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Bioinformatics Basics : Applications in Biological Science and Medicine /

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Bibliographic Details
Corporate Author: Taylor & Francis
Other Authors: Buehler, Lukas K. (Editor), Rashidi, Hooman H. (Editor)
Format: eBook
Language:English
Published: Boca Raton, FL : Taylor & Francis, 2005.
Edition:Second edition.
Subjects:
Bioinformatics.
Gene mapping.
Life sciences > Data processing.
Gene mapping > Data processing.
Computational biology.
Computer science.
Electronic data processing.
Computational Biology
Chromosome Mapping
Electronic Data Processing
Sequence Analysis, DNA
Bio-informatique.
Sciences de la vie > Informatique.
Cartes chromosomiques > Informatique.
Cartes chromosomiques.
Informatique.
data processing.
computer science.
SCIENCE > Life Sciences > Biochemistry.
Life sciences > Data processing
Gene mapping > Data processing
Gene mapping
Electronic data processing
Computer science
Computational biology
Bioinformatics
Bioinformatik
Bio-informatica.
Electronic books.
Online Access:Connect to the full text of this electronic book
Table of Contents:
  • Cover
  • Half Title
  • Title Page
  • Copyright Page
  • Title Page
  • 1: Biology and Information
  • 1.1 Bioinformatics-A Rapidly Maturing Science
  • 1.1.1 From Genes to Proteins
  • 1.1.2 Bioinformatics in the Public Domain
  • 1.2 Computers in Biology and Medicine
  • 1.2.1 Computational Tools
  • 1.2.2 Limitations of Computational Tools
  • References
  • 1.3 The Virtual Doctor
  • 1.3.1 Mapping the Human Brain
  • References
  • 1.4 Biological Macromolecules as Information Carriers
  • References
  • 1.5 Proteins: From Sequence to Structure to Function
  • 1.5.1 Molecular Interaction in Protein Structures
  • 1.5.1.1 The Peptide Bond
  • 1.5.1.2 Characteristics of the Peptide Bond
  • 1.5.1.3 The Hydrophobic Effect and How It Contributes to Protein Folding
  • 1.5.1.4 Electrostatic Interactions
  • 1.5.1.5 Hydrogen Bonding
  • 1.5.1.6 Conformational Entropy
  • 1.5.1.7 Van der Waals Interactions (Packing)
  • 1.5.1.8 Covalent Bonds (e.g., Disulfide Bridge)
  • 1.5.2 Protein Functions
  • 1.5.2.1 Enzymes
  • 1.5.2.2 Regulatory Proteins
  • 1.5.2.3 Storage
  • 1.5.2.4 Transportation
  • 1.5.2.5 Signaling
  • 1.5.2.6 Immunity
  • 1.5.2.7 Structural
  • References
  • 1.6 DNA and RNA Structure
  • 1.6.1 The DNA Double Helix
  • 1.6.2 Genomic Size of DNA
  • References
  • 1.7 DNA Cloning and Sequencing
  • 1.7.1 DNA Cloning
  • 1.7.2 Transcriptional Profiling
  • 1.7.3 Positional Cloning and Chromosome Mapping
  • 1.7.4 Polymerase Chain Reaction (PCR)
  • 1.7.5 Sequencing Technologies
  • References
  • 1.8 Genes, Taxonomy, and Evolution
  • References
  • 2: Biological Databases
  • 2.1 Biological Database Organization
  • 2.1.1 Database Content and Management
  • 2.1.2 Data Submissions
  • 2.1.3 The Growth of Public Databases
  • 2.1.4 Data Retrieval
  • References
  • 2.1.5 Data Annotation and Database Connectivity
  • 2.1.5.1 Annotation
  • 2.1.5.2 Redundancy
  • 2.2 Public Databases.
  • 2.2.1 National Center for Biotechnology Information (NCBI)
  • 2.2.1.1 Who is Employed by NCBI?
  • 2.2.1.2 What Kind of Research is Conducted at NCBI?
  • 2.2.1.3 What Types of Databases are Supported by NCBI?
  • 2.2.1.4 What Do We Mean by Redundancy?
  • 2.2.1.5 What are Some of the Services Offered by NCBI?
  • References
  • 2.2.2 European Bioinformatics Institute (EBI)
  • 2.2.2.1 Who is Employed by EBI?
  • 2.2.2.2 What Kind of Research is Conducted at EBI?
  • 2.2.2.3 What Are Some Of The Services Offered By EBI?
  • References
  • 2.2.3 Kyoto Encyclopedia of Genes and Genomes (KEGG)
  • 2.2.3.1 Classification of Biological Molecules
  • 2.2.3.2 Cellular Processes at KEGG
  • References
  • 2.3. Database Mining Tools
  • 2.3.1 Sequence Similarity Search Tools: BLAST and FASTA
  • 2.3.1.1 Shared Characteristics in Both Sequence Alignment Tools
  • 2.3.1.2 How are Sequence Alignments Useful?
  • 2.3.1.3 Basic Local Alignment Search Tool (BLAST)
  • 2.3.2 An Overview of Database Sequence Searching
  • References
  • 2.3.3 Pattern Recognition Tools (Prosite)
  • 2.3.3.1 The Significance of Embedded Symbols within Each Signature and How to Read and Construct Signatures
  • References
  • 2.3.4 Multiple Alignment and Phylogenetic Tree Analysis
  • References
  • 3: Genome Analysis
  • 3.1 The Genomic Organization of Genes
  • 3.1.1 What are Genomes?
  • 3.1.2 Mapping and Navigating Genomes
  • 3.1.2.1 Genetic Linkage Maps
  • 3.1.2.2 Physical Maps
  • 3.1.2.3 From Sequence Maps to Gene Function Maps
  • References
  • 3.1.2 The Genome Projects
  • 3.1.2.1 How Many Genes are in a Genome?
  • References
  • 3.1.3 The Human Genome
  • References
  • 3.2 Comparative Genomics
  • 3.2.1 Cluster of Orthologous Groups (COGs)
  • 3.2.2 Homologene at NCBI
  • 3.2.2.1 Gene Order and Chromosome Rearrangements
  • 3.2.2.2 MapViewer
  • References
  • References
  • 3.3 Functional Genomics.
  • 3.3.1 The Transcriptome
  • 3.4 Microarray and Bioarray Technology
  • 3.4.1 Concept and Use
  • 3.4.2 Summary of a Typical Experiment Using Microarray Technology
  • 3.4.3 Microarray Bioinformatics
  • 3.4.4 Image Processing
  • References
  • 3.4.5 Data Annotation
  • References
  • 3.4.6 Data Analysis
  • 3.4.6.1 Experiment Design/Plan
  • 3.4.6.2 Volume of Data
  • 3.4.6.3 Dimensionality of Data
  • 3.4.6.4 Quality of Data
  • 3.4.7 Normalization
  • 3.4.8 Statistical Analysis
  • 3.4.9 Explorative Analysis
  • 3.4.9.1 Aim of Clustering
  • 3.4.9.2 Biological Interpretation of Clustering Results
  • 3.4.9.3 Theory of Clustering
  • 3.4.9.4 Clustering vs. Classification (Unsupervised vs. Supervised)
  • 3.4.10 Main Types of Clustering
  • 3.4.10.1 Hierarchical Clustering
  • 3.4.10.2 Nonhierarchical Clustering
  • 3.4.10.3 Other Clustering or Classification Algorithms
  • 3.4.10.4 Advice on Using Clustering
  • References
  • 3.4.11 Data Storage
  • References
  • 3.4.12 Data Mining
  • 3.4.13 Protein Arrays
  • 3.4.14 Concluding Remarks
  • 3.5 Genomes as Gene Networks
  • References
  • 4: Proteome Analysis
  • 4.1 Proteomics
  • 4.1.1 What is a Proteome?
  • 4.1.1.1 2-D Gels and Mass Spectrometry Tools
  • 4.1.1.2 2-D PAGE at Expasy (Swiss Bioinformatics Institute)
  • References
  • 4.2 Hydrodynamic Methods
  • 4.2.1 Introduction
  • 4.2.2 Analytical Ultracentrifugation
  • 4.2.2.1 Experimental Setup and Instrumentation
  • 4.2.2.2 Transport Processes in The AUC Cell
  • 4.2.2.3 Analytical Ultracentrifuge (AUC) Experiments
  • 4.2.3 Light Scattering
  • 4.2.3.1 Experimental Setup and Instrumentation
  • 4.2.3.2 Dynamic Light Scattering
  • 4.2.3.3 Static Light Scattering
  • 4.2.4 Global Analysis
  • 4.2.5 Appendix
  • References
  • 4.3 Predictive Biology
  • 4.3.1 Protein Structure Prediction
  • 4.3.1.1 Structure Prediction Software
  • References
  • 4.3.2 Structural Genomics
  • References.
  • 4.3.3 Rational Drug Design
  • References
  • 4.4 Systems Biology
  • 4.4.1 Protein Interaction Networks
  • References
  • 4.4.2 Metabolic Reconstruction
  • References
  • 5: The Bioinformatics Revolution in Medicine
  • 5.1 Genes and Diseases
  • 5.1.1 From Molecules to Diseases
  • References
  • 5.1.2 Online Mendelian Inheritance in Man (OMIM)
  • References
  • 5.1.3 Pharmacogenomics
  • 5.2 Agricultural Genomics
  • 5.2.1 Genetically Modified Organisms
  • References
  • 5.2.2 Biopharming
  • References
  • Appendix A: Glossary of Biological Terms
  • Appendix B: Bioinformatics Web Sites
  • Index.