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Bioinformatics and Functional Genomics, Second Edition

Book Description

The bestselling introduction to bioinformatics and functional genomics—now in an updated edition

Widely received in its previous edition, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded Second Edition, it continues to be the go-to source for students and professionals involved in biomedical research.

This edition provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include:

  • Several fundamentally important proteins, such as globins, histones, insulin, and albumins, are included to better show how to apply bioinformatics tools to basic biological questions.

  • A completely updated companion web site, which will be updated as new information becomes available - visit www.wiley.com/go/pevsnerbioinformatics

  • Descriptions of genome sequencing projects spanning the tree of life.

  • A stronger focus on how bioinformatics tools are used to understand human disease.

  • The book is complemented by lavish illustrations and more than 500 figures and tables—fifty of which are entirely new to this edition. Each chapter includes a Problem Set, Pitfalls, Boxes explaining key techniques and mathematics/statistics principles, Summary, Recommended Reading, and a list of freely available software. Readers may visit a related Web page for supplemental information at www.wiley.com/go/pevsnerbioinformatics.

    Bioinformatics and Functional Genomics, Second Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.

    Praise for the first edition:

    "...ideal both for biologists who want to master the application of bioinformatics to real-world problems and for computer scientists who need to understand the biological questions that motivate algorithms." Quarterly Review of Biology

    "... an excellent textbook for graduate students and upper level undergraduate students." Annals of Biomedical Engineering

    "...highly recommended for academic and medical libraries, and for researchers as an introduction and reference..." E-Streams

    Table of Contents

    1. Cover Page
    2. Title Page
    3. Copyright
    4. Dedication
    5. Contents in Brief
    6. Contents
    7. Preface to the Second Edition
    8. Preface to the First Edition
      1. ORIGINS OF THIS BOOK
      2. COMPARISON
      3. THE CHALLENGE OF HUMAN DISEASE
      4. NOTE TO READERS
      5. ACKNOWLEDGMENTS
    9. Foreword
    10. Part I: Analyzing DNA, RNA, and Protein Sequences in Databases
      1. 1: Introduction
        1. ORGANIZATION OF THE BOOK
        2. BIOINFORMATICS: THE BIG PICTURE
        3. A CONSISTENT EXAMPLE: HEMOGLOBIN
        4. ORGANIZATION OF THE CHAPTERS
        5. A TEXTBOOK FOR COURSES ON BIOINFORMATICS AND GENOMICS
        6. KEY BIOINFORMATICS WEBSITES
        7. SUGGESTED READING
        8. REFERENCES
      2. 2: Access to Sequence Data and Literature Information
        1. INTRODUCTION TO BIOLOGICAL DATABASES
        2. GENBANK: DATABASE OF MOST KNOWN NUCLEOTIDE AND PROTEIN SEQUENCES
        3. NATIONAL CENTER FOR BIOTECHNOLOGY INFORMATION
        4. THE EUROPEAN BIOINFORMATICS INSTITUTE (EBI)
        5. ACCESS TO INFORMATION: ACCESSION NUMBERS TO LABEL AND IDENTIFY SEQUENCES
        6. ACCESS TO INFORMATION VIA ENTREZ GENE AT NCBI
        7. ACCESS TO INFORMATION: PROTEIN DATABASES
        8. ACCESS TO INFORMATION: THE THREE MAIN GENOME BROWSERS
        9. EXAMPLES OF HOW TO ACCESS SEQUENCE DATA
        10. ACCESS TO BIOMEDICAL LITERATURE
        11. PERSPECTIVE
        12. PITFALLS
        13. WEB RESOURCES
        14. DISCUSSION QUESTIONS
        15. PROBLEMS
        16. SELF-TEST QUIZ
        17. SUGGESTED READING
        18. REFERENCES
      3. 3: Pairwise Sequence Alignment
        1. INTRODUCTION
        2. SCORING MATRICES
        3. ALIGNMENT ALGORITHMS: GLOBAL AND LOCAL
        4. THE STATISTICAL SIGNIFICANCE OF PAIRWISE ALIGNMENTS
        5. PERSPECTIVE
        6. PITFALLS
        7. WEB RESOURCES
        8. DISCUSSION QUESTIONS
        9. PROBLEMS/COMPUTER LAB
        10. SELF-TEST QUIZ
        11. SUGGESTED READING
        12. REFERENCES
      4. 4: Basic Local Alignment Search Tool (BLAST)
        1. INTRODUCTION
        2. BLAST SEARCH STEPS
        3. BLAST ALGORITHM USES LOCAL ALIGNMENT SEARCH STRATEGY
        4. BLAST SEARCH STRATEGIES
        5. PERSPECTIVE
        6. PITFALLS
        7. WEB RESOURCES
        8. DISCUSSION QUESTIONS
        9. COMPUTER LAB/PROBLEMS
        10. SELF-TEST QUIZ
        11. SUGGESTED READING
        12. REFERENCES
      5. 5: Advanced Database Searching
        1. INTRODUCTION
        2. SPECIALIZED BLAST SITES
        3. FINDING DISTANTLY RELATED PROTEINS: POSITION-SPECIFIC ITERATED BLAST (PSI-BLAST)
        4. PROFILE SEARCHES: HIDDEN MARKOV MODELS
        5. BLAST-LIKE ALIGNMENT TOOLS TO SEARCH GENOMIC DNA RAPIDLY
        6. USING BLAST FOR GENE DISCOVERY
        7. PERSPECTIVE
        8. PITFALLS
        9. WEB RESOURCES
        10. DISCUSSION QUESTIONS
        11. PROBLEMS/COMPUTER LAB
        12. SELF-TEST QUIZ
        13. SUGGESTED READING
        14. REFERENCES
      6. 6: Multiple Sequence Alignment
        1. INTRODUCTION
        2. FIVE MAIN APPROACHES TO MULTIPLE SEQUENCE ALIGNMENT
        3. DATABASES OF MULTIPLE SEQUENCE ALIGNMENTS
        4. MULTIPLE SEQUENCE ALIGNMENTS OF GENOMIC REGIONS
        5. PERSPECTIVE
        6. PITFALLS
        7. WEB RESOURCES
        8. DISCUSSION QUESTIONS
        9. PROBLEMS/COMPUTER LAB
        10. SELF-TEST QUIZ
        11. SUGGESTED READING
        12. REFERENCES
      7. 7: Molecular Phylogeny and Evolution
        1. INTRODUCTION TO MOLECULAR EVOLUTION
        2. MOLECULAR PHYLOGENY: PROPERTIES OF TREES
        3. TYPE OF TREES
        4. FIVE STAGES OF PHYLOGENETIC ANALYSIS
        5. PHYLOGENETIC METHODS
        6. PERSPECTIVE
        7. PITFALLS
        8. WEB RESOURCES
        9. DISCUSSION QUESTIONS
        10. PROBLEMS/COMPUTER LAB
        11. SELF-TEST QUIZ
        12. SUGGESTED READING
        13. REFERENCES
    11. Part II: Genomewide Analysis of RNA and Protein
      1. 8: Bioinformatic Approaches to Ribonucleic Acid (RNA)
        1. INTRODUCTION TO RNA
        2. NONCODING RNA
        3. INTRODUCTION TO MESSENGER RNA
        4. MICROARRAYS: GENOMEWIDE MEASUREMENT OF GENE EXPRESSION
        5. INTERPRETATION OF RNA ANALYSES
        6. PERSPECTIVE
        7. PITFALLS
        8. WEB RESOURCES
        9. DISCUSSION QUESTIONS
        10. PROBLEMS
        11. SELF-TEST QUIZ
        12. SUGGESTED READING
        13. REFERENCES
      2. 9: Gene Expression: Microarray Data Analysis
        1. INTRODUCTION
        2. MICROARRAY DATA ANALYSIS: PREPROCESSING
        3. MlCROARRAY DATA ANALYSIS: INFERENTIAL STATISTICS
        4. MICROARRAY DATA ANALYSIS: DESCRIPTIVE STATISTICS
        5. FUNCTIONAL ANNOTATION OF MICROARRAY DATA
        6. PERSPECTIVE
        7. PITFALLS
        8. DISCUSSION QUESTIONS
        9. PROBLEMS/COMPUTER LAB
        10. SELF-TEST QUIZ
        11. SUGGESTED READING
        12. REFERENCES
      3. 10: Protein Analysis and Proteomics
        1. INTRODUCTION
        2. TECHNIQUES TO IDENTIFY PROTEINS
        3. FOUR PERSPECTIVES ON PROTEINS
        4. PERSPECTIVE 1. PROTEIN DOMAINS AND MOTIFS: MODULAR NATURE OF PROTEINS
        5. PERSPECTIVE 2. PHYSICAL PROPERTIES OF PROTEINS
        6. INTRODUCTION TO PERSPECTIVES 3 AND 4: GENE ONTOLOGY CONSORTIUM
        7. PERSPECTIVE 3: PROTEIN LOCALIZATION
        8. PERSPECTIVE 4: PROTEIN FUNCTION
        9. PERSPECTIVE
        10. PITFALLS
        11. WEB RESOURCES
        12. DISCUSSION QUESTIONS
        13. PROBLEMS/COMPUTER LAB
        14. SELF-TEST QUIZ
        15. SUGGESTED READING
        16. REFERENCES
      4. 11: Protein Structure
        1. OVERVIEW OF PROTEIN STRUCTURE
        2. PRINCIPLES OF PROTEIN STRUCTURE
        3. THE PROTEIN DATA BANK
        4. PROTEIN STRUCTURE PREDICTION
        5. INTRINSICALLY DISORDERED PROTEINS
        6. PROTEIN STRUCTURE AND DISEASE
        7. PERSPECTIVE
        8. PITFALLS
        9. DISCUSSION QUESTIONS
        10. PROBLEMS/COMPUTER LAB
        11. SELF-TEST QUIZ
        12. SUGGESTED READING
        13. REFERENCES
      5. 12: Functional Genomics
        1. INTRODUCTION TO FUNCTIONAL GENOMICS
        2. EIGHT MODEL ORGANISMS FOR FUNCTIONAL GENOMICS
        3. FUNCTIONAL GENOMICS USING REVERSE GENETICS AND FORWARD GENETICS
        4. FUNCTIONAL GENOMICS AND THE CENTRAL DOGMA
        5. PROTEOMICS APPROACHES TO FUNCTIONAL GENOMICS
        6. PERSPECTIVE
        7. PITFALLS
        8. DISCUSSION QUESTIONS
        9. PROBLEMS/COMPUTER LABORATORY
        10. SELF-TEST QUIZ
        11. SUGGESTED READING
        12. REFERENCES
    12. Part III: Genome Analysis
      1. 13: Completed Genomes
        1. INTRODUCTION
        2. GENOME-SEQUENCING PROJECTS: OVERVIEW
        3. GENOME ANALYSIS PROJECTS
        4. DNA SEQUENCING TECHNOLOGIES
        5. THE PROCESS OF GENOME SEQUENCING
        6. GENOME ANNOTATION: FEATURES OF GENOMIC DNA
        7. PERSPECTIVE
        8. PITFALLS
        9. DISCUSSION QUESTIONS
        10. PROBLEMS/COMPUTER LAB
        11. SELF-TEST QUIZ
        12. SUGGESTED READING
        13. REFERENCES
      2. 14: Completed Genomes: Viruses
        1. INTRODUCTION
        2. BIOINFORMATICS APPROACHES TO PROBLEMS IN VIROLOGY
        3. INFLUENZA VIRUS
        4. HERPESVIRUS: FROM PHYLOGENY TO GENE EXPRESSION
        5. HUMAN IMMUNODEFICIENCY VIRUS
        6. MEASLES VIRUS
        7. PERSPECTIVES
        8. PITFALLS
        9. WEB RESOURCES
        10. DISCUSSION QUESTIONS
        11. PROBLEMS/COMPUTER LAB
        12. SELF-TEST QUIZ
        13. SUGGESTED READING
        14. REFERENCES
      3. 15: Completed Genomes: Bacteria and Archaea
        1. INTRODUCTION
        2. CLASSIFICATION OF BACTERIA AND ARCHAEA
        3. ANALYSIS OF PROKARYOTIC GENOMES
        4. COMPARISON OF PROKARYOTIC GENOMES
        5. PERSPECTIVE
        6. PITFALLS
        7. WEB RESOURCES
        8. DISCUSSION QUESTIONS
        9. PROBLEMS/COMPUTER LAB
        10. SELF-TEST QUIZ
        11. SUGGESTED READING
        12. REFERENCES
      4. 16: The Eukaryotic Chromosome
        1. INTRODUCTION
        2. GENERAL FEATURES OF EUKARYOTIC GENOMES AND CHROMOSOMES
        3. REPETITIVE DNA CONTENT OF EUKARYOTIC CHROMOSOMES
        4. GENE CONTENT OF EUKARYOTIC CHROMOSOMES
        5. REGULATORY REGIONS OF EUKARYOTIC CHROMOSOMES
        6. COMPARISON OF EUKARYOTIC DNA
        7. VARIATION IN CHROMOSOMAL DNA
        8. TECHNIQUES TO MEASURE CHROMOSOMAL CHANGE
        9. PERSPECTIVE
        10. PITFALLS
        11. WEB RESOURCES
        12. DISCUSSION QUESTIONS
        13. PROBLEMS/COMPUTER LAB
        14. SELF-TEST QUIZ
        15. SUGGESTED READING
        16. REFERENCES
      5. 17: Eukaryotic Genomes: Fungi
        1. INTRODUCTION
        2. INTRODUCTION TO BUDDING YEAST SACCHAROMYCES CEREVISIAE
        3. GENE DUPLICATION AND GENOME DUPLICATION OF S. CEREVISIAE
        4. COMPARATIVE ANALYSES OF HEMIASCOMYCETES
        5. ANALYSIS OF FUNGAL GENOMES
        6. PERSPECTIVE
        7. PITFALLS
        8. WEB RESOURCES
        9. DISCUSSION QUESTIONS
        10. PROBLEMS/COMPUTER LAB
        11. SELF-TEST QUIZ
        12. SUGGESTED READING
        13. REFERENCES
      6. 18: Eukaryotic Genomes: From Parasites to Primates
        1. INTRODUCTION
        2. PROTOZOANS AT THE BASE OF THE TREE LACKING MITOCHONDRIA
        3. GENOMES OF UNICELLULAR PATHOGENS: TRYPANOSOMES AND LEISHMANIA
        4. THE CHROMALVEOLATES
        5. PLANT GENOMES
        6. SLIME AND FRUITING BODIES AT THE FEET OF METAZOANS
        7. METAZOANS
        8. PERSPECTIVE
        9. PITFALLS
        10. WEB RESOURCES
        11. DISCUSSION QUESTIONS
        12. PROBLEMS/COMPUTER LAB
        13. SELF-TEST QUIZ
        14. SUGGESTED READING
        15. REFERENCES
      7. 19: Human Genome
        1. INTRODUCTION
        2. MAIN CONCLUSIONS OF HUMAN GENOME PROJECT
        3. GATEWAYS TO ACCESS THE HUMAN GENOME
        4. THE HUMAN GENOME PROJECT
        5. 24 HUMAN CHROMOSOMES
        6. VARIATION: SEQUENCING INDIVIDUAL GENOMES
        7. VARIATION: SNPS TO COPY NUMBER VARIANTS
        8. PERSPECTIVE
        9. PITFALLS
        10. DISCUSSION QUESTIONS
        11. PROBLEMS/COMPUTER LAB
        12. SELF-TEST QUIZ
        13. SUGGESTED READING
        14. REFERENCES
      8. 20: Human Disease
        1. HUMAN GENETIC DISEASE: A CONSEQUENCE OF DNA VARIATION
        2. FOUR CATEGORIES OF DISEASE
        3. DISEASE DATABASES
        4. FOUR APPROACHES TO IDENTIFYING DISEASE-ASSOCIATED GENES
        5. HUMAN DISEASE GENES IN MODEL ORGANISMS
        6. FUNCTIONAL CLASSIFICATION OF DISEASE GENES
        7. PERSPECTIVE
        8. PITFALLS
        9. WEB RESOURCES
        10. DISCUSSION QUESTIONS
        11. PROBLEMS
        12. SELF-TEST QUIZ
        13. SUGGESTED READING
        14. REFERENCES
    13. Glossary
      1. A
      2. B
      3. C
      4. D
      5. E
      6. F
      7. G
      8. H
      9. I
      10. J
      11. K
      12. L
      13. M
      14. N
      15. O
      16. P
      17. Q
      18. R
      19. S
      20. T
      21. U
      22. V
      23. W
      24. X
      25. Y
      26. Z
    14. Answersto Self-Test Quizzes
    15. Author Index
    16. Subject Index