolly, R.A., K.M. Goldstein, T. Wei, H. Gao, P. Chen, S. Huang, J.M. Colet, T.P. Ryan, C.E. Thomas, and S.T. Estrem. 2005. Pooling samples within microarray studies: A comparative analysis of rat liver transcription response to prototypical toxicants. Physiol. Genomics 22(3):346-355. Jones, J.A., L. Kaphalia, M. Treinen-Moslen, and D.C. Liebler. 2003. Proteomic charac- terization of metabolites, protein adducts, and biliary proteins in rats exposed to 1,1-dichloroethylene or diclofenac. Chem. Res. Toxicol. 16(10):1306-1317. Julka, S., and F. Regnier. 2004. Quantification in proteomics through stable isotope cod- ing: A review. J. Proteome Res. 3(3):350-363. Kahn, J.D. 2005. From disparity to difference: How race-specific medicines may under- mine policies to address inequalities in health care. Southern California Interdisci- plinary Law Journal 15:105-130. Kane, M.D., T.A. Jatkoe, C.R. Stumpf, J. Lu, J.D. Thomas, and S.J. Madore. 2000. As- sessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res. 28(22):4552-4557. Kanno, J. K.I. Aisaki, K. Igarashi, N. Nakatsu, S. Kitajima, and Y. Kodama. 2005. Percellome” and “Mille-Feuille data” System for Toxicogenomics [abstract]. 5th World Congress on Alternatives & Animal Use in the Life Sciences, 5.12 Work- shop: Toxicogenomics - Potenial, Validation, and Case Studies, August 24, 2005, Berlin, Germany [online]. Available: http://www.ctw-congress.de/scripts/abs- view/abstract.php?id=25649&topic=383&kid=37-%20http://www.ctw-congress. de/scripts/abs-view/abstract.php?id=25649&topic=383&kid=37 [accessed Nov. 8, 2005]. Kardia, S.L., and C. Wang. 2005. The role of health education and behavior in public health genetics. Health Educ. Behav. 32(5):583-588. Kelleher, N.L. 2004. Top-down proteomics. Anal. Chem. 76(11):197A-203A. Keller, A., A.I. Nesvizhskii, E. Kolker, and R. Aebersold. 2002. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and da- tabase search. Anal. Chem. 74(20):5383-5392. Keller-Seitz, M.U., U. Certa, C. Sengstag, F.E. Wurgler, M. Sun, and M. Fasullo. 2004. Transcriptional response of yeast to aflatoxin B1: Recombinational repair involv- ing RAD51 and RAD1. Mol. Biol. Cell. 15(9):4321-4336. Kendziorski, C., R.A. Irizarry, K.S. Chen, J.D. Haag, and M.N. Gould. 2005. On the utility of pooling biological samples in microarray experiments. Proc. Natl. Acad Sci. USA 102(12):4252-4257. Keun, H.C., T.M. Ebbels, M.E. Bollard, O. Beckonert, H. Antti, E. Holmes, J.C. Lindon, and J.K. Nicholson. 2004. Geometric trajectory analysis of metabolic responses to toxicity can define treatment specific profiles. Chem. Res. Toxicol. 17(5):579-587.

References 231 Kiechl, S., E. Lorenz, M. Reindl, C.J. Wiedermann, F. Oberhollenzer, E. Bonora, J. Willeit, and D.A. Schwartz. 2002. Toll-like receptor 4 polymorphisms and athero- genesis. N. Engl. J. Med. 347(3):185-192. Kikkawa, R., T. Yamamoto, T. Fukushima, H. Yamada, and I. Horii. 2005. Investigation of a hepatotoxicity screening system in primary cell cultures –“What biomarkers would need to be addressed to estimate toxicity in conventional and new ap- proaches?” J. Toxicol. Sci. 30(1):61-72. Kim, H-L. 2003. Comparison of oligonucleotide-microarray and serial analysis of gene expression (SAGE) in transcript profiling analysis of megakaryocytes derived from CD34+ cells. EMM 35(5):460-466. Kim, J.Y., J. Kwon, J.E. Kim, W.S. Koh, M.K. Chung, S. Yoon, C.W. Song, and M. Lee. 2005. Identification of potential biomarkers of genotoxicity and carcinogenicity in L5178Y mouse lymphoma cells by cDNA microarray analysis. Environ. Mol. Mutagen. 45(1):80-89. Kim, S.K., J. Lund, M. Kiraly, K. Duke, M. Jiang, J.M. Stuart, A. Eizinger, B.N. Wylie, and G.S. Davidson. 2001. A gene expression map for Caenorhabditis elegans. Sci- ence 293(5537):2087-2092. Kirby, R., E.J. Cho, B. Gehrke, T. Bayer, Y.S. Park, D.P. Neikirk, J.T. McDevitt, and A.D. Ellington. 2004. Aptamer-based sensor arrays for the detection and quantita- tion of proteins. Anal. Chem. 76(14):4066-4075. Kirkpatrick, D.S., S.F. Weldon, G. Tsaprailis, D.C. Liebler, and A.J. Gandolfi. 2005. Proteomic identification of ubiquitinated proteins from human cells expressing His-tagged ubiquitin. Proteomics 5(8):2104-2111. Kleeberger, S.R. 1991. Understanding biological variability in susceptibility to respira- tory disease: Animal models. Pharmacogenetics 1(2):114-118. Kleeberger, S.R. 2003. Genetic aspects of susceptibility to air pollution. Eur. Respir. J Suppl. 40:52s-56s. Kleeberger, S.R., and B.B. Hudak. 1992. Acute ozone-induced change in airway perme- ability: Role of infiltrating leukocytes. J. Appl. Physiol. 72(2):670-676. Kleeberger, S.R., R.C. Levitt, and L.Y. Zhang. 1993a. Susceptibility to ozone-induced inflammation. I. Genetic control of the response to subacute exposure. Am. J. Physiol. 264(1 Pt 1):L15-L20. Kleeberger, S.R., R.C. Levitt, and L.Y. Zhang. 1993b. Susceptibility to ozone-induced inflammation. II. Separate loci control responses to acute and subacute exposures. Am. J. Physiol. 264(1 Pt 1):L21-L26. Kleeberger, S.R., R.C. Levitt, L.Y. Zhang, M. Longphre, J. Harkema, A. Jedlicka, S.M. Eleff, D. DiSilvestre, and K.J. Holroyd. 1997. Linkage analysis of susceptibility to ozone-induced lung inflammation in inbred mice. Nat. Genet. 17(4):475-478. Klein, A.R. 1999. A model for enhanced risk recovery in tort. Wash. Lee Law Rev. 56(4):1173-1210. Klein, R.J., C. Zeiss, E.Y. Chew, J.Y. Tsai, R.S. Sackler, C. Haynes, A.K. Henning, J.P. SanGiovanni, S.M. Mane, S.T. Mayne, M.B. Bracken, F.L. Ferris, J. Ott, C. Barnstable, and J. Hoh. 2005. Complement factor H polymorphism in age-related macular degeneration. Science 308(5720):385-389. Knoppers, B.M. 2005. Biobanking: International norms. J. Law Med. Ethics 33(1):7-14. Koskinen, H., P. Pehkonen, E. Vehniainen, A. Krasnov, C. Rexroad, S. Afanasyev, H. Molsa, and A. Oikari. 2004. Response of rainbow trout transcriptome to model chemical contaminants. Biochem. Biophys. Res. Commun. 320(3):745-753. Kramer, J.A., S.D. Pettit, R.P. Amin, T.A. Bertram, B. Car, M. Cunningham, S.W. Curtiss, J.W. Davis, C. Kind, M. Lawton, J.M. Naciff, V. Oreffo, R.J. Roman, F.D.

232 Applications of Toxicogenomic Technologies Sistare, J. Stevens, K. Thompson, A.E. Vickers, S. Wild, and C.A. Afshari. 2004. Overview on the application of transcription profiling using selected nephrotoxi- cants for toxicology assessment. Environ. Health Perspect. 112(4):460-464. Kultima, K., A.M. Nystrom, B. Scholz, A.L. Gustafson, L. Dencker, and M. Stigson. 2004. Valproic acid teratogenicity: A toxicogenomics approach. Environ. Health Perspect. 112(12):1225-1235. Kuo, W.P., T.K. Jenssen, A.J. Butte, L. Ohno-Machado, and I.S. Kohane. 2002. Analysis of matched mRNA measurements from two different microarray technologies. Bioinformatics 18(3):405-412. Kurachi, M., S. Hashimoto, A. Obata, S. Nagai, T. Nagahata, H. Inadera, H. Sone, C. Tohyama, S. Kaneko, K. Kobayashi, and K. Matsushima. 2002. Identification of 2,3,7,8-tetrachlorodibenzo-p-dioxin-responsive genes in mouse liver by serial analysis of gene expression. Biochem. Biophys. Res. Commun. 292(2):368-377. La Caze, A. 2005. Does pharmacogenomics provide an ethical challenge to the utilisation of cost-effectiveness analysis by public health systems? Pharmacoeconomics 23(5):445-447. Lakin, N.D., and S.P. Jackson. 1999. Regulation of p53 in response to DNA damage. Oncogene 18(53):7644-7655. Lam, S.H., Y.L. Wu, V.B. Vega, L.D. Miller, J. Spitsbergen, Y. Tong, H. Zhan, K.R. Govindarajan, S. Lee, S. Mathavan, K.R. Murthy, D.R. Buhler, E.T. Liu, and Z. Gong. 2006. Conservation of gene expression signatures between zebrafish and human liver tumors and tumor progression. Nat. Biotechnol. 24(1):73-75. Lame, M.W., A.D. Jones, D.W. Wilson, S.K. Dunston, and H.J. Segall. 2000. Protein targets of monocrotaline pyrrole in pulmonary artery endothelial cells. J. Biol. Chem. 275(37):29091-29099. Lander, E.S., and D. Botstein. 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121(1):185-199. Larkin, J.E., B.C. Frank, H. Gavras, R. Sultana, and J. Quackenbush. 2005. Independence and reproducibility across microarray platforms. Nat. Methods 2(5):337-344. Le, Q.T., P.D. Sutphin, S. Raychaudhuri, S.C. Yu, D.J. Terris, H.S. Lin, B. Lum, H.A. Pinto, A.C. Koong, and A.J. Giaccia. 2003. Identification of osteopontin as a prog- nostic plasma marker for head and neck squamous cell carcinomas. Clin. Cancer Res. 9(1):59-67. Le Corre, P., R.J. Parmer, M.T. Kailasam, B.P. Kennedy, T.P. Skaar, H. Ho, R. Leverge, D.W. Smith, M.G. Ziegler, P.A. Insel, N.J. Schork, D.A. Flockhart, and D.T. O’Connor. 2004. Human sympathetic activation by α2-adrenergic blockade with yohimbine: Bimodal, epistatic influence of cytochrome P450-mediated drug me- tabolism. Clin. Pharmacol. Ther. 76(2):139-153. Lee, J.S., I.S. Chu, A. Mikaelyan, D.F. Calvisi, J. Heo, J.K. Reddy, and S.S. Thorgeirsson. 2004. Application of comparative functional genomics to identify best-fit mouse models to study human cancer. Nat. Genet. 36(12):1306-1311. Lerman, C., K. Gold, J. Audrain, T.H. Lin, N.R. Boyd, C.T. Orleans, B. Wilfond, G. Louben, and N. Caporaso. 1997. Incorporating biomarkers of exposure and genetic susceptibility into smoking cessation treatment: Effects on smoking-related cogni- tions, emotions, and behavior change. Health Psychol. 16(1):87-99. Li, W.F., L.G. Costa, and C.E. Furlong. 1993. Serum paraoxonase status: A major factor in determining resistance to organophosphates. J. Toxicol. Environ. Health. 40(2- 3):337-346. Liebler, D.C. 2002a. Introduction to Proteomics: Tools for the New Biology. Totowa, NJ: Humana Press.

References 233 Liebler, D.C., and F.P. Guengerich. 2005. Elucidating mechanisms of drug-induced tox- icity. Nat. Rev. Drug Discov. 4(5):410-420. Liebler, D.C., B.T. Hansen, S.W. Davey, L. Tiscareno, and D.E. Mason. 2002. Peptide sequence motif analysis of tandem MS data with the SALSA algorithm. Anal. Chem. 74(1):203-210. Liebler, D.C., B.T. Hansen, J.A. Jones, H. Badghisi, and D.E. Mason. 2003. Mapping protein modifications with liquid chromatography-mass spectrometry and the SALSA algorithm. Adv. Protein Chem. 65:195-216. Liedberg, B., C. Nylander, and I. Lundstrom. 1995. Biosensing with surface plasmon resonance--how it all started. Biosens. Bioelectron. 10(8):i-ix. 454 Life Sciences. 2006. The 454 Genome Sequencer 20 Sequencing System [online]. Available: http://www.454.com/ [accessed Jan. 3, 2006]. Lindahl, M., B. Stahlbom, and C. Tagesson. 1995. Two-dimensional gel electrophoresis of nasal and bronchoalveolar lavage fluids after occupational exposure. Electro- phoresis 16(7):1199-1204. Lindahl, M., B. Stahlbom, and C. Tagesson. 1999. Newly identified proteins in human nasal and bronchoalveolar lavage fluids: Potential biomedical and clinical applica- tions. Electrophoresis 20(18):3670-3676. Lindon, J.C., J.K. Nicholson, E. Holmes, H. Antti, M.E. Bollard, H. Keun, O. Beckonert, T.M. Ebbels, M.D. Reily, D. Robertson, G.J. Stevens, P. Luke, A.P. Breau, G.H. Cantor, R.H. Bible, U. Niederhauser, H. Senn, G. Schlotterbeck, U.G. Sidelmann, S.M. Laursen, A. Tymiak, B.D. Car, L. Lehman-McKeeman, J.M. Colet, A. Loukaci, and C. Thomas. 2003. Contemporary issues in toxicology the role of me- tabonomics in toxicology and its evaluation by the COMET project. Toxicol. Appl. Pharmacol. 187(3):137-146. Lindon, J.C., J.K. Nicholson, E. Holmes, H.C. Keun, A. Craig, J.T. Pearce, S.J. Bruce, N. Hardy, S.A. Sansone, H. Antti, P. Jonsson, C. Daykin, M. Navarange, R.D. Beger, E.R. Verheij, A. Amberg, D. Baunsgaard, G.H. Cantor, L. Lehman-McKeeman, M. Earll, S. Wold, E. Johansson, J.N. Haselden, K. Kramer, C. Thomas, J. Lindberg, I. Schuppe-Koistinen, I.D. Wilson, M.D. Reily, D.G. Robertson, H. Senn, A. Krotzky, S. Kochhar, J. Powell, F. van der Ouderaa, R. Plumb, H. Schaefer, and M. Spraul. 2005a. Summary recommendations for standardization and reporting of metabolic analyses. Nat. Biotechnol. 23(7):833-838. Lindon, J.C., H.C. Keun, T.M. Ebbels, J.M. Pearce, E. Holmes, and J.K. Nicholson. 2005b. The Consortium for Metabonomic Toxicology (COMET): Aims, activities and achievements. Pharmacogenomics 6(7):691-699. Link, A.J., J. Eng, D.M. Schieltz, E. Carmack, G.J. Mize, D.R. Morris, B.M. Garvik, and J.R. Yates III. 1999. Direct analysis of protein complexes using mass spectrome- try. Nat. Biotechnol. 17(7):676-682. Lipshutz, R.J., S.P. Fodor, T.R. Gingeras, and D.J. Lockhart. 1999. High density syn- thetic oligonucleotide arrays. Nat. Genet. 21(Suppl. 1):20-24. Liu, H., R.G. Sadygov, and J.R. Yates III. 2004. A model for random sampling and esti- mation of relative protein abundance in shotgun proteomics. Anal. Chem. 76(14):4193-4201. Liu, J., T.M. Fujiwara, N.T. Buu, F.O. Sanchez, M. Cellier, A.J. Paradis, D. Frappier, E. Skamene, P. Gros, K. Morgan, and E. Schurr. 1995. Identification of polymor- phisms and sequence variants in the human homologue of the mouse natural resis- tance-associated macrophage protein gene. Am. J. Hum. Genet. 56(4):845-853. Livak, K.J. 1999. Allelic discrimination using fluorogenic probes and the 5' nuclease assay. Genet Anal. 14(5-6):143-149.

234 Applications of Toxicogenomic Technologies Livingston, R.J., A. von Niederhausern, A.G. Jegga, D.C. Crawford, C.S. Carlson, M.J. Rieder, S. Gowrisankar, B.J. Aronow, R.B. Weiss, and D.A. Nickerson. 2004. Pat- tern of sequence variation across 213 environmental response genes. Genome Res. 14(10A):1821-1831. Lo, H.S., Z. Wang, Y. Hu, H.H. Yang, S. Gere, K.H. Buetow, and M.P. Lee. 2003. Alle- lic variation in gene expression is common in the human genome. Genome Res.13(8):1855-1862. Lobenhofer, E.K., X. Cui, L. Bennett, P.L. Cable, B.A. Merrick, G.A. Churchill, and C.A. Afshari. 2004. Exploration of low-dose estrogen effects: Identification of No Observed Transcriptional Effect Level (NOTEL). Toxicol. Pathol. 32(4):482-492. Long, A.D., H.J. Mangalam, B.Y. Chan, L. Tolleri, G.W. Hatfield, and P. Baldi. 2001. Improved statistical inference from DNA microarray data using analysis of vari- ance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276(23):19937-19944. Lu, X., and D.P. Lane. 1993. Differential induction of transcriptionally active p53 follow- ing UV or ionizing radiation: defects in chromosome instability syndromes? Cell 75(4):765-778. Lum, P.Y., C.D. Armour, S.B. Stepaniants, G. Cavet, M.K. Wolf, J.S. Butler, J.C. Hin- shaw, P. Garnier, G.D. Prestwich, A. Leonardson, P. Garrett-Engele, C.M. Rush, M. Bard, G. Schimmack, J.W. Phillips, C.J. Roberts, and D.D. Shoemaker. 2004. Discovering modes of action for therapeutic compounds using a genome-wide screen of yeast heterozygotes. Cell 116(1):121-137. Luyendyk, J.P., W.B. Mattes, L.D. Burgoon, T.R. Zacharewski, J.F. Maddox, G.N. Cosma, P.E. Ganey, and R.A. Roth. 2004. Gene expression analysis points to he- mostasis in livers of rats cotreated with lipopolysaccharide and ranitidine. Toxicol. Sci. 80(1):203-213. MacCoss, M.J. 2005. Computational analysis of shotgun proteomics data. Curr. Opin. Chem. Biol. 9(1):88-94. MacCoss, M.J., W.H. McDonald, A. Saraf, R. Sadygov, J.M. Clark, J.J. Tasto, K.L. Gould, D. Wolters, M. Washburn, A. Weiss, J.I. Clark, and J.R. Yates III. 2002. Shotgun identification of protein modifications from protein complexes and lens tissue. Proc. Natl. Acad. Sci. USA 99(12):7900-7905. MacDonald, N., S. Chevalier, R. Tonge, M. Davison, R. Rowlinson, J. Young, S. Rayner, and R. Roberts. 2001. Quantitative proteomic analysis of mouse liver response to the peroxisome proliferator diethylhexylphthalate (DEHP). Arch. Toxicol. 75(7): 415-424. MacPhee, M., K.P. Chepenik, R.A. Liddell, K.K. Nelson, L.D. Siracusa, and A.M. Buchberg. 1995. The secretory phospholipase A2 gene is a candidate for the Mom1 locus, a major modifier of ApcMin-induced intestinal neoplasia. Cell 81(6):957-966. Mah, N., A. Thelin, T. Lu, S. Nikolaus, T. Kuhbacher, Y. Gurbuz, H. Eickhoff, G. Kloppel, H. Lehrach, B. Mellgard, C.M. Costello, and S. Schreiber. 2004. A com- parison of oligonucleotide and cDNA-based microarray systems. Physiol. Genom- ics 16(3):361-370. Mahadevan, B., C. Keshava, T. Musafia-Jeknic, A. Pecaj, A. Weston, and W.M. Baird. 2005. Altered gene expression patterns in MCF-7 cells induced by the urban dust particulate complex mixture standard reference material 1649a. Cancer Res. 65(4):1251-1258. Maitra, A., N.V. Adsay, P. Argani, C. Iacobuzio-Donahue, A. De Marzo, J.L. Cameron, C.J. Yeo, and R.H. Hruban. 2003. Multicomponent analysis of the pancreatic ade-

References 235 nocarcinoma progression model using a pancreatic intraepithelial neoplasia tissue microarray. Mod. Pathol. 16(9):902-912. Majumder, M.A. 2005. Cyberbanks and other virtual research repositories. J. Law Med. Ethics 33(1):31-39. Malek, R.L., R.B. Irby, Q.M. Guo, K. Lee, S. Wong, M. He, J. Tsai, B. Frank, E.T. Liu, J. Quackenbush, R. Jove, T.J. Yeatman, and N.H. Lee. 2002. Identification of Src transformation fingerprint in human colon cancer. Oncogene 21(47):7256-7265. Malinowski, M.J. 2005. Technology transfer in biobanking: Credits, debits, and population health futures. J. Law Med. Ethics 33(1):54-69. Malo, D., K. Vogan, S. Vidal, J. Hu, M. Cellier, E. Schurr, A. Fuks, N. Bumstead, K. Morgan, and P. Gros. 1994. Haplotype mapping and sequence analysis of the mouse Nramp gene predict susceptibility to infection with intracellular parasites. Genomics 23(1):51-61. Manly, K.F., and J.M. Olson. 1999. Overview of QTL mapping software and introduction to map manager QT. Mamm. Genome 10(4):327-334. Mann, M., and O.N. Jensen. 2003. Proteomic analysis of post-translational modifications. Nat. Biotechnol. 21(3):255-261. Manza, L.L., S.G. Codreanu, S.L. Stamer, D.L. Smith, K.S. Wells, R.L. Roberts, and D.C. Liebler. 2004. Global shifts in protein sumoylation in response to electrophile and oxidative stress. Chem. Res. Toxicol. 17(12):1706-1715. Marchant, G.E. 2000. Genetic susceptibility and biomarkers in toxic injury litigation. Jurimetrics 41(1):67-109. Marchant, G.E. 2002. Toxicogenomics and toxic torts. Trends Biotechnol. 20(8):329-332. Marchant, G.E. 2003a. Genomics and toxic substances: Part I – Toxicogenomics. Envi- ron. Law Rep. News Anal. 33(1):10071-10093. Marchant, G.E. 2003b. Genomics and toxic substances: Part II – Toxicogenomics. Envi- ron. Law Rep. News Anal. 33(9):10641-10667. Marchant, G.E. 2005. Property rights and benefit-sharing for DNA donors? Jurimetrics J. 45(2):153–178. Marchant, G.E. 2006. Genetic data in toxic tort litigation. J. Law Policy14:7-37. Margulies, M., M. Egholm, W.E. Altman, S. Attiya, J.S. Bader, L.A. Bemben, J. Berka, M.S. Braverman, Y.J. Chen, Z. Chen, S.B. Dewell, L. Du, J.M. Fierro, X.V. Gomes, B.C. Godwin, W. He, S. Helgesen, C.H. Ho, G.P. Irzyk, S.C. Jando, M.L. Alenquer, T.P. Jarvie, K.B. Jirage, J.B. Kim, J.R. Knight, J.R. Lanza, J.H. Leamon, S.M. Lefkowitz, M. Lei, J. Li, K.L. Lohman, H. Lu, V.B. Makhijani, K.E. McDade, M.P. McKenna, E.W. Myers, E. Nickerson, J.R. Nobile, R. Plant, B.P. Puc, M.T. Ronan, G.T. Roth, G.J. Sarkis, J.F. Simons, J.W. Simpson, M. Srinivasan, K.R. Tartaro, A. Tomasz, K.A. Vogt, G.A. Volkmer, S.H. Wang, Y. Wang, M.P. Weiner, P. Yu, R.F. Begley, and J.M. Rothberg. 2005. Genome se- quencing in microfabricated high-density picolitre reactors. Nature 437(7057):376- 380. Marras, S.A., F.R. Kramer, and S. Tyagi. 1999. Multiplex detection of single-nucleotide variations using molecular beacons. Genet. Anal. 14(5-6):151-156. Marsh, S., and H.L. McLeod. 2004. Pharmacogenetics of irinotecan toxicity. Pharmaco- genomics 5(7):835-843. Marsh, S., M. Xiao, J. Yu, R. Ahluwalia, M. Minton, R.R. Freimuth, P.Y. Kwok, and H.L. McLeod. 2004. Pharmacogenomic assessment of carboxylesterases 1 and 2. Genomics 84(4):661-668. Marshall, J., P. Kupchak, W. Zhu, J. Yantha, T. Vrees, S. Furesz, K. Jacks, C. Smith, I. Kireeva, R. Zhang, M. Takahashi, E. Stanton, and G. Jackowski. 2003. Processing

236 Applications of Toxicogenomic Technologies of serum proteins underlies the mass spectral fingerprinting of myocardial infarc- tion. J. Proteome Res. 2(4):361-372. Mattes, W.B. 2004. Annotation and cross-indexing of array elements on multiple plat- forms. Environ. Health Perspect. 112(4):506-510. Mattes, W.B., S.D. Pettit, S.A. Sansone, P.R. Bushel, and M.D. Waters. 2004. Database development in toxicogenomics: Issues and efforts. Environ. Health Perspect. 112(4):495-505. Mattingly, C.J., G.T. Colby, J.N. Forrest, and J.L. Boyer. 2003. The Comparative Toxi- cogenomics Database (CTD). Environ. Health. Perspect. 111(6):793-795. McCanlies, E.C., K. Kreiss, M. Andrew, and A. Weston. 2003. HLA-DPB1 and chronic beryllium disease: A HuGE review. Am. J. Epidemiol. 157(5):388-398. McGuire, A.L., and R.A. Gibbs. 2006. Genetics: No longer de-identified. Science 312(5772):370-371. McKeown-Eyssen, G., C. Baines, D.E. Cole, N. Riley, R.F. Tyndale, L. Marshall, and V. Jazmaji. 2004. Case-control study of genotypes in multiple chemical sensitivity: CYP2D6, NAT1, NAT2, PON1, PON2, and MTHFR. Int. J. Epidemiol. 33(5):971-978. Medeiros, A.M., M.G. Bird, and G. Witz. 1997. Potential biomarkers of benzene expo- sure. J. Toxicol. Environ. Health 51(6):519-539. Meek, M.E., J.R. Bucher, S.M. Cohen, V. Dellarco,R.N. Hill, L.D. Lehman-McKeeman, D.G. Longfellow, T. Pastoor, J. See, and D.E. Patto. 2003a. A framework for hu- man relevance analysis of information on carcinogenic modes of action. Crit. Rev. Toxicol. 33(6):591-653. Meek, B., A. Renwick, and C. Sonich-Mullin. 2003b. Practical application of kinetic data in risk assessment—an IPCS initiative. International Programme on Chemical Safety. Toxicol. Lett. 138(1-2):151-160. MGED Society. 2005. Microarray Gene Expression Data Society [online]. Available: http://www.mged.org [accessed Nov. 9, 2005]. MIAME. 2002. Minimum Information About a Microarray Experiment – MIAME 1.1 DRAFT 6. Version 1.1. April 1, 2002 [online]. Available: http://www.mged.org/ Workgroups/MIAME/miame_1.1.html [accessed Jan. 13, 2005]. MIAME. 2003. Minimum Information About a Microarray Experiment – MIAME for Toxicogenomics (MIAME/Tox). February 12, 2003 [online]. Available: http:// www.mged.org/MIAME1.1-DenverDraft.DOC [accessed Jan. 13, 2006]. MIAME. 2005. Minimum Information About a Microarray Experiment – MIAME. Mi- croarray Gene Expression Data Society [online]. Available: http://www.mged.org/ Workgroups/MIAME/miame.html [accessed Nov. 8, 2005]. Miller, D.P., G. Liu, I. De Vivo, T.J. Lynch, J.C. Wain, L. Su, and D.C. Christiani. 2002. Combinations of the variant genotypes of GSTP1, GSTM1 and p53 are associated with an increased lung cancer risk. Cancer Res. 62(10):2819-2823. Miller, J.C., H. Zhou, J. Kwekel, R. Cavallo, J. Burke, E.B. Butler, B.S. Teh, and B.B. Haab. 2003. Antibody microarray profiling of human prostate cancer sera: Anti- body screening and identification of potential biomarkers. Proteomics 3(1):56-63. Mimura, J., K. Yamashita, K. Nakamura, M. Morita, T.N. Takagi, K. Nakao, M. Ema, K. Sogawa, M. Yasuda, M. Katsuki, and Y. Fujii-Kuriyama. 1997. Loss of terato- genic response to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in mice lacking the Ah (dioxin) receptor. Genes Cells 2(10):645-654. Moggs, J.G., H. Tinwell, T. Spurway, H.S. Chang, I. Pate, F.L. Lim, D.J. Moore, A. Soames, R. Stuckey, R. Currie, T. Zhu, I. Kimber, J. Ashby, and G. Orphanides.

References 237 2004. Phenotypic anchoring of gene expression changes during estrogen-induced uterine growth. Environ. Health Perspect. 112(16):1589-1606. Moggs, J.G., T.C. Murphy, F.L. Lim, D.J. Moore, R. Stuckey, K. Antrobus, I. Kimber, and G. Orphanides. 2005. Anti-proliferative effect of estrogen in breast cancer cells that re-express ERalpha is mediated by aberrant regulation of cell cycle genes. J. Mol. Endocrinol. 34(2):535-551. Mohlke, K.L., W.C. Nichols, R.J. Westrick, E.K. Novak, K.A. Cooney, R.T. Swank, and D. Ginsburg. 1996. A novel modifier gene for plasma von Willebrand factor level maps to distal mouse chromosome 11. Proc. Natl. Acad. Sci. USA 93(26):15352- 15357. Montesano, R., A.E. Pegg, and G.P. Margison. 1980. Alkylation of DNA and carcino- genicity of N-nitroso compounds. J. Toxicol. Environ. Health 6(5-6): 1001-1008. Monticelli, S., K.M. Ansel, C. Xiao, N.D. Socci, A.M. Krichevsky, T.H. Thai, N. Ra- jewsky, D.S. Marks, C. Sander, K. Rajewsky, A. Rao, and K.S. Kosik. 2005. Mi- croRNA profiling of the murine hematopoietic system. Genome Biol. 6(8):R71. Mortishire-Smith, R.J., G.L. Skiles, J.W. Lawrence, S. Spence, A.W. Nicholls, B.A. Johnson, and J.K. Nicholson. 2004. Use of metabonomics to identify impaired fatty acid metabolism as the mechanism of a drug-induced toxicity. Chem. Res. Toxicol. 17(2):165-173. MSU (Michigan State University). 2007. dbZach System. Zacharewski Laboratory Bioinformatics Group, National Food Safety & Toxicology Center, Michigan State University, East Lansing MI [online]. Available: http://dbzach.fst.msu.edu/ [ac- cessed May 9, 2007]. Mukherjee, S., P. Tamayo, S. Rogers, R. Rifkin, A. Engle, C. Campbell, T.R. Golub, and J.P. Mesirov. 2003. Estimating dataset size requirements for classifying DNA mi- croarray data. J. Comput. Biol. 10(2):119-142. Myers, T.G., E.C. Dietz, N.L. Anderson, E.A. Khairallah, S.D. Cohen, and S.D. Nelson. 1995. A comparative study of mouse liver proteins arylated by reactive metabolites of acetaminophen and its nonhepatotoxic regioisomer, 3'-hydroxyacetanilide. Chem. Res. Toxicol. 8(3):403-413. Naciff, J.M., M.L. Jump, S.M. Torontali, G.J. Carr, J.P. Tiesman, G.J. Overmann, and G.P. Daston. 2002. Gene expression profile induced by 17alpha-ethynyl estradiol, bisphenol A, and genistein in the developing female reproductive system of the rat. Toxicol. Sci. 68(1):184-199. Naciff, J.M., K.A. Hess, G.J. Overmann, S.M. Torontali, G.J. Carr, J.P. Tiesman, L.M. Foertsch, B.D. Richardson, J.E. Martinez, and G.P. Daston. 2005a. Gene expres- sion changes induced in the testis by transplacental exposure to high and low doses of 17{alpha}-ethynyl estradiol, genistein, or bisphenol A. Toxicol. Sci. 86(2):396- 416. Naciff, J.M., S.M. Torontali, G.I. Overmann, G.J. Carr, J.P. Tiesman, G.P. Daston. 2005b. Evaluation of the gene expression changes induced by 17-alpha-ethynyl es- tradiol in the immature uterus/ovaries of the rat using high density oligonucleotide arrays. Birth Defects Res. B Dev. Reprod. Toxicol. 74(2):164-184. Natsoulis, G., L. El Ghaoui, G.R. Lanckriet, A.M. Tolley, F. Leroy, S. Dunlea, B.P. Eynon, C.I. Pearson, S. Tugendreich, and K. Jarnagin. 2005. Classification of a large microarray data set: Algorithm comparison and analysis of drug signatures. Genome Res. 15(5):724-736. NBAC (National Bioethics Advisory Commission). 1999. Research Involving Human Biological Materials: Ethical Issues and Policy Guidance, Vol. 1. Report and Rec- ommendations of the National Bioethics Advisory Commission. National Bio-

238 Applications of Toxicogenomic Technologies ethics Advisory Commission, Rockville, MD. August 1999 [online]. Available: http://www.georgetown.edu/research/nrcbl/nbac/hbm.pdf [accessed Aug. 29, 2006]. NCI (National Cancer Institute). 2006a. Occupational and Environmental Epidemiology Branch Overview. Division of Cancer, Epidemiology and Genetics, National Can- cer Institute [online]. Available: http://dceg.cancer.gov/occu-overview.html [ac- cessed Aug. 24, 2006]. NCI (National Cancer Institute). 2006b. Clinical Proteomic Technologies for Cancer. National Cancer Institute [online]. Available: http://proteomics.cancer.gov/ [ac- cessed Aug. 24, 2006]. NCI (National Cancer Institute). 2006c. The Mouse Models of Human Cancers Consor- tium (MMHCC). National Cancer Institute [online]. Available: http://emice.nci. nih.gov/ [accessed Aug. 13, 2006]. NCI (National Cancer Institute). 2006d. Cancer Biomedical Informatics Grid (caBIG). National Cancer Institute [online]. Available: https://cabig.nci.nih.gov/ [accessed Aug. 24, 2006]. NCSL (National Conference of State Legislatures). 2005a. State Genetic Privacy Laws [online]. Available: http://www.ncsl.org/programs/health/genetics/prt.htm [ac- cessed Nov. 8, 2005]. NCSL (National Conference of State Legislatures). 2005b. Genetic and Health Insurance State Anti-Discrimination Laws [online]. Available: http://www.ncsl.org/pro grams/health/genetics/ndishlth.htm [accessed Nov. 14, 2005]. NCSL (National Conference of State Legislatures). 2005c. State Genetic Employment Laws [online]. Available: http://www.ncsl.org/programs/health/genetics/ndiscrim. htm [accessed Nov. 14, 2005]. NCVHS (National Committee on Vital and Health Statistics). 2006. Privacy and Confi- dentiality in the Nationwide Health Information Network. Letter to Michael O. Leavitt, Secretary, U.S. Department of Health and Human Services, Washington, DC, from Simon P. Cohn, Chairman, National Committee on Vital and Health Sta- tistics. June 22, 2006 [online]. Available: http://www.ncvhs.hhs.gov/060622lt.htm [accessed Aug. 30, 2006]. Nemeth, K.A., A.V. Singh, and T.B. Knudsen. 2005. Searching for biomarkers of devel- opmental toxicity with microarrays: Normal eye morphogenesis in rodent em- bryos. Toxicol. Appl. Pharmacol. 206(2):219-228. Nesvizhskii, A.I., and R. Aebersold. 2004. Analysis, statistical validation and dissemina- tion of large-scale proteomics datasets generated by tandem MS. Drug Discov. Today 9(4):173-181. Nesvizhskii, A.I., A. Keller, E. Kolker, and R. Aebersold. 2003. A statistical model for identifying proteins by tandem mass spectrometry. Anal. Chem. 75(17):4646- 4658. Newton, R.K., M. Aardema, and J. Aubrecht. 2004. The utility of DNA microarrays for characterizing genotoxicity. Environ Health Perspect. 112(4):420-422. Nguyen, D.V., and D.M. Rocke. 2002. Tumor classification by partial least squares using microarray gene expression data. Bioinformatics 18(1):39-50. Nicholls, A.W., E. Holmes, J.C. Lindon, J.P. Shockcor, R.D. Farrant, J.N. Haselden, S.J. Damment, C.J. Waterfield, and J.K. Nicholson. 2001. Metabonomic investigations into hydrazine toxicity in the rat. Chem. Res. Toxicol. 14(8):975-987. Nicholls, A.W., R.J. Mortishire-Smith, and J.K. Nicholson. 2003. NMR spectroscopic- based metabonomic studies of urinary metabolite variation in acclimatizing germ- free rats. Chem. Res. Toxicol. 16(11):1395-1404.

References 239 Nicholson, J.K., J. Connelly, J.C. Lindon, and E. Holmes. 2002. Metabonomics: A plat- form for studying drug toxicity and gene function. Nat. Rev. Drug Discov. 1(2):153-161. Nicholson, J.K., E. Holmes, and I.D. Wilson. 2005. Gut microorganisms, mammalian metabolism and personalized health care. Nat. Rev. Microbiol. 3(5):431-438. NIH (National Institute of Health). 2007. NIH Mission [online]. Available: http://www. nih.gov/about/ [accessed April 13, 2007]. Noble, H.B. 2000. Concerns grow over reactions to lyme shots. N.Y. Times Nov. 21, 2000, F1. NRC (National Research Council). 1983. Risk Assessment in the Federal Government: Managing the Process. Washington, DC: National Academy Press. NRC (National Research Council). 1984. Toxicity Testing: Strategies to Determine Needs and Priorities. Washington, DC: National Academy Press. NRC (National Research Council). 1989. Improving Risk Communication. Washington, DC: National Academy Press. NRC (National Research Council). 1994. Science and Judgment in Risk Assessment. Washington, DC: National Academy Press. NRC (National Research Council). 2005a. Health Implications of Perchlorate Ingestion. Washington, DC: National Academy Press. NRC (National Research Council). 2005b. Reaping the Benefits of Genomic and Proteo- mic Research: Intellectual Property Rights, Innovation, and Public Health. Wash- ington, DC: The National Academies Press. NRC (National Research Council). 2005c. Toxicogenomic Technologies and Risk As- sessment of Environmental Carcinogens, A Workshop Summary. Washington, DC: The National Academies Press. NRC (National Research Council). 2005d. Communicating Toxicogenomics Information to Nonexperts. Washington, DC: The National Academies Press. NRC (National Research Council). 2006a. Toxicity Testing for Assessment of Environ- mental Agents: Interim Report. Washington, DC: The National Academies Press. NRC (National Research Council). 2006b. Health Risk from Dioxin and Related Com- pounds: Evaluation of the EPA Reassessment. Washington, DC: The National Academies Press. NRC (National Research Council). 2006d. Human Biomonitoring for Environmental Chemicals. Washington, DC: The National Academies Press. Nuwaysir, E.F., M. Bittner, J. Trent, J.C. Barrett, and C.A. Afshari. 1999. Microarrays and toxicology: The advent of toxicogenomics. Mol. Carcinog. 24(3):153-159. OECD (Organisation for Economic Co-operation and Development). 2001. Draft Guid- ance Document on the Development, Validation and Regulatory Acceptance of New and Updated Internationally Acceptable Test Methods in Hazard Assessment. Series on Testing and Assessment. OECD Environmental Health and Safety Publi- cations, Paris. OECD (Organisation for Economic Co-operation and Development). 2006. Manual for Investigation of HPV Chemicals, Chapter 2: SIDS, the SIDS Plan and the SIDS Dossier. Organisation for Economic Co-operation and Development [online]. Available: http://www.oecd.org/dataoecd/13/18/36045056.pdf [accessed May 1, 2007]. Okey, A.B., L.M. Vella, and P.A. Harper. 1989. Detection and characterization of a low affinity form of cytosolic Ah receptor in livers of mice nonresponsive to induction of cytochrome P1-450 by 3-methylcholanthrene. Mol. Pharmacol. 35(6):823-830.

240 Applications of Toxicogenomic Technologies Okey, A.B., M.A. Franc, I.D. Moffat, N. Tijet, P.C. Boutros, M. Korkalainen, J. Tuomisto, and R. Pohjanvirta. 2005. Toxicological implications of polymorphisms in receptors for xenobiotic chemicals: The case of the aryl hydrocarbon receptor. Toxicol. Appl. Pharmacol. 207(Suppl. 2):43-51. Oliver, S.G., M.K. Winson, D.B. Kell, and F. Baganz. 1998. Systematic functional analy- sis of the yeast genome. Trends Biotechnol. 16(9):373-378. Olle, E.W., A. Sreekumar, R.L. Warner, S.D. McClintock, A.M. Chinnaiyan, M.R. Bleavins, T.D. Anderson, and K.J. Johnson. 2005. Development of an internally controlled antibody microarray. Mol. Cell Proteomics 4(11):1664-1672. Ong, S.E., B. Blagoev, I. Kratchmarova, D.B. Kristensen, H. Steen, A. Pandey, and M. Mann. 2002. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1(5):376-386. Orchard, S., H. Hermjakob, R.K. Julian, Jr., K. Runte, D. Sherman, J. Wojcik, W. Zhu, and R. Apweiler. 2004. Common interchange standards for proteomics data: Pub- lic availability of tools and schema. Proteomics 4(2):490-491. Orentlicher, D. 1997. Genetic privacy in the patient-physician relationship. Pp. 77-92 in Genetic Secrets: Protecting Privacy and Confidentiality in the Genetic Era, M.A. Rothstein, ed. New Haven: Yale University Press. Orr, M.S., and U. Scherf. 2002. Large-scale gene expression analysis in molecular target discovery. Leukemia 16(4):473-477. Osmond, C., and D.J. Barker. 2000. Fetal, infant, and childhood growth are predictors of coronary heart disease, diabetes, and hypertension in adult men and women. Environ. Health Perspect. 108(Suppl. 3):545-553. Ossorio, P.N. 2004. Societal and ethical issues in pharmacogenomics. Module 2: Funda- mentals of Pharmacogenomics in Pharmacogenomics: Applications to Patient Care, R.T. Scheife, ed. Thousand Oaks, CA: Sage. Ossorio, P., and T. Duster. 2005. Race and genetics: Controversies in biomedical, behav- ioral, and forensic sciences. Am. Psychol. 60(1):115-128. Palmer, L.I. 2003. Medical liability for pharmacogenomics. Pp. 187-206 in Pharmacoge- nomics: Social, Ethical, and Clinical Dimensions, M.A. Rothstein, ed. Hoboken, NJ: John-Wiley & Sons. Palmer, L.I. 2005. Should liability play a role in social control of biobanks? J. Law Med. Ethics 33(1):70–78. Park, P.J., Y.A. Cao, S.Y. Lee, J.W. Kim, M.S. Chang, R. Hart, and S. Choi. 2004. Cur- rent issues for DNA microarrays: Platform comparison, double linear amplifica- tion, and universal RNA reference. J. Biotechnol. 112(3):225-245. Paweletz, C.P., L. Charboneau, V.E. Bichsel, N.L. Simone, T. Chen, J.W. Gillespie, M.R. Emmert-Buck, M.J. Roth, E.F. Petricoin III, and L.A. Liotta. 2001. Reverse phase protein microarrays which capture disease progression show activation of pro- survival pathways at the cancer invasion front. Oncogene 20(16):1981-1989. Pease, A.C., D. Solas, E.J. Sullivan, M.T. Cronin, C.P. Holmes, and S.P. Fodor. 1994. Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Proc. Natl. Acad. Sci. U.S.A. 91(11):5022-5026. Peden, D.B. 2000. Development of atopy and asthma: Candidate environmental influ- ences and important periods of exposure. Environ. Health Perspect. 108(Suppl 3):475-482. Pedrioli, P.G., J.K. Eng, R. Hubley, M. Vogelzang, E.W. Deutsch, B. Raught, B. Pratt, E. Nilsson, R.H. Angeletti, R. Apweiler, K. Cheung, C.E. Costello, H. Hermjakob, S. Huang, R.K. Julian, E. Kapp, M.E. McComb, S.G. Oliver, G. Omenn, N.W. Paton,

References 241 R. Simpson, R. Smith, C.F. Taylor, W. Zhu, and R. Aebersold. 2004. A common open representation of mass spectrometry data and its application to proteomics re- search. Nat. Biotechnol. 22(11):1459-1466. Pegg, A.E. 2000. Repair of O(6)-alkylguanine by alkyltransferases. Mutat. Res. 462(2- 3):83-100. Peng, J., J.E. Elias, C.C. Thoreen, L.J. Licklider, and S.P. Gygi. 2003. Evaluation of mul- tidimensional chromatography coupled with tandem mass spectrometry (LC/LC- MS/MS) for large scale protein analysis: the yeast proteome. J.Proteome Res. 2(1):43-50. Pennie, W., S.D. Pettit, and P.G. Lord. 2004. Toxicogenomics in risk assessment: An overview of an HESI collaborative research program. Environ. Health Perspect. 112(4):417-419. Pepe, M.S., R. Etzioni, Z. Feng, J.D. Potter, M.L. Thompson, M. Thornquist, M. Winget, and Y. Yasui. 2001. Phases of biomarker development for early detection of can- cer. J. Natl. Cancer Inst, 93(14):1054-1061. Perera, F., R. Santella, and M. Poirier. 1986. Biomonitoring of workers exposed to car- cinogens: Immunoassays to benzo(a)pyrene-DNA adducts as a prototype. J. Oc- cup. Med. 28(10):1117-1123. Perkins, D.N., D.J. Pappin, D.M. Creasy, and J.S. Cottrell. 1999. Probability-based pro- tein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20(18):3551-3567. Pesavento, J.J., Y.B. Kim, G.K. Taylor, and N.L. Kelleher. 2004. Shotgun annotation of histone modifications: A new approach for streamlined characterization of proteins by top down mass spectrometry. J. Am. Chem. Soc. 126(11):3386-3387. Petricoin, E.F., A.M. Ardekani, B.A. Hitt, P.J. Levine, V.A. Fusaro, S.M. Steinberg, G.B. Mills, C. Simone, D.A. Fishman, E.C. Kohn, and L.A. Liotta. 2002a. Use of pro- teomic patterns in serum to identify ovarian cancer. Lancet 359(9306):572-527. Petricoin, E.F., D.K. Ornstein, C.P. Paweletz, A. Ardekani, P.S. Hackett, B.A. Hitt, A. Velassco, C. Trucco, L. Wiegand, K. Wood, C.B. Simone, P.J. Levine, W.M. Linehan, M.R. Emmert-Buck, S.M. Steinberg, E.C. Kohn, and L.A. Liotta. 2002b. Serum proteomic patterns for detection of prostate cancer. J. Natl. Cancer Inst. 94(20):1576-1578. Petricoin, E.F., J.L. Hackett, L.J. Lesko, R.K. Puri, S.I. Gutman, K. Chumakov, J. Woodcock, D.W. Feigal, Jr., K.C. Zoon, and F.D. Sistare. 2002c. Medical applica- tions of microarray technologies: A regulatory science perspective. Nat. Genet. 32(Suppl.):474-479. Phillips, M.S., R. Lawrence, R. Sachidanandam, A.P. Morris, D.J. Balding, M.A. Donaldson, J.F. Studebaker, W.M. Ankener, S.V. Alfisi, F.S. Kuo, A.L. Camisa, V. Pazorov, K.E. Scott, B.J. Carey, J. Faith, G. Katari, H.A. Bhatti, J.M. Cyr, V. Derohannessian, C. Elosua, A.M. Forman, N.M. Grecco, C.R. Hock, J.M. Kuebler, J.A. Lathrop, M.A. Mockler, E.P. Nachtman, S.L. Restine, S.A. Varde, M.J. Hozza, C.A. Gelfand, J. Broxholme, G.R. Abecasis, M.T. Boyce-Jacino, and L.R. Cardon. 2003. Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet. 33(3):382-387. Pinkerton, K.E., and J.P. Joad. 2000. The mammalian respiratory system and critical windows of exposure for children's health. Environ. Health Perspect. 108(Suppl. 3):457-462. Plumb, R.S., C.L. Stumpf, M.V. Gorenstein, J.M. Castro-Perez, G.J. Dear, M. Anthony, B.C. Sweatman, S.C. Connor, and J.N. Haselden. 2002. Metabonomics: The use of electrospray mass spectrometry coupled to reversed-phase liquid chromatography

242 Applications of Toxicogenomic Technologies shows potential for the screening of rat urine in drug development. Rapid Com- mun. Mass Spectrom. 16(20):1991-1996. Potter, J.D. 2004. Toward the last cohort. Cancer Epidemiol. Biomarkers Prev. 13(6):895-897. Prows, D.R., and G.D. Leikauf. 2001. Quantitative trait analysis of nickel-induced acute lung injury in mice. Am. J. Respir. Cell. Mol. Biol. 24(6):740-746. Prows, D.R., H.G. Shertzer, M.J. Daly, C.L. Sidman, and G.D. Leikauf. 1997. Genetic analysis of ozone-induced acute lung injury in sensitive and resistant strains of mice. Nat. Genet. 17(4):471-474. Prows, D.R., M.J. Daly, H.G. Shertzer, and G.D. Leikauf. 1999. Ozone-induced acute lung injury: Genetic analysis of F(2) mice generated from A/J and C57BL/6J strains. Am. J. Physiol. 277(2 Pt 1):L372-L380. Puga, A., A. Maier, and M. Medvedovic. 2000. The transcriptional signature of dioxin in human hepatoma HepG2 cells. Biochem. Pharmacol. 60(8):1129-1142. Qian, X., B.W. Scheithauer, K. Kovacs, and R.V. Lloyd. 2005. DNA microarrays: Recent developments and applications to the study of pituitary tissues. Endocrine 28(1):49-56. Qiu, Y., L.Z. Benet, and A.L. Burlingame. 1998. Identification of the hepatic protein targets of reactive metabolites of acetaminophen in vivo in mice using two- dimensional gel electrophoresis and mass spectrometry. J. Biol. Chem. 273(28): 17940-17953. Radich, J.P., M. Mao, S. Stepaniants, M. Biery, J. Castle, T. Ward, G. Schimmack, S. Kobayashi, M. Carleton, J. Lampe, and P.S. Linsley. 2004. Individual-specific variation of gene expression in peripheral blood leukocytes. Genomics 83(6):980- 988. Ramachandran, N., E. Hainsworth, B. Bhullar, S. Eisenstein, B. Rosen, A.Y. Lau, J.C. Walter, and J. LaBaer. 2004. Self-assembling protein microarrays. Science 305(5680):86-90. Ramaswamy, S., P. Tamayo, R. Rifkin, S. Mukherjee, C.H. Yeang, M. Angelo, C. Ladd, M. Reich, E. Latulippe, J.P. Mesirov, T. Poggio, W. Gerald, M. Loda, E.S. Lander, and T.R. Golub. 2001. Multiclass cancer diagnosis using tumor gene expression signatures. Proc. Natl. Acad. Sci. USA 98(26):15149-15154. Ramsahoye, B.H. 2002. Measurement of genome wide DNA methylation by reversed- phase high-performance liquid chromatography. Methods 27(2):156-161. Ranish, J.A., E.C. Yi, D.M. Leslie, S.O. Purvine, D.R. Goodlett, J. Eng, and R. Aebersold. 2003. The study of macromolecular complexes by quantitative pro- teomics. Nat. Genet. 33(3):349-355. Raychaudhuri, S., J.M. Stuart, and R.B. Altman. 2000. Principal components analysis to summarize microarray experiments: Application to sporulation time series. Pac. Symp. Biocomput. (2000):455-466. Reeder, C.E., and W.M. Dickson. 2003. Economic implications on pharmacogenomics. Pp. 229-250 in Pharmacogenomics: Social, Ethical, and Clinical Dimensions, M.A. Rothstein, ed. Hoboken, NJ: John-Wiley & Sons. Renegar, G., C.J. Webster, S. Stuerzebecher, L. Harty, S.E. Ide, B. Balkite, T.A. Rogalski-Salter, N. Cohen, B.B. Spear, D.M. Barnes, and C. Brazell. 2006. Re- turning genetic research results to individuals: Points-to-consider. Bioethics 20(1):24-36. Renwick, A.G., and N.P. Lazarus. 1998. Human variability and noncancer risk assess- ment-an analysis of the default uncertainty factor. Regul. Toxicol. Pharmacol. 27(1 Pt. 1):3-20.

References 243 Righetti, P.G., and A. Bossi. 1997. Isoelectric focusing in immobilized pH gradients: Recent analytical and preparative developments. Anal. Biochem. 247(1):1-10. Robosky, L.C., D.F. Wells, L.A. Egnash, M.L. Manning, M.D. Reily, and D.G. Robertson. 2005. Metabonomic identification of two distinct phenotypes in Spra- gue-Dawley (Crl:CD[SD]) rats. Toxicol. Sci. 87(1):277-284. Rogojina, A.T., W.E. Orr, B.K. Song, and E.E. Geisert, Jr. 2003. Comparing the use of Affymetrix to spotted oligonucleotide microarrays using two retinal pigment epi- thelium cell lines. Mol. Vis. 9:482-496. Rose, G. 1994. The Strategy of Preventive Medicine. New York: Oxford University Press. Rothstein, M.A. 1996. Preventing the discovery of plaintiff genetic profiles by defendants seeking to limit damages in personal injury litigation. Indiana Law J. 71(4):877- 910. Rothstein, M.A. 1997. Genetic secrets: A policy framework. Pp. 461-495 in Genetic Se- crets: Protecting Privacy and Confidentiality in the Genetic Era, M.A. Rothstein, ed. New Haven: Yale University Press. Rothstein, M.A. 1998. Genetic privacy and confidentiality: Why they are so hard to pro- tect. J. Law Med. Ethics 26(3):198-201. Rothstein, M.A. 2000a. Ethical guidelines for medical research on workers. J. Occup. Environ. Med. 42(12):1166-1171. Rothstein, M.A. 2000b. Genetics and the work force of the next hundred years. Columbia Bus. Law Rev. 3:371-402. Rothstein, M.A. 2003. Epilogue: Policy prescriptions. Pp. 319-336 in Pharmacogenom- ics: Social, Ethical, and Clinical Dimensions, M.A. Rothstein, ed. Hoboken, NJ: John-Wiley & Sons. Rothstein, M.A. 2005a. Currents in contemporary ethics: Research privacy under HIPAA and the common rule. J. Law Med. Ethics 33(1):154-159. Rothstein, M.A. 2005b. Expanding the ethical analysis of biobanks. J. Law Med. Ethics 33(1):89-101. Rothstein, M.A., and P.G. Epps. 2001a. Pharmacogenomics and the (ir)relevance of race. Pharmacogenomics J. 1(2):104-108. Rothstein, M.A., and P.G. Epps. 2001b. Ethical and legal implications of pharmacoge- nomics. Nat. Rev. Genet. 2(3):228-231. Rothstein, M.A., and C.A. Hornung. 2004. Public attitudes. Pp. 1-25 in Genetics and Life Insurance: Medical Underwriting and Social Policy, M.A. Rothstein, ed. Cam- bridge, MA: MIT Press. Rothstein, M.A., and M.K. Talbott. 2006. Compelled disclosure of health information: Protecting against the greatest potential threat to privacy. JAMA 295(24):2882- 2885. Royal Society. 2005. Personalized Medicine: Hopes and Realities. Policy report. The Royal Society, London. September 2005 [online]. Available: http://www.royal soc.ac.uk/displaypagedoc.asp?id=17570. Ruepp, S.U., R.P. Tonge, J. Shaw, N. Wallis, and F. Pognan. 2002. Genomics and pro- teomics analysis of acetaminophen toxicity in mouse liver. Toxicol. Sci. 65(1):135-150. Ruepp, S., F. Boess, L. Suter, M.C. de Vera, G. Steiner, T. Steele, T. Weiser, and S. Al- bertini. 2005. Assessment of hepatotoxic liabilities by transcript profiling. Toxicol. Appl. Pharmacol. 207(2 Suppl.):161-170.

244 Applications of Toxicogenomic Technologies Saal, L.H., C. Troein, J. Vallon-Christersson, S. Gruvberger, A. Borg, and C. Peterson. 2002. BioArray Software Environment (BASE): A platform for comprehensive management and analysis of microarray data. Genome Biol. 3(8):SOFTWARE 0003. Sadygov, R.G., D. Cociorva, and J.R. Yates III. 2004. Large-scale database searching using tandem mass spectra: Looking up the answer in the back of the book. Nat. Methods 1(3):195-202. Saeed, A.I., V. Sharov, J. White, J. Li, W. Liang, N. Bhagabati, J. Braisted, M. Klapa, T. Currier, M. Thiagarajan, A. Sturn, M. Snuffin, A. Rezantsev, D. Popov, A. Ryltsov, E. Kostukovich, I. Borisovsky, Z. Liu, A. Vinsavich, V. Trush, and J. Quackenbush. 2003. TM4: A free, open-source system for microarray data man- agement and analysis. Biotechniques 34(2):374-378. Safe, S. 1990. Polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs) and related compounds: Environmental and mechanistic considerations which support the development of toxic equivalency factors (TEFs). CRC Crit. Rev. Toxicol. 21(1):51-88. Said, M.R., T.J. Begley, A.V. Oppenheim, D.A. Lauffenburger, and L.D. Samson. 2004. Global network analysis of phenotypic effects: Protein networks and toxicity modulation in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 101(52): 18006-18011. Salerno, R.A., and L.J. Lesko. 2004. Pharmacogenomics in Drug Development and Regulatory Decision-making: The Genomic Data Submission (GDS) Proposal. Pharmacogenomics 5(1):25-30. Sanger, F., S. Nicklen, and A.R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74(12):5463-5467. Sansone, S.A., N. Morrison, P. Rocca-Serra, and J. Fostel. 2004. Standardization initia- tives in the (eco)toxicogenomics domain: A review. Comp. Funct. Genomics 5(8):633-641. Saul, S. 2005. U.S. to Review Drug Intended for One Race. N.Y. Times, P.1. June 13, 2005. Savoie, C.J., S. Aburatani, S. Watanabe, Y. Eguchi, S. Muta, S. Imoto, S. Miyano, S. Kuhara, and K. Tashiro. 2003. Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades. DNA Res. 10(1):19-25. Sawada, H., K. Takami, and S. Asahi. 2005. A toxicogenomic approach to drug-induced phospholipidosis: Analysis of its induction mechanism and establishment of a novel in vitro screening system. Toxicol. Sci. 83(2):282-292. Scarano, M.I., M. Strazzullo, M.R. Matarazzo, and M. D'Esposito. 2005. DNA methyla- tion 40 years later: Its role in human health and disease. J. Cell Physiol. 204(1):21- 35. Schadt, E.E., C. Li, B. Ellis, and W.H. Wong. 2001. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell Biochem. (Suppl 37):120-125. Schechtman, L.M. 2005. Toxicogenomics: ICCVAM Fundamentals for Validation and Regulatory Acceptance. Presentation at NAS Workshop onValidation of Toxico- genomic Technologies: A Focus on Chemical Classification Strategies, July 7-8, 2005, Washington, DC. Schena, M., D. Shalon, R.W. Davis, and P.O. Brown. 1995. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467-470.

References 245 Schena, M., D. Shalon, R. Heller, A. Chai, P.O. Brown, and R.W. Davis. 1996. Parallel human genome analysis: Microarray-based expression monitoring of 1000 genes. Proc. Natl. Acad. Sci. U.S.A. 93(20):10614-10619. Schubert, E.L., L. Hsu, L.A. Cousens, J. Glogovac, S. Self, B.J. Reid, P.S. Rabinovitch, and P.L. Porter. 2002. Single nucleotide polymorphism array analysis of flow- sorted epithelial cells from frozen versus fixed tissues for whole genome analysis of allelic loss in breast cancer. Am. J. Pathol. 160(1):73-79. Searfoss, G.H., W.H. Jordan, D.O. Calligaro, E.J. Galbreath, L.M. Schirtzinger, B.R. Berridge, H. Gao, M.A. Higgins, P.C. May, and T.P. Ryan. 2003. Adipsin, a bio- marker of gastrointestinal toxicity mediated by a functional gamma-secretase in- hibitor. J. Biol. Chem. 278(46):46107-46116. Searle, S., and J.M. Blackwell. 1999. Evidence for a functional repeat polymorphism in the promoter of the human NRAMP1 gene that correlates with autoimmune versus infectious disease susceptibility. J. Med. Genet. 36(4):295-299. Searfoss, G.H., Jordan, W.H., Calligaro, D.O., Galbreath, E.J., Schirtzinger, L.M., Ber- ridge, B.R., Gao, H., Higgins, M.A., May, P.C., and Ryan, T.P. 2003. Adipsin, a Biomarker of Gastrointestinal Toxicity Mediated by a Functional -Secretase In- hibitor. J. Biol. Chem. 278:46107-46116. Sen, B., A. Wang, S.D. Hester, JL. Robertson, and D.C. Wolf. 2005. Gene expression profiling of responses to dimethylarsinic acid in female F344 rat urothelium. Toxi- cology 215(3):214-226. Shannon, P., A. Markiel, O. Ozier, N.S. Baliga, J.T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: A software environment for inte- grated models of biomolecular interaction networks. Genome Res. 13(11):2498- 2504. Shaw, M.A., D. Clayton, S.E. Atkinson, H. Williams, N. Miller, D. Sibthorpe, and J.M. Blackwell. 1996. Linkage of rheumatoid arthritis to the candidate gene NRAMP1 on 2q35. J. Med. Genet. 33(8):672-677. Shendure, J., G.J. Porreca, N.B. Reppas, X. Lin, J.P. McCutcheon, A.M. Rosenbaum, M.D. Wang, K. Zhang, R.D. Mitra, and G.M. Church. 2005. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309(5741):1728-1732. Shiloh, S. 1996. Decision-making in the context of genetic risk. Pp. 82-103 in The Trou- bled Helix: Social and Psychological Implications of the New Human Genetics, T. Marteau, and M. Richards, eds. Cambridge: Cambridge University Press. Shingara, J., K. Keiger, J. Shelton, W. Laosinchai-Wolf, P. Powers, R. Conrad, D. Brown, and E. Labourier. 2005. An optimized isolation and labeling platform for accurate microRNA expression profiling. RNA 11(9):1461-1470. Shippy, R., T.J. Sendera, R. Lockner, C. Palaniappan, T. Kaysser-Kranich, G. Watts, and J. Alsobrook. 2004. Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. BMC Genomics 5(1):61. Shmulevich, I., E.R. Dougherty, S. Kim, and W. Zhang. 2002a. Probabilistic Boolean Networks: A rule-based uncertainty model for gene regulatory networks. Bioin- formatics 18(2):261-274. Shmulevich, I., E.R. Dougherty, and W. Zhang. 2002b. Gene perturbation and interven- tion in probabilistic Boolean networks. Bioinformatics 18(10):1319-1331. Shugart, L., J.M. Holland, and R.O. Rahn. 1983. Dosimetry of PAH skin carcinogenesis: Covalent binding of benzo[a]pyrene to mouse epidermal DNA. Carcinogenesis 4(2):195-198.

246 Applications of Toxicogenomic Technologies Shukla, S.J., and M.E. Dolan. 2005. Use of CEPH and non-CEPH lymphoblast cell lines in pharmacogenetic studies. Pharmacogenomics 6(3):303-310. Sidransky, D., R. Irizarry, J.A. Califano, X. Li, H. Ren, N. Benoit, and L. Mao. 2003. Serum protein MALDI profiling to distinguish upper aerodigestive tract cancer pa- tients from control subjects. J. Natl. Cancer Inst. 95(22):1711-1717. Silver, L.M. 1995. Mouse Genetics: Concepts and Applications. New York: Oxford Uni- versity Press. Simon, R., M.D. Radmacher, and K. Dobbin. 2002. Design of studies using DNA mi- croarrays. Genet. Epidemiol. 23(1):21-36. Simon, R., M.D. Radmacher, K. Dobbin, and L.M. McShane. 2003. Pitfalls in the use of DNA microarray data for diagnostic and prognostic classification. J. Natl. Cancer. Inst. 95(1):14-18. Skipper, P.L., X. Peng, C.K. Soohoo, and S.R. Tannenbaum. 1994. Protein adducts as biomarkers of human carcinogen exposure. Drug Metab. Rev. 26(1-2):111-124. SMD. 2006. Stanford MicroArray Database. Departments of Biochemistry and Genetics at the School of Medicine, Stanford University [online]. Available: http://genome- www5.stanford.edu/ [accessed Aug. 24, 2006]. Smith, D., B.D. Collins, J. Heil, and T.H. Koch. 2003. Sensitivity and specificity of photoaptamer probes. Mol. Cell. Proteomics 2(1):11-18. Smith, R.D. 2002. Trends in mass spectrometry instrumentation for proteomics. Trends Biotechnol. 20(Suppl. 12):S3-S7. Soinov, L.A. 2003. Supervised classification for gene network reconstruction. Biochem. Soc. Trans. 31(Pt 6):1497-1502. Sorenson, J.R., and B. Cheuvront. 1993. The Human Genome Project and health behavior and health education research. Health Educ. Res. 8(4):589-593. Soukas, A., P. Cohen, N.D. Socci, and J.M. Friedman. 2000. Leptin-specific patterns of gene expression in white adipose tissue. Genes. Dev. 14(8):963-980. Spellman, P.T., M. Miller, J. Stewart, C. Troup, U. Sarkans, S. Chervitz, D. Bernhart, G. Sherlock, C. Ball, M. Lepage, M. Swiatek, W.L. Marks, J. Goncalves, S. Markel, D. Iordan, M. Shojatalab, A. Pizarro, J. White, R. Hubley, E. Deutsch, M. Senger, B.J. Aronow, A. Robinson, D. Bassett, C.J. Stoeckert, Jr., and A. Brazma. 2002. Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3(9):RESEARCH0046. Stahl, D.C., K.M. Swiderek, M.T. Davis, and T.D. Lee. 1996. Data-controlled automation of liquid chromatography/tandem mass spectrometry analysis of peptide mixtures. J. Am. Soc. Mass Spectrom. 7(6):532-540. Stearman, R.S., L. Dwyer-Nield, L. Zerbe, S.A. Blaine, Z. Chan, P.A. Bunn, Jr., G.L. Johnson, F.R. Hirsch, D.T. Merrick, W.A. Franklin, A.E. Baron, R.L. Keith, R.A. Nemenoff, A.M. Malkinson, and M.W. Geraci. 2005. Analysis of orthologous gene expression between human pulmonary adenocarcinoma and a carcinogen- induced murine model. Am. J. Pathol. 167(6):1763-1775. Steiner, G., L. Suter, F. Boess, R. Gasser, M.C. de Vera, S. Albertini, and S. Ruepp. 2004. Discriminating different classes of toxicants by transcript profiling. Environ. Health Perspect. 112(12):1236-1248. Stoyanova, R., J.K. Nicholson, J.C. Lindon, and T.R. Brown. 2004. Sample classification based on Bayesian spectral decomposition of metabonomic NMR data sets. Anal. Chem. 76(13):3666-3674. Stribinskis, V., and K.S. Ramos. 2006. Activation of human long interspersed nuclear element 1 retrotransposition by benzo(a)pyrene, an ubiquitous environmental car- cinogen. Cancer Res. 66(5):2616-2620.

References 247 Strouse, D.S. 2005. Informed consent to genetic research on banked human tissue. Juri- metrics 45:135-152. Stuart, J.M., E. Segal, D. Koller, and S.K. Kim. 2003. A gene-coexpression network for global discovery of conserved genetic modules. Science 302(5643):249-255. Suchard, M.A., P. Yudkin, and J.S. Sinsheimer. 1999. Are general practitioners willing and able to provide genetic services for common diseases? J. Genet. Couns. 8(5):301-311. Sun, Y.V., D.R. Boverhof, L.D. Burgoon, M.R. Fielden, and T.R. Zacharewski. 2004. Comparative analysis of dioxin response elements in human, mouse and rat ge- nomic sequences. Nucl. Acids Res. 32(15):4512-4523. Suter, L., M. Haiker, M.C. De Vera, and S. Albertini. 2003. Effect of two 5-HT6 receptor antagonists on the rat liver: A molecular approach. Pharmacogenomics J. 3(6):320- 334. Suter, L., L.E. Babiss, and E.B. Wheeldon. 2004. Toxicogenomics in predictive toxicol- ogy in drug development. Chem. Biol. 11(2):161-171. Sutherland, J.E., and M. Costa. 2003. Epigenetics and the environment. Ann. N.Y. Acad. Sci. 983:151-160. Sweet-Cordero, A., S. Mukherjee, A. Subramanian, H. You, J.J. Roix, C. Ladd-Acosta, J. Mesirov, T.R. Golub, and T. Jacks. 2005. An oncogenic KRAS2 expression signa- ture identified by cross-species gene-expression analysis. Nat. Genet. 37(1):48-55. Syka, J.E., J.A. Marto, D.L. Bai, S. Horning, M.W. Senko, J.C. Schwartz, B. Ueberheide, B. Garcia, S. Busby, T. Muratore, J. Shabanowitz, and D.F. Hunt. 2004a. Novel linear quadrupole ion trap/FT mass spectrometer: Performance characterization and use in the comparative analysis of histone H3 post-translational modifications. J. Proteome Res. 3(3):621-626. Syka, J.E., J.J. Coon, M.J. Schroeder, J. Shabanowitz, and D.F. Hunt. 2004b. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl. Acad. Sci. USA 101(26):9528-9533. Syvanen, A.C. 2005. Toward genome-wide SNP genotyping. Nat. Genet. 37 (Suppl.):S5- S10. Tamada, Y., S. Kim, H. Bannai, S. Imoto, K. Tashiro, S. Kuhara, and S. Miyano. 2003. Estimating gene networks from gene expression data by combining Bayesian net- work model with promoter element detection. Bioinformatics 19(Suppl. 2):II227- II236. Tamayo, P., D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E.S. Lander, and T.R. Golub. 1999. Interpreting patterns of gene expression with self- organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. USA 96(6):2907-2912. Tan, P.K., T.J. Downey, E.L. Spitznagel, Jr., P. Xu, D. Fu, D.S. Dimitrov, R.A. Lempicki, B.M. Raaka, and M.C. Cam. 2003. Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res. 31(19):5676-5684. Taylor, C.F., N.W. Paton, K.L. Garwood, P.D. Kirby, D.A. Stead, Z. Yin, E.W. Deutsch, L. Selway, J. Walker, I. Riba-Garcia, S. Mohammed, M.J. Deery, J.A. Howard, T. Dunkley, R. Aebersold, D.B. Kell, K.S. Lilley, P. Roepstorff, J.R. Yates III, A. Brass, A.J. Brown, P. Cash, S.J. Gaskell, S.J. Hubbard, and S.G. Oliver. 2003. A systematic approach to modeling, capturing, and disseminating proteomics ex- perimental data. Nat. Biotechnol. 21(3):247-254.

248 Applications of Toxicogenomic Technologies Tennant, R.W. 2002. The National Center for Toxicogenomics: Using new technologies to inform mechanistic toxicology [editorial]. Environ. Health Perspect.110(1):A8- A10. Teuschler, L., J. Klaunig, E. Carney, J. Chambers, R. Conolly, C. Gennings, J. Giesy, R. Hertzberg, C. Klaassen, R. Kodell, D. Paustenbach, and R. Yang. 2002. Support of science-based decisions concerning the evaluation of the toxicology of mixtures: A new beginning. Regul. Toxicol. Pharmacol. 36(1):34-39. Thackaberry, E.A., Z. Jiang, C.D. Johnson, K.S. Ramos, and M.K. Walker. 2005. Toxi- cogenomic profile of 2,3,7,8-tetrachlorodibenzo-p-dioxin in the murine fetal heart: Modulation of cell cycle and extracellular matrix genes. Toxicol. Sci. 88(1):231- 241. Theilhaber, J., T. Connolly, S. Roman-Roman, S. Bushnell, A. Jackson, K. Call, T. Garcia, and R. Baron. 2002. Finding genes in the C2C12 osteogenic pathway by k- nearest-neighbor classification of expression data. Genome Res. 12(1):165-176. Thomas, D.B., D.L. Gao, S.G. Self, C.J. Allison, Y. Tao, J. Mahloch, R. Ray, Q. Qin, R. Presley, and P. Porter. 1997. Randomized trial of breast self-examination in Shanghai: Methodology and preliminary results. J. Natl. Cancer Inst. 89(5):355- 365. Thomas, R.S., D.R. Rank, S.G. Penn, G.M. Zastrow, K.R. Hayes, K. Pande, E. Glover, T. Silander, M.W. Craven, J.K. Reddy, S.B. Jovanovich, and C.A. Bradfield. 2001. Identification of toxicologically predictive gene sets using cDNA microarrays. Mol. Pharmacol. 60(6):1189-1194. Thompson, K.L., C.A. Afshari, R.P. Amin, T.A. Bertram, B. Car, M. Cunningham, C. Kind, J.A. Kramer, M. Lawton, M. Mirsky, J.M. Naciff , V. Oreffo, P.S. Pine, and F.D. Sistare. 2004. Identification of platform-independent gene expression markers of cisplatin nephrotoxicity. Environ. Health Perspect. 112(4):488-494. Thorgeirsson, S.S., J.S. Lee, and J.W. Grisham. 2006. Functional genomics of hepatocel- lular carcinoma. Hepatology 43(2 Suppl. 1):S145-S150. Thukral, S.K., P.J. Nordone, R. Hu, L. Sullivan, E. Galambos, V.D. Fitzpatrick, L. Healy, M.B. Bass, M.E. Cosenza, and C.A. Afshari. 2005. Prediction of nephrotoxicant action and identification of candidate toxicity-related biomarkers. Toxicol. Pathol. 33(3):343-355. Timchalk, C., A. Kousba, and T. S. Poet. 2002. Monte Carlo analysis of the human chlorpyrifos-oxonase (PON1) polymorphism using a physiologically based phar- macokinetic and pharmacodynamic (PBPK/PD) model. Toxicol. Lett. 135(1-2):51- 59. Todd, J.A., T.J. Aitman, R.J. Cornall, S. Ghosh, J.R. Hall, C.M. Hearne, A.M. Knight, J.M. Love, M.A. McAleer, J.B. Prins, M. Rodriguez, A. Lathrop, A. Pressey, N.H. DeLarato, L.B. Peterson, and L.S. Wicker. 1991. Genetic analysis of autoimmune type 1 diabetes mellitus in mice. Nature 351(6327):542-547. Tonge, R., J. Shaw, B. Middleton, R. Rowlinson, S. Rayner, J. Young, F. Pognan, E. Hawkins, I. Currie, and M. Davison. 2001. Validation and development of fluores- cence two-dimensional differential gel electrophoresis proteomics technology. Pro- teomics 1(3):377-396. Toronen, P., M. Kolehmainen, G. Wong, and E. Castren. 1999. Analysis of gene expres- sion data using self-organizing maps. FEBS Lett. 451(2):142-146. TRC (Toxicogenomics Research Consortium). 2003. TRC Member Publications. Toxi- cogenomics Research Consortium. Division of Extramural Research and Training, National Institute of Environmental Health Sciences [online]. Available: http:// www.niehs.nih.gov/dert/trc/pub-mem.htm [accessed May 9, 2007].

References 249 TRC (Toxicogenomics Research Consortium). 2005. Toxicogenomics Research Consor- tium. Division of Extramural Research and Training, National Institute of Envi- ronmental Health Sciences [online]. Available: http://www.niehs.nih.gov/dert/trc/ home.htm [accessed Feb. 28, 2006]. Tusher, V.G., R. Tibshirani, and G. Chu. 2001. Significance analysis of microarrays ap- plied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98(9):5116- 5121. UK Biobank Limited. 2007. Biobank: Improving the Health of Future Generation [online]. Available: http://www.ukbiobank.ac.uk/ [accessed Sept. 28, 2007]. Ulrich, R., and S.H. Friend. 2002. Toxicogenomics and drug discovery: Will new tech- nologies help us produce better drugs? Nat. Rev. Drug Discov. 1(1):84-88. Ulrich, R.G., J.C. Rockett, G.G. Gibson, and S.D. Pettit. 2004. Overview of an interlabo- ratory collaboration on evaluating the effects of model hepatotoxicants on hepatic gene expression. Environ. Health Perspect. 112(4):423-427. Urushidani, T., and T. Nagao. 2005. Toxicogenomics: Japanese initiative. Pp. 623-631 in Handbook of Toxicogenomics: Strategies and Applications, J. Borlak, ed. Wein- heim: Wiley-VCH. UW-Madison (University of Wisconsin at Madison). 2006. Edge2: The Environment, Drugs and Gene Expression. Bradfield Laboratory, University of Wisconsin at Madison [online]. Available: http://edge.oncology.wisc.edu/edge.php [accessed May 9, 2007]. Uzumcu, M., H. Suzuki, and M.K. Skinner. 2004. Effect of the anti-androgenic endocrine disruptor vinclozolin on embryonic testis cord formation and postnatal testis de- velopment and function. Reprod. Toxicol. 18(6):765-774. van Delft, J.H., E. van Agen, S.G. van Breda, M.H. Herwijnen, Y.C. Staal, and J.C. Kleinjans. 2005. Comparison of supervised clustering methods to discriminate genotoxic from non-genotoxic carcinogens by gene expression profiling. Mutat. Res. 575(1-2):17-33. van de Peppel, J., P. Kemmeren, H. van Bakel, M. Radonjic, D. van Leenen, F.C. Holstege. 2003. Monitoring global messenger RNA changes in externally con- trolled microarray experiments. EMBO Rep. 4(4):387-393. van de Vijver, M.J., Y.D. He, L.J. van't Veer, H. Dai, A.A. Hart, D.W. Voskuil, G.J. Schreiber, J.L. Peterse, C. Roberts, M.J. Marton, M. Parrish, D. Atsma, A. Witteveen, A. Glas, L. Delahaye, T. van der Velde, H. Bartelink, S. Rodenhuis, E.T. Rutgers, S.H. Friend, and R. Bernards. 2002. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347(25):1999-2009. van de Waterbeemd, H., and E. Gifford. 2003. ADMET in silico modelling: Towards prediction paradise? Nat. Rev. Drug Discov. 2(3):192-204. van Leeuwen, A., P.I. Schrier, M.J. Giphart, I.A. Noordermeer, D.J. Ruiter, P. Rubin- stein, and J.J. van Rood. 1986. TCA: A polymorphic genetic marker in leukemias and melanoma cell lines. Blood 67(4):1139-1142. van 't Veer, L.J., H. Dai, M.J. van de Vijver, Y.D. He, A.A. Hart, M. Mao, H.L. Peterse, K. van der Kooy, M.J. Marton, A.T. Witteveen, G.J. Schreiber, R.M. Kerkhoven, C. Roberts, P.S. Linsley, R. Bernards, and S.H. Friend. 2002. Gene expression pro- filing predicts clinical outcome of breast cancer. Nature 415(6871):530-536. Venter, J.C., H.O. Smith, and L. Hood. 1996. A new strategy for genome sequencing. Nature 381(6581):364-366. Vezina, C.M., N.J. Walker, and J.R. Olson. 2004. Subchronic exposure to TCDD, PeCDF, PCB126, and PCB153: Effect on hepatic gene expression. Environ. Health Perspect. 112(16):1636-1644.

250 Applications of Toxicogenomic Technologies Villanueva, J., J. Philip, D. Entenberg, C.A. Chaparro, M.K. Tanwar, E.C. Holland, and P. Tempst. 2004. Serum peptide profiling by magnetic particle-assisted, automated sample processing and MALDI-TOF mass spectrometry. Anal. Chem. 76(6):1560- 1570. Von Eggeling, F., A. Gawriljuk, W. Fiedler, G. Ernst, U. Claussen, J. Klose, and I. Ro- mer. 2001. Fluorescent dual colour 2D-protein gel electrophoresis for rapid detec- tion of differences in protein pattern with standard image analysis software. Int. J. Mol. Med. 8(4):373-377. Wagner, J.A. 2002. Overview of biomarkers and surrogate endpoints in drug develop- ment. Dis. Markers 18(2):41-46. Walum, E., J. Hedander, and P. Garberg. 2005. Research perspectives for pre-screening alternatives to animal experimentation on the relevance of cytotoxicity measure- ments, barrier passage determinations and high throughput screening in vitro to se- lect potentially hazardous compounds in large sets of chemicals. Toxicol. Appl. Pharmacol. 207(2 Suppl.):393-397. Wang, C., R. Gonzalez, and S.D. Merajver. 2004. Assessment of genetic testing and re- lated counseling services: Current research and future directions. Soc. Sci. Med. 58(7):1427-1442. Wang, C., D.J. Bowen, and S.L. Kardia. 2005. Research and practice opportunities at the intersection of health education, health behavior, and genomics. Health Educ. Be- hav. 32(5):686-701. Wang, H.T., J.P. Kong, F. Ding, X.Q. Wang, M.R. Wang, L.X. Liu, M. Wu, and Z.H. Liu. 2003. Analysis of gene expression profile induced by EMP-1 in esophageal cancer cells using cDNA Microarray. World J. Gastroenterol. 9(3):392-398. Wang, J., J. Delabie, H. Aasheim, E. Smeland, and O. Myklebost. 2002. Clustering of the SOM easily reveals distinct gene expression patterns: Results of a reanalysis of lymphoma study. BMC Bioinformatics 3(1):36. Wang, W., H. Zhou, H. Lin, S. Roy, T.A. Shaler, L.R. Hill, S. Norton, P. Kumar, M. Anderle, and C.H. Becker. 2003. Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards. Anal. Chem. 75(18):4818-4826. Wang, X., D.J. Tomso, X. Liu, and D.A. Bell. 2005. Single nucleotide polymorphism in transcriptional regulatory regions and expression of environmentally responsive genes. Toxicol. Appl. Pharmacol. 207(Suppl. 2):S84-S90. Wang, Y., M.E. Bollard, H. Keun, H. Antti, O. Beckonert, T.M. Ebbels, J.C. Lindon, E. Holmes, H. Tang, and J.K. Nicholson. 2003. Spectral editing and pattern recogni- tion methods applied to high-resolution magic-angle spinning 1H nuclear magnetic resonance spectroscopy of liver tissues. Anal. Biochem. 323(1):26-32. Wang, Y., J. Hayakawa, F. Long, Q. Yu, A.H. Cho, G. Rondeau, J. Welsh, S. Mittal, I. De Belle, E. Adamson, M. McClelland, and D. Mercola. 2005a. Promoter array studies identify cohorts of genes directly regulated by methylation, copy number change, or transcription factor binding in human cancer cells. Ann. N.Y. Acad. Sci. 1058:162-185. Wang, Y., H. Tang, J.K. Nicholson, P.J. Hylands, J. Sampson, and E. Holmes. 2005b. A metabonomic strategy for the detection of the metabolic effects of chamomile (Matricaria recutita L.) ingestion. J. Agric. Food Chem. 53(2):191-196. Wang, Z., H. Fan, H.H. Yang, Y. Hu, K.H. Buetow, and M.P. Lee. 2004. Comparative sequence analysis of imprinted genes between human and mouse to reveal imprint- ing signatures. Genomics 83(3):395-401.

References 251 Wang, Z., D. Neuburg, C. Li, L. Su, J.Y. Kim, J.C. Chen, and D.C. Christiani. 2005. Global gene expression profiling in whole-blood samples from individuals ex- posed to metal fumes. Environ. Health Perspect. 113(2):233-241. Waring, J.F., R.A. Jolly, R. Ciurlionis, P.Y. Lum, J.T. Praestgaard, D.C. Morfitt, B. Buratto, C. Roberts, E. Schadt, and R.G. Ulrich. 2001. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol. Appl. Pharmacol. 175(1):28-42. Waring, J.F., R. Gum, D. Morfitt, R.A. Jolly, R. Ciurlionis, M. Heindel, L. Gallenberg, B. Buratto, and R.G. Ulrich. 2002. Identifying toxic mechanisms using DNA microar- rays: Evidence that an experimental inhibitor of cell adhesion molecule expression signals through the aryl hydrocarbon nuclear receptor. Toxicology 181-182:537- 550. Waring, J.F., R.G. Ulrich, N. Flint, D. Morfitt, A. Kalkuhl, F. Staedtler, M. Lawton, J.M. Beekman, and L. Suter. 2004. Interlaboratory evaluation of rat hepatic gene ex- pression changes induced by methapyrilene. Environ. Health Perspect. 112(4):439- 448. Washburn, M.P., D. Wolters, and J.R. Yates III. 2001. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19(3):242-247. Washburn, M.P., R. Ulaszek, C. Deciu, D.M. Schieltz, and J.R. Yates III. 2002. Analysis of quantitative proteomic data generated via multidimensional protein identifica- tion technology. Anal. Chem. 74(7):1650-1657. Washington, HA. 1994. Henrietta Lacks: An unsung hero. Emerge (Oct.):29. Waterland, R.A., and R.L. Jirtle. 2004. Early nutrition, epigenetic changes at transposons and imprinted genes, and enhanced susceptibility to adult chronic diseases. Nutri- tion 20(1):63-68. Waters, M., G. Boorman, P. Bushel, M. Cunningham, R. Irwin, A. Merrick, K. Olden, R. Paules, J. Selkirk, S. Stasiewicz, B. Weis, B. Van Houten, N. Walker, and R. Tennant. 2003b. Systems toxicology and the Chemical Effects in Biological Sys- tems (CEBS) knowledge base. EHP Toxicogenomics 111(1T):15-28. Waters, N.J, S. Garrod, R.D. Farrant, J.N. Haselden, S.C. Connor, J. Connelly, J.C. Lindon, E. Holmes, and J.K. Nicholson. 2000. High-resolution magic angle spin- ning (1)H NMR spectroscopy of intact liver and kidney: Optimization of sample preparation procedures and biochemical stability of tissue during spectral acquisi- tion. Anal. Biochem. 282(1):16-23. Waters, N.J., E. Holmes, A. Williams, C.J. Waterfield, R.D. Farrant, and J.K. Nicholson. 2001. NMR and pattern recognition studies on the time-related metabolic effects of alpha-naphthylisothiocyanate on liver, urine, and plasma in the rat: An integrative metabonomic approach. Chem. Res. Toxicol. 14(10):1401-1412. Waters, N.J., E. Holmes, C.J. Waterfield, R.D. Farrant, and J.K. Nicholson. 2002. NMR and pattern recognition studies on liver extracts and intact livers from rats treated with alpha-naphthylisothiocyanate. Biochem. Pharmacol. 64(1):67-77. Waters, N.J., C.J. Waterfield, R.D. Farrant, E. Holmes, and J.K. Nicholson. 2005. Me- tabonomic deconvolution of embedded toxicity: Application to thioacetamide hepato- and nephrotoxicity. Chem. Res. Toxicol. 18(4):639-654. Weber, W.W. 1997. Pharmacogenetics. Oxford: Oxford University Press. Weijer, C., and P.B. Miller. 2004. Protecting communities in pharmacogenetic and phar- macogenomic research. Pharmacogenomics J. 4(1):9-16. Weinstein, J.N., T.G. Myers, P.M. O'Connor, S.H. Friend, A.J. Fornace Jr, K.W. Kohn, T. Fojo, S.E. Bates, L.V. Rubinstein, N.L. Anderson, J.K. Buolamwini, W.W. van

252 Applications of Toxicogenomic Technologies Osdol, A.P. Monks, D.A. Scudiero, E.A. Sausville, D.W. Zaharevitz, B. Bunow, V.N. Viswanadhan, G.S. Johnson, R.E. Wittes, and K.D. Paull. 1997. An informa- tion-intensive approach to the molecular pharmacology of cancer. Science 275(5298):343-349. Welch, K.D., B. Wen, D.R. Goodlett, E.C. Yi, H. Lee, T.P. Reilly, S.D. Nelson, and L.R. Pohl. 2005. Proteomic identification of potential susceptibility factors in drug- induced liver disease. Chem. Res. Toxicol. 18(6):924-933. Wen, X., S. Fuhrman, G.S. Michaels, D.B. Carr, S. Smith, J.L. Barker, and R. Somogyi. 1998. Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl. Acad. Sci USA 95(1):334-339. Wesselkamper, S.C., L.M. Case, L.N. Henning, M.T. Borchers, J.W. Tichelaar, J.M. Mason, N. Dragin, M. Medvedovic, M.A. Sartor, C.R. Tomlinson, and G.D. Leikauf. 2005. Gene expression changes during the development of acute lung in- jury: Role of TGF-{beta}. Am. J. Respir. Crit. Care Med. 172(11):1399-1411. Weston, W.M., E.E. LeClair, W. Trzyna, K.M. McHugh, P. Nugent, C.M. Lafferty, L. Ma, R.S. Tuan, and R.M. Greene. 1999. Differential display identification of plunc, a novel gene expressed in embryonic palate, nasal epithelium, and adult lung. J. Biol. Chem. 274(19):13698-13703. Wiback, S.J., R. Mahadevan, and B.O. Palsson. 2004. Using metabolic flux data to fur- ther constrain the metabolic solution space and predict internal flux patterns: The Escherichia coli spectrum. Biotechnol. Bioeng. 86(3):317-331. Wilkinson, C.F., G.R. Christoph, E. Julien, J.M. Kelley, J. Kronenberg, J. McCarthy, and R. Reiss. 2000. Assessing the risks of exposures to multiple chemicals with a common mechanism of toxicity: How to cumulate? Regul. Toxicol. Pharmacol. 31(1):30-43. Williams, R.E., H. Major, E.A. Lock, E.M. Lenz, and I.D. Wilson. 2005. D-Serine- induced nephrotoxicity: A HPLC-TOF/MS-based metabonomics approach. Toxi- cology 207(2):179-190. Wilson, I.D., and J.K. Nicholson. 2003. Topics in xenobiochemistry: Do metabolic path- ways exist for xenobiotics? The micro-metabolism hypothesis. Xenobiotica 33(9):887-901. Wilson, I.D., R. Plumb, J. Granger, H. Major, R. Williams, and E.M. Lenz. 2005a. HPLC-MS-based methods for the study of metabonomics. J. Chromatogr. B Ana- lyt. Technol. Biomed. Life Sci. 817(1):67-76. Wilson, I.D., J.K. Nicholson, J. Castro-Perez, J.H. Granger, K.A. Johnson, B.W. Smith, and R.S. Plumb. 2005b. High resolution “ultra performance” liquid chromatogra- phy coupled to oa-TOF mass spectrometry as a tool for differential metabolic pathway profiling in functional genomic studies. J. Proteome Res. 4(2):591-598. Wiltse, J. 2005. Mode of action: Inhibition of histone deacetylase, altering WNT- dependent gene expression, and regulation of beta-catenin – developmental effects of valproic acid. Crit. Rev. Toxicol. 35(8-9):727-738. Witte, K. 1994. Fear control and danger control: A test of the Extended Parallel Process Model (EPPM). Commun. Monogr. 61(2):113-134. Wolpert, D.H., and W.G. MacReady. 1997. No free lunch theorems for optimization, IEEE T. Evolut. Comput. 1(1):67-82. Wolters, D.A., M.P. Washburn, and J.R.Yates, III. 2001. An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73(23): 5683-5690.

References 253 Workman, C.T., H.C. Mak, S. McCuine, J.B. Tagne, M. Agarwal, O. Ozier, T.J. Begley, L.D. Samson, and T. Ideker. 2006. A systems approach to mapping DNA damage response pathways. Science 312(5776):1054-1059. Wu, M.T., B. Demple, R.A. Bennett, D.C. Christiani, R. Fan, and H. Hu. 2000. Individ- ual variability in the zinc inducibility of metallothionein-IIA mRNA in human lymphocytes. J. Toxicol. Environ. Health A 61(7):553-567. Wu, S.L., J. Kim, W.S. Hancock, and B. Karger. 2005. Extended Range Proteomic Analysis (ERPA): A new and sensitive LC-MS platform for high sequence cover- age of complex proteins with extensive post-translational modifications- comprehensive analysis of beta-casein and epidermal growth factor receptor (EGFR). J. Proteome Res. 4(4):1155-1170. Xenarios, I., L. Salwinski, X.J. Duan, P. Higney, S.M. Kim, and D. Eisenberg. 2002. DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30(1):303-305. Xiao, G.G., M. Wang, N. Li, J.A. Loo, and A.E. Nel. 2003. Use of proteomics to demon- strate a hierarchical oxidative stress response to diesel exhaust particle chemicals in a macrophage cell line. J. Biol. Chem. 278(50):50781-50790. Xu, X.Q., C.K. Leow, X. Lu, X. Zhang, J.S. Liu, W.H. Wong, A. Asperger, S. Deininger, and H.C. Eastwood Leung. 2004. Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics. Proteomics 4(10):3235-3245. Yamamoto, T., R. Kikkawa, H. Yamada, and I. Horii. 2005. Identification of oxidative stress-related proteins for predictive screening of hepatotoxicity using a proteomic approach. J. Toxicol. Sci. 30(3):213-227. Yang, I., I.Y. Park, S.M. Jang, L.H. Shi, H.K. Ku, and S.R. Park. 2006. Rapid quantifica- tion of DNA methylation through dNMP analysis following bisulfite-PCR. Nucleic Acids Res. 34(8):e61. Yang, I.V., E. Chen, J.P. Hasseman, W. Liang, B.C. Frank, S. Wang, V. Sharov, A.I. Saeed, J. White, J. Li, N.H. Lee, T.J. Yeatman, and J. Quackenbush. 2002. Within the fold: Assessing differential expression measures and reproducibility in mi- croarray assays. Genome Biol. 3(11):RESEARCH0062. Yang, R.S.H. 1994. Toxicology of Chemical Mixtures: Case Studies, Mechanisms, and Novel Approaches. San Diego: Academic Press. Yang, Y.H., S. Dudoit, P. Luu, D.M. Lin, V. Peng, J. Ngai, and T.P. Speed. 2002. Nor- malization for cDNA microarray data: A robust composite method addressing sin- gle and multiple slide systematic variation. Nucleic Acids Res. 30(4):e15. Yao, G., M. Craven, N. Drinkwater, and C.A. Bradfield. 2004. Interaction networks in yeast define and enumerate the signaling steps or the vertebrate aryl hydrocarbon receptor. PloS Biol. 2(3):E65. Yates, J.R. III. 1998. Mass spectrometry and the age of the proteome. J. Mass. Spectrom. 33(1):1-19. Yates, J.R. III. 2000. Mass spectrometry: From genomics to proteomics. Trends Genet. 16(1):5-8. Yauk, C.L., M.L. Berndt, A. Williams, and G.R. Douglas. 2004. Comprehensive com- parison of six microarray technologies. Nucleic Acids Res. 32(15):e124. Yuen, T., E. Wurmbach, R.L. Pfeffer, B.J. Ebersole, and S.C. Sealfon. 2002. Accuracy and calibration of commercial oligonucleotide and custom cDNA microarrays. Nucleic Acids Res. 30(10):E48. Yuk, J.S., and K.S. Ha. 2005. Proteomic applications of surface plasmon resonance bio- sensors: Analysis of protein arrays. Exp. Mol. Med. 37(1):1-10.

254 Applications of Toxicogenomic Technologies Yuk, J.S., S.H. Jung, J.W. Jung, D.G. Hong, J.A. Han, Y.M. Kim, and K.S. Ha. 2004. Analysis of protein interactions on protein arrays by a wavelength interrogation- based surface plasmon resonance biosensor. Proteomics 4(11):3468-3476. Zarbl, H. 2001. DNA microarrays: An overview of technologies and applications to toxi- cology. Curr. Protocol. Toxicol. (Suppl. 9):1.4.2-1.4.16. Zeeberg, B.R., W. Feng, G. Wang, M.D. Wang, A.T. Fojo, M. Sunshine, S. Narasimhan, D.W. Kane, W.C. Reinhold, S. Lababidi, K.J. Bussey, J. Riss, J.C. Barrett, and J.N. Weinstein. 2003. GoMiner: A resource for biological interpretation of ge- nomic and proteomic data. Genome Biol. 4(4):R28. Zeiger, E. 2003. Validation and acceptance of new and revised tests: A flexible but trans- parent process. Toxicol. Lett. (140-141):31-35. Zhang, K., Z.S. Qin, J.S. Liu, T. Chen, M.S. Waterman, and F. Sun. 2004. Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res. 14(5):908-916. Zhou, H., J.A. Ranish, J.D. Watts, and R. Aebersold. 2002. Quantitative proteome analy- sis by solid-phase isotope tagging and mass spectrometry. Nat. Biotechnol. 20(5):512-515. Zhou, W., G. Liu, D.P. Miller, S.W. Thurston, L.L. Xu, J.C. Wain, T.J. Lynch, L. Su, and D.C. Christiani. 2003. Polymorphisms in the DNA repair genes XRCC1 and ERCC2, smoking, and lung cancer risk. Cancer Epidemiol. Biomarkers Prev. 12(4):359-365. Zhou, W., J.J. Ryan, and H. Zhou. 2004. Global analyses of sumoylated proteins in Sac- charomyces cerevisiae. Induction of protein sumoylation by cellular stresses. J. Biol. Chem. 279(31):32262-32268. Zhu, H., M. Bilgin, R. Bangham, D. Hall, A. Casamayor, P. Bertone, N. Lan, R. Jansen, S. Bidlingmaier, T. Houfek, T. Mitchell, P. Miller, R.A. Dean, M. Gerstein, and M. Snyder. 2001. Global analysis of protein activities using proteome chips. Sci- ence 293(5537):2101-2105. Zou, M., and S.D. Conzen. 2005. A new dynamic Bayesian network (DBN) approach for identifying gene regulatory networks from time course microarray data. Bioinfor- matics 21(1):71-79.

Next: Appendix A: Biographic Information on the Committee on Applications of Toxicogenomic Technologies to Predictive Toxicology »
Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment Get This Book
×
Buy Paperback | $84.00 Buy Ebook | $64.99
MyNAP members save 10% online.
Login or Register to save!
Download Free PDF

The new field of toxicogenomics presents a potentially powerful set of tools to better understand the health effects of exposures to toxicants in the environment. At the request of the National Institute of Environmental Health Sciences, the National Research Council assembled a committee to identify the benefits of toxicogenomics, the challenges to achieving them, and potential approaches to overcoming such challenges. The report concludes that realizing the potential of toxicogenomics to improve public health decisions will require a concerted effort to generate data, make use of existing data, and study data in new ways—an effort requiring funding, interagency coordination, and data management strategies.

  1. ×

    Welcome to OpenBook!

    You're looking at OpenBook, NAP.edu's online reading room since 1999. Based on feedback from you, our users, we've made some improvements that make it easier than ever to read thousands of publications on our website.

    Do you want to take a quick tour of the OpenBook's features?

    No Thanks Take a Tour »
  2. ×

    Show this book's table of contents, where you can jump to any chapter by name.

    « Back Next »
  3. ×

    ...or use these buttons to go back to the previous chapter or skip to the next one.

    « Back Next »
  4. ×

    Jump up to the previous page or down to the next one. Also, you can type in a page number and press Enter to go directly to that page in the book.

    « Back Next »
  5. ×

    To search the entire text of this book, type in your search term here and press Enter.

    « Back Next »
  6. ×

    Share a link to this book page on your preferred social network or via email.

    « Back Next »
  7. ×

    View our suggested citation for this chapter.

    « Back Next »
  8. ×

    Ready to take your reading offline? Click here to buy this book in print or download it as a free PDF, if available.

    « Back Next »
Stay Connected!