Bioinformatics - From Genomes to Therapies

Copyright © 2007 WILEY-VCH Verlag GmbH & Co. KGaA

Bioinformatics - From Genomes to Therapies

Editor(s): Thomas Lengauer

Published Online: 5 FEB 2008

Print ISBN: 9783527312788

Online ISBN: 9783527619368

DOI: 10.1002/9783527619368

About this Book

Product Information

About The Product

Once again, Thomas Lengauer has succeeded in creating a comprehensive and immensely useful bioinformatics resource that meets even the high standards of professionals in the pharmaceutical and medical sector.
By extending the classical application areas of bioinformatics to the most recent approaches in analyzing molecular networks and in predicting molecular function, this handbook serves as a first-stop resource for every bioinformatics user in the life sciences. With contributions by more than 40 of the world's leading bioinformaticians, it is unrivalled in terms of scientific authority and accuracy.
The best single information source available, written by professionals for professionals.

Table of contents

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      Frontmatter (pages I–XXXVII)

  2. Part 1: Introduction

    1. Chapter 1

      Bioinformatics — From Genomes to Therapies (pages 1–24)

      Thomas Lengauer

  3. Part 2: Sequencing Genomes

    1. Chapter 2

      Bioinformatics Support for Genome-Sequencing Projects (pages 25–55)

      Knut Reinert and Daniel Huson

  4. Part 3: Sequence Analysis

    1. Chapter 3

      Sequence Alignment and Sequence Database Search (pages 57–82)

      Martin Vingron

    2. Chapter 4

      Phylogeny Reconstruction (pages 83–128)

      Ingo Ebersberger, Arndt von Haeseler and Heiko A. Schmidt

    3. Chapter 5

      Finding Protein-coding Genes (pages 129–158)

      David C. Kulp

    4. Chapter 6

      Analyzing Regulatory Regions in Genomes (pages 159–195)

      Thomas Werner

    5. Chapter 7

      Finding Repeats in Genome Sequences (pages 197–233)

      Brian J. Haas and Steven L. Salzberg

    6. Chapter 8

      Analyzing Genome Rearrangements (pages 235–260)

      Guillaume Bourque

  5. Part 4: Molecular Structure Prediction

    1. Chapter 9

      Predicting Simplified Features of Protein Structure (pages 261–295)

      Dariusz Przybylski and Burkhard Rost

    2. Chapter 10

      Homology Modeling in Biology and Medicine (pages 297–349)

      Roland L. Dunbrack

    3. Chapter 11

      Protein Fold Recognition Based on Distant Homologs (pages 351–388)

      Ingolf Sommer

    4. Chapter 12

      De Novo Structure Prediction: Methods and Applications (pages 389–418)

      Richard Bonneau

    5. Chapter 13

      Structural Genomics (pages 419–438)

      Philip E. Bourne and Adam Godzik

    6. Chapter 14

      RNA Secondary Structures (pages 439–489)

      Ivo L. Hofacker and Peter F. Stadler

    7. Chapter 15

      RNA Tertiary Structure Prediction (pages 491–539)

      François Major and Philippe Thibault

  6. Part 5: Analysis of Molecular Interactions

    1. Chapter 16

      Docking and Scoring for Structure-based Drug Design (pages 541–599)

      Matthias Rarey, Jörg Degen and Ingo Reulecke

    2. Chapter 17

      Modeling Protein-Protein and Protein-DNA Docking (pages 601–650)

      Andreas Hildebrandt, Oliver Kohlbacher and Hans-Peter Lenhof

    3. Chapter 18

      Lead Identification by Virtual Screening (pages 651–704)

      Andreas Kämper, Didier Rognan and Thomas Lengauer

    4. Chapter 19

      Efficient Strategies for Lead Optimization by Simultaneously Addressing Affinity, Selectivity and Pharmacokinetic Parameters (pages 705–754)

      Karl-Heinz Baringhaus and Hans Matter

  7. Part 6: Molecular Networks

    1. Chapter 20

      Modeling and Simulating Metabolic Networks (pages 755–805)

      Stefan Schuster and David Fell

    2. Chapter 21

      Inferring Gene Regulatory Networks (pages 807–827)

      Michael Q. Zhang

    3. Chapter 22

      Modeling Cell Signaling Networks (pages 829–860)

      Anthony Hasseldine, Azi Lipshtat, Ravi Iyengar and Avi Máayan

    4. Chapter 23

      Dynamics of Virus-Host Cell Interaction (pages 861–898)

      Udo Reichl and Yury Sidorenko

  8. Part 7: Analysis of Expression Data

    1. Chapter 24

      DNA Microarray Technology and Applications — An Overview (pages 899–928)

      John Quackenbush

    2. Chapter 25

      Low-level Analysis of Microarray Experiments (pages 929–956)

      Wolfgang Huber, Anja von Heydebreck and Martin Vingron

    3. Chapter 26

      Classification of Patients (pages 957–991)

      Claudio Lottaz, Dennis Kostka and Rainer Spang

    4. Chapter 27

      Classification of Genes (pages 993–1021)

      Jörg Rahnenführer and Thomas Lengauer

    5. Chapter 28

      Proteomics: Beyond cDNA (pages 1023–1059)

      Patricia M. Palagi, Yannick Brunner, Jean-Charles Sanchez and Ron D. Appel

  9. Part 8: Protein Function Prediction

    1. Chapter 29

      Ontologies for Molecular Biology (pages 1061–1086)

      Chris Wroe and Robert Stevens

    2. Chapter 30

      Inferring Protein Function from Sequence (pages 1087–1119)

      Douglas Lee Brutlag

    3. Chapter 31

      Analyzing Protein Interaction Networks (pages 1121–1177)

      Johannes Goll and Peter Uetz

    4. Chapter 32

      Inferring Protein Function from Genomic Context (pages 1179–1210)

      Christian von Mering

    5. Chapter 33

      Inferring Protein Function from Protein Structure (pages 1211–1252)

      Francisco S. Domingues and Thomas Lengauer

    6. Chapter 34

      Mining Information on Protein Function from Text (pages 1253–1295)

      Martin Krallinger and Alfonso Valencia

    7. Chapter 35

      Integrating Information for Protein Function Prediction (pages 1297–1314)

      William Stafford Noble and Asa Ben-Hur

    8. Chapter 36

      The Molecular Basis of Predicting Druggability (pages 1315–1334)

      Bissan Al-Lazikani, Anna Gaulton, Gaia Paolini, Jerry Lanfear, John Overington and Andrew Hopkins

  10. Part 9: Comparative Genomics and Evolution of Genomes

    1. Chapter 37

      Comparative Genomics (pages 1335–1374)

      Martin S. Taylor and Richard R. Copley

    2. Chapter 38

      Association Studies of Complex Diseases (pages 1375–1426)

      Momiao Xiong and Li Jin

    3. Chapter 39

      Pharmacogenetics/Pharmacogenomics (pages 1427–1455)

      Xing Jian Lou, Russ B. Altman and Teri E. Klein

    4. Chapter 40

      Evolution of Drug Resistance in HIV (pages 1457–1495)

      Niko Beerenwinkel, Kirsten Roomp and Martin Däumer

    5. Chapter 41

      Analyzing the Evolution of Infectious Bacteria (pages 1497–1524)

      Dawn Field, Edward J. Feil, Gareth Wilson and Paul Swift

  11. Part 10: Basic Bioinformatics Technologies

    1. Chapter 42

      Integrating Biological Databases (pages 1525–1571)

      Zoé Lacroix, Bertram Ludäscher and Robert Stevens

    2. Chapter 43

      Visualization of Biological Data (pages 1573–1626)

      Harry Hochheiser, Kevin W. Eliceiri and Ilya G. Goldberg

    3. Chapter 44

      Using Distributed Data and Tools in Bioinformatics Applications (pages 1627–1650)

      Robert Stevens, Phillip Lord and Duncan Hull

  12. Part 11: Outlook - Outlook

    1. Chapter 45

      Future Trends (pages 1651–1686)

      Thomas Lengauer

    1. You have free access to this content
      Index (pages 1687–1726)

    1. You have free access to this content
      Name Index (pages 1727–1732)

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