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References

A set of references for the seminar documents.

Afshari CA, Nuwaysir EF and Barrett JC (1999). Application of complementary DNA microarray technology to carcinogen identification, toxicology, and drug safety evaluation. Cancer Research, 59, 4759-4760.

Aicher L, Wahl D, Arce A, Grenet O and Steiner S. (1998). New insights into cyclosporine A nephrotoxicity by proteome analysis. Electrophoresis 19, 1998-2003.

Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JG, Sabet H, Tran T, Yu X, Powell JI, Yang LM, Marti GE, Moore T, Hudson J, Lu LS, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 2000;403:503-511.

Anderson L, Steele VK, Kellof GJ, Sharma S, (1995) Effects of oltipraz and related chemoprevention compounds on gene expression in rat liver. J. Cell. Biochem. Suppl. 22, 108 -116

Bartosiewicz M, Trounstine M, Barker D, Johnston R and Buckpitt A. (2000). Development of a toxicological gene arrays and quantitative assessment of this technology. Arch Biochem Biophys. 376 (1), 66-73.

Blanchard K, DiSorbo O, Burris R, Dunn R, Farr S and Stoll R. (2000). Toxicogenomics: Understanding the use of microarrays for toxicology studies in vivo. Toxicologist, 54, 195.

Bowtell., D. D. L. (1999) Options available - from start to finish – for obtaining expression data by microarray. Nat. Genet. Supp. 21, 25.

Brown CS, Goodwin PC, Sorger PK. Image metrics in the statistical analysis of DNA microarray data. Proc Natl Acad Sci USA 2001;98:8944-8949.

Bulera SJ, Eddy SM, Ferguson E, Jatkoe TA, Reindel JF, Bleavins MR and De La Iglesia FA. (2001). RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays. Hepatology, 33 (5), 1239-1258.

Burchiel SW et al. (2001). Analysis of genetic and epigenetic mechanisms of toxicity: Potential roles of toxicogenomics and proteomics in toxicology. Toxicological Sciences, 59, 193-195.

Burczynski ME et al. (2000). Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells.Toxicological Sciences, 58 (2), 399-415.

Ciphergen Biosystems Ltd. and SmithKline Beecham (2001) Correlating ProteinChip¿ Protein Profiles with Drug Treatment: A Powerful New Strategy for Safety Assessment. http://www.ciphergen.com/F1_case1.html

Corton JC and Stauber AJ. (2000). Toward construction of a transcript profile database predictive of chemical toxicity. Toxicological Sciences, 58, 217-219.

ECETOC Document No. 42 (2000) Genomics, Transcript Profiling, Proteomics and Metabonomics (GTPM) - An Introduction. Ed. Carpanini, F. M.

Farr S and Dunn RT (1999). Concise Review: Gene expression applied to toxicology. Toxicological Sciences, 50, 1-9.

Fielden MR and Zacharewski TR (2001). Challenges and Limitations of gene expression profiling in mechanistic and predictive toxicology. Toxicological Sciences, 60, 6-10.

Fountoulakis M, Berndt P, Boelsterli UA, Crameri F, Winter M, Albertini S and Suter L. (2000). Two-dimensional database of mouse liver proteins: Changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioisomer 3-acetamidophenol. Electrophoresis 21, 2148-2161.

GlaxoWellcome and Ciphergen Biosystems, Inc . (2000) ProteinChip¿ Case Study: Detection, Identification and Validation of a Protein Marker in Urine for TMPD Induced Skeletal Muscle Toxicity. http://www.ciphergen.com/F1_case1.html

Greene LA. (2001). New Centre a Stroke of Gene-ius. Environmental Health Perspectives, 109 (1), A22-A23.

Harries HM, Fletcher ST, Duggan CM and Baker VA. (2001). The use of genomics technology to investigate gene expression changes in cultured human liver cells. Toxicology In Vitro (in press).

Hughes, T. R., et al., (2000) Functional discovery via a compendium of expression profiles. Cell, 102. 109.

Iannaccone PM. (2001). Toxicogenomics: The call of the wild chip. Environmental Health Perspectives, 109 (1), A8-A11.

Kane MD, Jatkoe TA, Stumpf CR, Lu J, Thomas JD, Madore SJ. Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucl Acids Res 2000;28:4552-4557.

Kennedy S. (2001). Proteomic profiling from human samples: the body fluid alternative. Toxicol Lett. 120, 379-384.

Kerr and Churchill(2001), Experimental design for gene expression microarrays, Biostatistics, 2:183-201.

http://www.le.ac.uk/cmht/twg1/array-fp.html Gives links to other array sites.

Khan J, Wei JS, Ringner M, Saal LH, Ladanyi M, Westermann F, Berthold F, Antonescu CR, Peterson C, Meltzer PS. Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nature Medicine 2001;7:673-679

Lauerman JF. (2001). Arrays cast toxicology in a new light. Environmental Health Perspectives, 109 (1), A20-A22.

Lewis, T. S., Hunt, J. B., Aveline, L. D., Jonsher, K. R., Louie, D. F., Yeh, J. M., Nahreini, T. S., Resing, K. A. and Ahn, N. G. (2000) Identification of novel MAP kinase signalling targets by functional proteomics and mass spectrometry. Mol. Cell, 6, 1343.

Lobenhofer EK, Bushel PR, Afshari CA and Hamedeh HK (2001). Progress in the application of DNA microarrays. Environmental Health Perspectives. 109 (9), 881-892.

Lockhart DL, Winzeler E. Genomics, gene expression and DNA arrays. Nature 2000;405:827-836.

Lovett RA. (2000). Toxicologists brace for genomics revolution. Science, 389, 536-537.

Medlin JF. (1999). Timely toxicology. Environmental Health Perspect, 107(5), A256-8.

Moller A, Soldan M, Volker U and Maser E. (2001). Two-dimensional gel electrophoresis: a powerful method to elucidate cellular responses to toxic compounds. Toxicology 160, 129-138.

Nadadur SS, Schladweiler MC and Kodavanti UP (2000). A pulmonary rat gene array for screening altered expression profiles in air pollutant-induced lung injury. Inhalation Toxicology, 12(12): 1239-1254.

Newsholme S.J, Maleeff BF, Steiner S, Anderson NL and Schwartz LW. (2000). Two-dimensional electrophoresis of liver proteins: characterization of a drug-induced hepatomegaly in rats. Electrophoresis 21, 2122-2128.

Nuwaysir EF, Bittner M, Trent J, Barrett JC, Afshari CA.(1999). Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog, 24(3), 153-9.

Pandey, A. and Mann, M., (2000) Proteomics to study genes and genomes. Nature, 405, 837.

Pennie WD (2000). Use of cDNA microarrays to probe and understand the toxicological consequences of altered gene expression. Toxicology Letters, 112-113: 473-477.

Pennie WD, Tugwood JD, Oliver GJ and Kimber I. (2000). The Principles and Practice of Toxicogenomics; Applications and opportunities. Toxicological Sciences, 54, 277-283.

Pennie WD, Woodyatt NJ, Aldridge TC and Orphanides G (2001). Application of genomics to the definition of the molecular basis for toxicity. Toxicology Letters, 120, 353-358.

Rockett JC, Dix DJ. (1999). Application of DNA Arrays to Toxicology. Environ Health Perspect Aug;107(8), 681-685.

Rockett JC, Esdaile DJ, Gibson GG. (1999). Differential gene expression in drug metabolism and toxicology: practicalities, problems and potential. Xenobiotica Jul;29(7), 655-91

Rockett, J. C. and Dix D. J., (2000) DNA arrays: technology, options and toxicological applications. Xenobiot. 30, 155.

Rodi CP, Bunch RT, Curtiss SW, Kier LD, Cabonce MA, Davila JC, Mitchell MD, Alden CL, Morris DL. (1999). Revolution through genomics in investigative and discovery toxicology. Toxicol Pathol , Jan-Feb;27(1), 107-10.

Schulze, A. and Downward, J., (2001) Navigating gene expression using microarrays – a technology review. Nat. Cell Biol. 3, E190.

Smith, L. L., (2001) Key challenges for toxicologists in the 21st century. Trends, Pharm. Sci. 22, 281.

Steiner S and Anderson N L (2000). Expression profiling in toxicology – potentials and limitations. Toxicology Letters, 112-113: 467-471.

Turton NJ, Judah DJ, Riley J, Davies R, Lipson D, Styles JA, Smith AG, Gant TW. Gene expression and amplification in breast carcinoma cells with intrinsic and acquired doxorubicin resistance. Oncogene 2001;20:1300-1306.

Waring JF, Ciurlionis R, Jolly RA, Heindel M and Ulrich RG (2001). Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicology Letters, 120, 359-368.

Waring JF, Jolly RA, Ciurlionis R, Lum PY, Praestgaard JT, Morfitt DC, Buratto B, Robers C, Schadt E and Ulrich RG. (2001). Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicology and Applied Pharmacology, 175 (1), 28-42.

Wittes J, Friedman HP. Searching for evidence of altered gene expression: a comment on statistical analysis of microarray data. J Natl Cancer Institute 1999;91:400-401.