How molecular profiling could revolutionize drug discovery (original) (raw)

• Stoughton, R. Applications of DNA microarrays in biology. Annu. Rev. Biochem. 13 Jan 2005 (10.1146/annurev.biochem.74.082803.133212).
• de Hoog, C. L. & Mann, M. Proteomics. Annu. Rev. Genomics Hum. Genet. 5, 267–293 (2004).
  Article CAS Google Scholar
• Lindon, J. C., Holmes, E., Bollard, M. E., Stanley, E. G. & Nicholson, J. K. Metabonomics technologies and their applications in physiological monitoring, drug safety assessment and disease diagnosis. Biomarkers 9, 1–31 (2004).
  Article CAS Google Scholar
• Nicholson, J. K. & Wilson, I. D. Opinion: understanding 'global' systems biology: metabonomics and the continuum of metabolism. Nature Rev. Drug Discov. 2, 668–676 (2003).
  Article CAS Google Scholar
• Lindsay, M. A. Target discovery. Nature Rev. Drug Discov. 2, 831–838 (2003).
  Article CAS Google Scholar
• Weinshilboum, R. & Wang, L. Pharmacogenomics: bench to bedside. Nature Rev. Drug Discov. 3, 739–748 (2004).
  Article CAS Google Scholar
• Roth, A., Gill, R. & Certa, U. Temporal and spatial gene expression patterns after experimental stroke in a rat model and characterization of PC4, a potential regulator of transcription. Mol. Cell. Neurosci. 22, 353–364 (2003).
  Article CAS Google Scholar
• Chuaqui, R. F. et al. Post-analysis follow-up and validation of microarray experiments. Nature Genet. 32 (Suppl.), 509–514 (2002).
  Article CAS Google Scholar
• Lock, C. et al. Gene-microarray analysis of multiple sclerosis lesions yields new targets validated in autoimmune encephalomyelitis. Nature Med. 8, 500–508 (2002).
  Article CAS Google Scholar
• Clare, A. & King, R. D. How well do we understand the clusters found in microarray data? In Silico Biol 2, 511–522 (2002).
  CAS PubMed Google Scholar
• Hughes, T. R. et al. Functional discovery via a compendium of expression profiles. Cell 102, 109–126 (2000).
  Article CAS Google Scholar
• Hardwick, J. et al. Identification of biomarkers for tumor endothelial cell proliferation through gene expression profiling. Mol. Canc. Ther. (in the press).
• Waring, J. F. et al. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol. Appl. Pharmacol. 175, 28–42 (2001).
  Article CAS Google Scholar
• Waring, J. F. et al. Identifying toxic mechanisms using DNA microarrays: evidence that an experimental inhibitor of cell adhesion molecule expression signals through the aryl hydrocarbon nuclear receptor. Toxicology 181–182, 537–550 (2002).
  Article Google Scholar
• Zielinski, N. et al. Expression profiling using DNA microarray reveals a functional antagonism of the peroxisome proliferator activated receptor alpha by the protease inhibitor, Ritonavir. Conf. Antimicrobial Agents Chemother. Chicago, Illinois (2001).
• Engelberg, A. Iconix Pharmaceuticals, Inc. - removing barriers to efficient drug discovery through chemogenomics. Pharmacogenomics 5, 741–744 (2004).
  Article Google Scholar
• Waring, J. F. et al. Development of a DNA microarray for toxicology based on hepatotoxin-regulated sequences. EHP Toxicogenomics 111, 53–60 (2003).
  CAS PubMed Google Scholar
• Steiner, G. et al. Discriminating different classes of toxicants by transcript profiling. Environ. Health Perspect. 112, 1236–1248 (2004).
  Article CAS Google Scholar
• Gunther, E. C., Stone, D. J., Gerwien, R. W., Bento, P. & Heyes, M. P. Prediction of clinical drug efficacy by classification of drug-induced genomic expression profiles in vitro. Proc. Natl Acad. Sci. USA 100, 9608–9613 (2003).
  Article CAS Google Scholar
• Marton, M. J. et al. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nature Med. 4, 1293–1301 (1998).
  Article CAS Google Scholar
• Roberts, C. J. et al. Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873–880 (2000).
  Article CAS Google Scholar
• van 't Veer, L. J. et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature 415, 530–536 (2002).
  Article CAS Google Scholar
• van 't Veer, L. J. et al. Expression profiling predicts outcome in breast cancer. Breast Cancer Res. 5, 57–58 (2003).
  Article Google Scholar
• Petricoin, E. F. et al. Use of proteomic patterns in serum to identify ovarian cancer. Lancet 359, 572–577 (2002).
  Article CAS Google Scholar
• Mariadason, J. M. et al. Gene expression profiling-based prediction of response of colon carcinoma cells to 5-fluorouracil and camptothecin. Cancer Res. 63, 8791–8812 (2003).
  CAS PubMed Google Scholar
• Ochi, K. et al. Prediction of response to neoadjuvant chemotherapy for osteosarcoma by gene-expression profiles. Int. J. Oncol. 24, 647–655 (2004).
  CAS PubMed Google Scholar
• Alizadeh, A. A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403, 503–511 (2000).
  Article CAS Google Scholar
• Berns, K. et al. A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature 428, 431–437 (2004).
  Article CAS Google Scholar
• Hartwell, L. H., Szankasi, P., Roberts, C. J., Murray, A. W. & Friend, S. H. Integrating genetic approaches into the discovery of anticancer drugs. Science 278, 1064–1068 (1997).
  Article CAS Google Scholar
• Houshmand, P. & Zlotnik, A. Targeting tumor cells. Curr. Opin. Cell Biol. 15, 640–644 (2003).
  Article CAS Google Scholar
• Christopher, R. et al. Data-driven computer simulation of human cancer cell. Ann. NY Acad. Sci. 1020, 132–153 (2004).
  Article CAS Google Scholar
• Schadt, E. E. et al. Genetics of gene expression surveyed in maize, mouse and man. Nature 422, 297–302 (2003).
  Article CAS Google Scholar
• Schadt, E. E., Monks, S. A. & Friend, S. H. A new paradigm for drug discovery: integrating clinical, genetic, genomic and molecular phenotype data to identify drug targets. Biochem. Soc. Trans. 31, 437–443 (2003).
  Article CAS Google Scholar
• Franke, L. et al. TEAM: a tool for the integration of expression, and linkage and association maps. Eur. J. Hum. Genet. 12, 633–638 (2004).
  Article CAS Google Scholar
• Boess, F. et al. Gene expression in two hepatic cell lines, cultured primary hepatocytes, and liver slices compared to the in vivo liver gene expression in rats: possible implications for toxicogenomics use of in vitro systems. Toxicol. Sci. 73, 386–402 (2003).
  Article CAS Google Scholar
• Clish, C. B. et al. Integrative biological analysis of the APOE*3-leiden transgenic mouse. Omics 8, 3–13 (2004).
  Article CAS Google Scholar
• Neumann, E. & Thomas, J. Knowledge assembly for the life sciences. Drug Discov. Today 7, S160–S162 (2002).
  Article Google Scholar
• Ekins, S. Predicting undesirable drug interactions with promiscuous proteins in silico. Drug Discov. Today 9, 276–285 (2004).
  Article CAS Google Scholar
• Wilson, A. G., White, A. C. & Mueller, R. A. Role of predictive metabolism and toxicity modeling in drug discovery — a summary of some recent advancements. Curr. Opin. Drug Discov. Devel. 6, 123–128 (2003).
  CAS PubMed Google Scholar
• Kola, I. & Landis, J. Can the pharmaceutical industry reduce attrition rates? Nature Rev. Drug Discov. 3, 711–715 (2004).
  Article CAS Google Scholar
• Deroubaix, X. & Coquette, A. The ins and outs of human ADME studies. Business Briefing: Pharmatech 2004 (2004).
• van de Vijver, M. J. et al. A gene-expression signature as a predictor of survival in breast cancer. N. Engl. J. Med. 347, 1999–2009 (2002).
  Article CAS Google Scholar
• Hongyue, D. et al. A cell proliferation signature is a marker of extremely poor outcomes in a subpopulation of breast cancer patients. Cancer Res. (in the press).
• Issa, A. M. Ethical perspectives on pharmacogenomic profiling in the drug development process. Nature Rev. Drug Discov. 1, 300–308 (2002).
  Article CAS Google Scholar
• Petricoin, E. F., 3rd et al. Medical applications of microarray technologies: a regulatory science perspective. Nature Genet. 32 (Suppl.), 474–479 (2002).
  Article CAS Google Scholar
• Christensen, C. M. The Innovator's Dilemma 252 (Harvard Business School Press, Boston, 1997).
  Google Scholar