Preface.

List of Contributors.

Part 1 Introduction.

1 Bioinformatics -- From Genomes to Therapies (Thomas Lengauer).

Part 2 Sequencing Genomes.

2 Bioinformatics Support for Genome-Sequencing Projects (Knut Reinert and Daniel Huson).

Part 3 Sequence Analysis.

3 Sequence Alignment and Sequence Database Search (Martin Vingron).

4 Phylogeny Reconstruction (Ingo Ebersberger, Arndt von Haeseler and Heiko A. Schmidt).

5 Finding Protein-coding Genes (David C. Kulp).

6 Analyzing Regulatory Regions in Genomes (Thomas Werner).

7 Finding Repeats in Genome Sequences (Brian J. Haas and Steven L. Salzberg).

8 Analyzing Genome Rearrangements (Guillaume Bourque).

Part 4 Molecular Structure Prediction.

9 Predicting Simplified Features of Protein Structure (Dariusz Przybylski and Burkhard Rost).

10 Homology Modeling in Biology and Medicine (Roland L. Dunbrack, Jr.).

11 Protein Fold Recognition Based on Distant Homologs (Ingolf Sommer).

12 De Novo Structure Prediction: Methods and Applications (Richard Bonneau).

13 Structural Genomics (Philip E. Bourne and Adam Godzik).

14 RNA Secondary Structures (Ivo L. Hofacker and Peter F. Stadler).

15 RNA Tertiary Structure Prediction (François Major and Philippe Thibault).

Volume 2.

Part 5 Analysis of Molecular Interactions.

16 Docking and Scoring for Structure-based Drug Design (Matthias Rarey, Jörg Degen and Ingo Reulecke).

17 Modeling Protein–Protein and Protein–DNA Docking (Andreas Hildebrandt, Oliver Kohlbacher and Hans-Peter Lenhof).

18 Lead Identification by Virtual Screening (Andreas Kämper, Didier Rognan and Thomas Lengauer).

19 Efficient Strategies for Lead Optimization by Simultaneously Addressing Affinity, Selectivity and Pharmacokinetic Parameters (Karl-Heinz Baringhaus and Hans Matter).

Part 6 Molecular Networks.

20 Modeling and Simulating Metabolic Networks (Stefan Schuster and David Fell).

21 Inferring Gene Regulatory Networks (Michael Q. Zhang).

22 Modeling Cell Signaling Networks (Anthony Hasseldine, Azi Lipshtat, Ravi Iyengar and Avi Ma’ayan).

23 Dynamics of Virus–Host Cell Interaction (Udo Reichl and Yury Sidorenko).

Part 7 Analysis of Expression Data.

24 DNA Microarray Technology and Applications – An Overview (John Quackenbush).

25 Low-level Analysis of Microarray Experiments (Wolfgang Huber, Anja von Heydebreck and Martin Vingron).

26 Classification of Patients (Claudio Lottaz, Dennis Kostka and Rainer Spang).

27 Classification of Genes (Jörg Rahnenführer and Thomas Lengauer).

28 Proteomics: Beyond cDNA (Patricia M. Palagi, Yannick Brunner, Jean-Charles Sanchez and Ron D. Appel).

Volume 3.

Part 8 Protein Function Prediction.

29 Ontologies for Molecular Biology (Chris Wroe and Robert Stevens).

30 Inferring Protein Function from Sequence (Douglas Lee Brutlag).

31 Analyzing Protein Interaction Networks (Johannes Goll and Peter Uetz).

32 Inferring Protein Function from Genomic Context (Christian von Mering).

33 Inferring Protein Function from Protein Structure (Francisco S. Domingues and Thomas Lengauer).

34 Mining Information on Protein Function from Text (Martin Krallinger and Alfonso Valencia).

35 Integrating Information for Protein Function Prediction (William Stafford Noble and Asa Ben-Hur).

36 The Molecular Basis of Predicting Druggability (Bissan Al-Lazikani, Anna Gaulton, Gaia Paolini, Jerry Lanfear, John Overington and Andrew Hopkins).

Part 9 Comparative Genomics and Evolution of Genomes.

37 Comparative Genomics (Martin S. Taylor and Richard R. Copley).

38 Association Studies of Complex Diseases (Momiao Xiong and Li Jin).

39 Pharmacogenetics/Pharmacogenomics (Xing Jian Lou, Russ B. Altman and Teri E. Klein).

40 Evolution of Drug Resistance in HIV (Niko Beerenwinkel, Kirsten Roomp and Martin Däumer).

41 Analyzing the Evolution of Infectious Bacteria (Dawn Field, Edward J. Feil, Gareth Wilson and Paul Swift).

Part 10 Basic Bioinformatics Technologies.

42 Integrating Biological Databases (Zoé Lacroix, Bertram Ludäscher and Robert Stevens).

43 Visualization of Biological Data (Harry Hochheiser, Kevin W. Eliceiri and Ilya G. Goldberg).

44 Using Distributed Data and Tools in Bioinformatics Applications (Robert Stevens, Phillip Lord and Duncan Hull).

Part 11 Outlook.

45 Future Trends (Thomas Lengauer).

Index.

Name Index.