Handbook of Toxicogenomics – Strategies and Applications

Jurgen Borlak received a degree in biochemistry and a PhD in biochemical toxicology at the University of Reading, UK, in 1988. He was a Cancer Research Campaign founded postdoctoral research scientist and in 1990 joined the Marion Merrel Dow Research Institute in Strasbourg, France, as Senior Research Biochemist. In 1998, he was appointed Director of the Center of Drug Research and Molecular Pharmacology at the Fraunhofer Institute of Toxicology and Experimental Medicine; the centre focuses largely on the molecular effects of drugs and xenobiotics, using a wide range of methods and technologies in cell biology, genomics and molecular biology. In 2000 Jurgen Borlak was habilitated in pharmacology and toxicology and received the venia legendi at the Medical School of Hannover. In 2002 he was appointed as full professor to the chair of Pharmaco and Toxicogenomics at the Medical School of Hannover. He was also appointed as Professor of Molecular Anatomy at the Medical Faculty of the University Leipzig in 2003. Jurgen Borlak is a member of, among others, the Biochemical Society, the Royal Society of Chemistry, the Society of Experimental Biology and the International Society for the Study of Xenobiotics. He is a reviewer for various scientific journals and appointed by the World Health Organisation as an expert on chemical and drug safety.

Preface. 1 Introduction (Jurgen Borlak). Technology Platforms in Toxicogenomics. 2 Expression Profiling using SAGE and cDNA Arrays (Andreas Bosio). 3 Oligo Arrays, Global Transcriptome Analysis (Jacques Retief, Earl Hubbell, and David Finkelstein). 4 Toxicogenomics Applications of Open platform High Density DNA Microarrays (Mark McCormick and Emile F. Nuwaysir). 5 Mass Spectrometry and Proteomics: Principles and Applications (Uwe Rapp). 6 Covalent Protein Modification Analysis by Electrospray Tandem Mass Spectrometry (Wolf D. Lehmann). 7 Chromatin Immunoprecipitation based Identification of Gene Regulatory Networks (Monika Niehof and Jurgen Borlak). 8 NMR Spectroscopy as a Versatile Analytical Platform for Toxicology Research (Olivia Corcoran). Bioinformatic Tools in Toxicogenomics. 9 Generation and Validation of a Reference System for Toxicogenomics DNA Microarray Experiments (Jurgen Cox, Hans Gmunder, Andreas Hohn, and Hubert Rehrauer). 10 The Chemical Effects in Biological Systems (CEBS) Knowledge Base (Michael D. Waters, Gary Boorman, Pierre Bushel, Michael Cunningham, Rick Irwin, Alex Merrick, Kenneth Olden, Richard Paules, James K. Selkirk, Stanley Stasiewicz, Ben Van Houten, Nigel Walker, Brenda Weis, Honghui Wan, and Raymond Tennant). 11 Investigating the Effective Range of Agents by Using Integrative Modelling (Andreas Freier, Ralf Hofestadt, and Thoralf Toepel). 12 Databases and Tools for in silico Analysis of Regulation of Gene Expression (Alexander Kel, Olga Kel Margoulis, and Edgar Wingender). 13 Systems Biology Applied to Toxicogenomics (Klaus Prank, Matthias Hochsmann, Bjorn Oleson, Thomas Schmidt, Leila Taher, and Dion Whitehead). Application of Toxicogenomic: Case Studies. 14 Regulatory Networks of Liver enriched Transcription Factors in Liver Biology and Disease (Jurgen Borlak, Jurgen Klempnauer, and Harald Schrem). 15 Toxicogenomics Applied to Understanding Cholestasis and Steatosis in the Liver (Timothy W. Gant, Peter Greaves, Andrew G. Smith, and Andreas Gescher). 16 Toxicogenomics Applied to Cardiovascular Toxicity (Thomas Thum and Jurgen Borlak). 17 Toxicogenomics Applied to Endocrine Disruption (Damian G. Deavall, Jonathan G. Moggs, and George Orphanides). 18 Toxicogenomics Applied to Teratogenicity Studies (Philip G. Hewitt, Peter J. Kramer, and Jurgen Borlak). 19 Toxicogenomics Applied to Nephrotoxicity (Anke Luhe and Heinz Hildebrand). 20 Toxicogenomic Analysis of Human Umbilical Cords to Establish a New Risk Assessment of Human Foetal Exposure to Multiple Chemicals (Masatoshi Komiyama and Chisato Mori). 21 Genetic Variability: Implications for Toxicogenomic Research (Gilbert Schonfelder, Dieter Schwarz, Thomas Gerloff, Martin Paul, and Ivar Roots). 22 Profiling of Peripheral Blood Gene Expression to Search for Biomarkers (Arno Kalkuhl and Mario Beilmann). 23 How Things Could Be Done Better Using Toxicogenomics: A Retrospective Analysis (Laura Suter and Rodolfo Gasser). 24 Toxicogenomics Applied to Hematotoxicology (Yoko Hirabayashi and Tohru Inoue). The National Toxicogenomic Program/Initiatives. 25 The National Toxicogenomics Program (James K. Selkirk, Michael D. Waters, and Raymond W. Tennant). 26 Toxicogenomics: Japanese Initiative (Tetsuro Urushidani and Taku Nagao). Point of View from Regulatory Authorities and Ethical Aspects. 27 Toxicogenomics in Need of an ICH Guideline? Experiences from the Past (Frauke Meyer and Gerd Bode). Subject Index.