Bioinformatics Basics: Applications in Biological Science and Medicine

Note: Supplemental materials are not guaranteed with Rental or Used book purchases.

ISBN: 9780849312830 | 0849312833
Cover: Hardcover
Copyright: 6/23/2005

Rent

(Recommended)

$94.09

Term

Due

Price

Semester

Dec 13

$104.55

Quarter

Aug 20

$99.32

Short Term

Jul 26

$94.09

*This item is part of an exclusive publisher rental program and requires an additional convenience fee. This fee will be reflected in the shopping cart.
Buy New

Usually Ships in 3-5 Business Days

$142.84
eBook

Available Instantly

Online: 180 Days

Downloadable: 180 Days

$51.36

Completely revised and updated, Bioinformatics Basics: Applications in Biological Science and Medicine, Second Edition will continue to serve as a tool that allows researchers to easily access and use databases to gather information on genes, proteins, and diseases. This new edition of a bestseller covers new approaches to data analysis using databases around the world. It identifies computing techniques that help readers manage the massive flow of information. The structure of this second edition will follow that of the first and its content will reflect the growth in information. New sections cover recent developments in genome projects, microarrays, proteomics, genome mapping, and more.

1 Biology and Information

(62)

1.1 Bioinformatics-A Rapidly Maturing Science

(11)

1.1.1 From Genes to Proteins

(5)

1.1.2 Bioinformatics in the Public Domain

(5)

1.2 Computers in Biology and Medicine

(11)

1.2.1 Computational Tools

(6)

1.2.2 Limitations of Computational Tools

(5)

References

(1)

1.3 The Virtual Doctor

(7)

1.3.1 Mapping the Human Brain

(5)

References

(1)

1.4 Biological Macromolecules as Information Carriers

(4)

References

(1)

1.5 Proteins: From Sequence to Structure to Function

(10)

1.5.1 Molecular Interaction in Protein Structures

(7)

1.5.1.1 The Peptide Bond

(2)

1.5.1.2 Characteristics of the Peptide Bond

(2)

1.5.1.3 The Hydrophobic Effect and How It Contributes to Protein Folding

(2)

1.5.1.4 Electrostatic Interactions

(1)

1.5.1.5 Hydrogen Bonding

(1)

1.5.1.6 Conformational Entropy

(1)

1.5.1.7 Van der Waals Interactions (Packing)

(1)

1.5.1.8 Covalent Bonds (e.g., Disulfide Bridge)

(1)

1.5.2 Protein Functions

(3)

1.5.2.1 Enzymes

(1)

1.5.2.2 Regulatory Proteins

(1)

1.5.2.3 Storage

(1)

1.5.2.4 Transportation

(1)

1.5.2.5 Signaling

(1)

1.5.2.6 Immunity

(1)

1.5.2.7 Structural

(1)

References

(1)

1.6 DNA and RNA Structure

(4)

1.6.1 The DNA Double Helix

(2)

1.6.2 Genomic Size of DNA

(1)

References

(1)

1.7 DNA Cloning and Sequencing

(7)

1.7.1 DNA Cloning

(1)

1.7.2 Transcriptional Profiling

(1)

1.7.3 Positional Cloning and Chromosome Mapping

(2)

1.7.4 Polymerase Chain Reaction (PCR)

(1)

1.7.5 Sequencing Technologies

(1)

References

(1)

1.8 Genes, Taxonomy, and Evolution

(5)

References

(2)

2 Biological Databases

(76)

2.1 Biological Database Organization

(11)

2.1.1 Database Content and Management

(1)

2.1.2 Data Submissions

(4)

2.1.3 The Growth of Public Databases

(2)

2.1.4 Data Retrieval

(4)

References

(5)

2.1.5 Data Annotation and Database Connectivity

(4)

2.1.5.1 Annotation

(2)

2.1.5.2 Redundancy

(1)

2.2 Public Databases

(10)

2.2.1 National Center for Biotechnology Information (NCBI)

(10)

2.2.1.1 Who is Employed by NCBI?

(1)

2.2.1.2 What Kind of Research is Conducted at NCBI?

(1)

2.2.1.3 What Types of Databases are Supported by NCBI?

(1)

2.2.1.4 What Do We Mean by Redundancy?

(2)

2.2.1.5 What are Some of the Services Offered by NCBI?

(5)

References

(12)

2.2.2 European Bioinformatics Institute (EBI)

(11)

2.2.2.1 Who is Employed by EBI?

(1)

2.2.2.2 What Kind of Research is Conducted at EBI?

(2)

2.2.2.3 What Are Some Of The Services Offered By EBI?

(9)

References

101

(16)

2.2.3 Kyoto Encyclopedia of Genes and Genomes (KEGG)

102

(16)

2.2.3.1 Classification of Biological Molecules

112

(2)

2.2.3.2 Cellular Processes at KEGG

114

(3)

References

117

(1)

2.3. Database Mining Tools

118

(13)

2.3.1 Sequence Similarity Search Tools: BLAST and FASTA

118

(11)

2.3.1.1 Shared Characteristics in Both Sequence Alignment Tools

120

(1)

2.3.1.2 How are Sequence Alignments Useful?

121

(1)

2.3.1.3 Basic Local Alignment Search Tool (BLAST)

122

(7)

2.3.2 An Overview of Database Sequence Searching

129

(2)

References

131

(3)

2.3.3 Pattern Recognition Tools (Prosite)

132

(2)

2.3.3.1 The Significance of Embedded Symbols within Each Signature and How to Read and Construct Signatures

133

(1)

References

134

(3)

2.3.4 Multiple Alignment and Phylogenetic Tree Analysis

134

(3)

References

137

(2)

3 Genome Analysis

139

(78)

3.1 The Genomic Organization of Genes

139

(15)

3.1.1 What are Genomes?

139

(3)

3.1.2 Mapping and Navigating Genomes

142

(12)

3.1.2.1 Genetic Linkage Maps

147

(2)

3.1.2.2 Physical Maps

149

(5)

3.1.2.3 From Sequence Maps to Gene Function Maps

154

(1)

References

154

(10)

3.1.2 The Genome Projects

155

(9)

3.1.2.1 How Many Genes are in a Genome?

158

(6)

References

164

(5)

3.1.3 The Human Genome

164

(5)

References

169

(1)

3.2 Comparative Genomics

170

(12)

3.2.1 Cluster of Orthologous Groups (COGs)

170

(6)

3.2.2 Homologene at NCBI

176

(6)

References

182

(3)

3.2.2.1 Gene Order and Chromosome Rearrangements

182

(1)

3.2.2.2 MapViewer

183

(2)

References

185

(1)

3.3 Functional Genomics

185

(5)

3.3.1 The Transcriptome

185

(5)

3.4 Microarray and Bioarray Technology

190

(5)

3.4.1 Concept and Use

190

(1)

3.4.2 Summary of a Typical Experiment Using Microarray Technology

191

(1)

3.4.3 Microarray Bioinformatics

191

(3)

3.4.4 Image Processing

194

(1)

References

195

(1)

3.4.5 Data Annotation

195

(1)

References

196

(11)

3.4.6 Data Analysis

196

(3)

3.4.6.1 Experiment Design/Plan

197

(1)

3.4.6.2 Volume of Data

197

(2)

3.4.6.3 Dimensionality of Data

199

(1)

3.4.6.4 Quality of Data

199

(1)

3.4.7 Normalization

199

(1)

3.4.8 Statistical Analysis

199

(3)

3.4.9 Explorative Analysis

202

(1)

3.4.9.1 Aim of Clustering

202

(1)

3.4.9.2 Biological Interpretation of Clustering Results

202

(1)

3.4.9.3 Theory of Clustering

202

(1)

3.4.9.4 Clustering vs. Classification (Unsupervised vs. Supervised)

203

(1)

3.4.10 Main Types of Clustering

203

(4)

3.4.10.1 Hierarchical Clustering

203

(1)

3.4.10.2 Nonhierarchical Clustering

204

(2)

3.4.10.3 Other Clustering or Classification Algorithms

206

(1)

3.4.10.4 Advice on Using Clustering

206

(1)

References

207

(2)

3.4.11 Data Storage

208

(1)

References

209

(2)

3.4.12 Data Mining

209

(1)

3.4.13 Protein Arrays

209

(2)

3.4.14 Concluding Remarks

211

(1)

3.5 Genomes as Gene Networks

211

(5)

References

216

(1)

4 Proteome Analysis

217

(80)

4.1 Proteomics

217

(8)

4.1.1 What is a Proteome?

217

(9)

4.1.1.1 2-D Gels and Mass Spectrometry Tools

219

(2)

4.1.1.2 2-D PAGE at Expasy (Swiss Bioinformatics Institute)

221

(4)

References

225

(1)

4.2 Hydrodynamic Methods

226

(29)

4.2.1 Introduction

226

(2)

4.2.2 Analytical Ultracentrifugation

228

(18)

4.2.2.1 Experimental Setup and Instrumentation

228

(1)

4.2.2.2 Transport Processes in The AUC Cell

229

(5)

4.2.2.3 Analytical Ultracentrifuge (AUC) Experiments

234

(12)

4.2.3 Light Scattering

246

(6)

4.2.3.1 Experimental Setup and Instrumentation

246

(1)

4.2.3.2 Dynamic Light Scattering

247

(3)

4.2.3.3 Static Light Scattering

250

(2)

4.2.4 Global Analysis

252

(2)

4.2.5 Appendix

254

(1)

References

255

(1)

4.3 Predictive Biology

256

(13)

4.3.1 Protein Structure Prediction

256

(13)

4.3.1.1 Structure Prediction Software

266

(3)

References

269

(7)

4.3.2 Structural Genomics

269

(7)

References

276

(9)

4.3.3 Rational Drug Design

276

(9)

References

285

(1)

4.4 Systems Biology

285

(5)

4.4.1 Protein Interaction Networks

285

(5)

References

290

(5)

4.4.2 Metabolic Reconstruction

290

(5)

References

295

(2)

5 The Bioinformatics Revolution in Medicine

297

(20)

5.1 Genes and Diseases

297

(6)

5.1.1 From Molecules to Diseases

297

(6)

References

303

(5)

5.1.2 Online Mendelian Inheritance in Man (OMIM)

303

(5)

References

308

(1)

5.1.3 Pharmacogenomics

308

(1)

5.2 Agricultural Genomics

309

(4)

5.2.1 Genetically Modified Organisms

312

(1)

References

313

(3)

5.2.2 Biopharming

313

(3)

References

316

(1)

Appendix A Glossary of Biological Terms

317

(6)

Appendix B Bioinformatics Web Sites

323

(2)

Index

325

Please wait while the item is added to your bag...

FREE SHIPPING

Amazon no longer offers textbook rentals. We do!

Bioinformatics Basics: Applications in Biological Science and Medicine

Summary

Table of Contents

Supplemental Materials