Genomics and proteomics : functional and computational aspects

1 . . . . and Counting: DNA-Microarrays . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 Jörg D. Hoheisel 2. Obtaining and Evaluating Gene Expression Profiles with cDNA Microarrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 Albert J. Fornace Jr., Edward R. Dougherty, Paul S. Meltzer, and Jeffrey M. Frent Michael Bittner, Yidong Chen, Sally A. Amundson, Javed Khan, 3. Large Scale Expression Screening Identifies Molecular Pathways and Predicts Gene Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 Nicolas Pollet, Volker Gawantka, Hajo Delius, and Christof Niehrs 4. The Glean Machine: What Can We Learn from DNA Sequence Daniel L. Hartl, E. Fidelma Boyd, Carlos D. Bustamante, Polymorphisms? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 and Stanley A. Sawyer 5. Automatic Assembly and Editing of Genomic Data . . . . . . . . . . . . . . . . . . 6. QUEST: An Iterated Sequence Databank Search Method . . . . . . . . . . . . . . . 51 B. Chevreux, T. Pfisterer, and S. Suhai 67 William R. Taylor and Nigel P. Brown 7. A n Essay on Individual Sequence Variatio n in Expressed Sequence Tags (ESTs) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83 Jens Reich, David Brett, and Jens Hanke 8. Sequence Similarity Based Gene Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95 Roderic Guigó, Moisés Burset, Pankaj Agarwal, Josep E Abril, Randall F. Smith and James W. Fickett 9. Functional Proteomics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107 Joachim Klose vii viii Contents 10. The Genome As a Flexible Polymer Chain: Recent Results from Simulations and Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121 Jörg Langowski, Carsten Mehring, Markus Hammermann, Konstantin Klenin, Christian Münkel, Katalin Tóth, and Gero Wedemann 1 1. Analysis of Chromosome Territory Architecture in the Human Cell Nucleus: Overview of Data from a Collaborative Study . . . . . . . . . . . 133 H. Bornfleth, C. Cremer, T. Cremer, S. Dietzel, P. Edelmann, R. Eils, W. Jäger, D. Kienle, G. Kreth, P. Lichter, G. Little, C. Münkel, J. Langowski, I. Solovei, E. H. K. Stelzer, and D. Zink 12. From Sequence to Structure and Function: Modelling and Simulation of Light-Activated Membrane Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141 Jerome Baudry, Serge Crouzy, Benoit Roux, and Jeremy C. Smith 13. SHOX Homeobox Gene and Turner Syndrome . . . . . . . . . . . . . . . . . . . . . . . . . . 149 E. Rao and G. A. Rappold 14. A Feature-Based Approach to Discrimination and Prediction of Protein Folding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 Boris Mirkin and Otto Ritter 15. Linking Structural Biology with Genome Research: The Berlin “Protein Udo Heinemann, Juergen Frevert, Klaus-Peter Hofmann, Gerd Illing, Structure Factory” Initiative . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179 Hartmut Oschkinat, Wolfram Saenger, and Rolf Zettl 16. G Protein-coupled Receptors, or the Power of Data . . . . . . . . . . . . . . . . . . . . . 191 Florence Horn, Mustapha Mokrane, Johnathon Weare, and Gerrit Vriend 17. Distributed Application Management in Bioinformatics . . . . . . . . . . . . . . . . . . 215 18. Is Human Genetics Becoming Dangerous to Society? . . . . . . . . . . . . . . . . . . . . 231 M. Senger, P. Ernst, and K.-H. Glatting Charles J. Epstein Contributors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249