Bioinformatics basics : applications in biological science and medicine /

Bioinformatics basics : applications in biological science and medicine /

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Bibliographic Details
Edition:2nd ed.
Imprint:Boca Raton : Taylor & Francis, 2005.
Description:335 p. : ill. ; 25 cm.
Language:English
Subject:
Bioinformatics.
Computational Biology.
Automatic Data Processing.
Chromosome Mapping.
Sequence Analysis, DNA.
Bioinformatics.
Format: Print Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/5727008
Hidden Bibliographic Details
Other authors / contributors:Buehler, Lukas K.
Rashidi, Hooman H.
ISBN:9780849312830 (hardcover : alk. paper)
0849312833 (hardcover : alk. paper)
Notes:Includes bibliographical references and index.
Table of Contents:
  • 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
  • References
  • 3.2.2.1. Gene Order and Chromosome Rearrangements
  • 3.2.2.2. MapViewer
  • 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
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