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Systems Bioinformatics: An Engineering Case-Based Approach Unabridged edition [Hardback]

Gil Alterovitz, Marco Ramoni

Formāts: Hardback, 398 pages
Izdošanas datums: 28-Feb-2007
Izdevniecība: Artech House Publishers
ISBN-10: 1596931248
ISBN-13: 9781596931244

Citas grāmatas par šo tēmu:

Biotechnology

Hardback
Cena: 114,54 €
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Formāts: Hardback, 398 pages
Izdošanas datums: 28-Feb-2007
Izdevniecība: Artech House Publishers
ISBN-10: 1596931248
ISBN-13: 9781596931244

Citas grāmatas par šo tēmu:

Biotechnology

Permanent link: https://www.kriso.lv/db/9781596931244.html

Keywords:

Beginning from an engineering perspective and written for engineering students, this textbook presents applications in systems bioinformatics, the intersection of systems biology and bioinformatics. The approach adopted by the editors (both of Harvard Medical School) is to match familiar engineering ideas, such as analysis, design, and reverse engineering with their applications in systems bioinformatics. Thus, a section on signal processing addresses biological signal processing and signal processing methods for mass spectrometry, a section on control and systems explores modeling cellular networks, and a section on probabilistic data networks and communications contains chapters on topological analysis of biomolecular networks and on Bayesian networks for genetic analysis. Other topics addressed include fundamentals of design for synthetic biology, applied cellular engineering, DNA/RNA sequence hybridization, biomolecular computing and cryptography, and chemotaxis. The CD-ROM contains a variety of computer programs for data analysis, modeling, and other purposes. Annotation ©2007 Book News, Inc., Portland, OR (booknews.com)

Preface

PART I Introduction: Molecular and Cellular Biology

(46)

Molecular and Cellular Biology: An Engineering Perspective

(12)

Cellular Structures and Functions

(1)

Introduction to Information Handling in Cells

(1)

The Importance and Diversity of Proteins

(1)

DNA Replication: Copying the Code

(1)

Transcription: Sending a Messenger

(2)

Translation: Protein Synthesis

(2)

Control of Gene Expression

(1)

Genetic Engineering

(1)

Summary

(2)

Proteomics: From Genome to Proteome

(32)

Defining the Proteome

(3)

From Genes to Proteins

(2)

What Is Proteomics?

(1)

Functional Proteomics

(1)

Building Gene Collections for Functional Proteomics Approaches

(17)

Selection of Target Genes for a Cloning Project

(4)

Clone Production

(7)

Sequencing and Analysis

(2)

Clone Maintenance and Distribution

(1)

Use of Clones in Functional Proteomics Approaches

(12)

High-Throughput Protein Production

(2)

Protein Arrays

(1)

Cell-Based Functional Proteomic Assays

(8)

PART II Analysis: Signal Processing

(78)

Introduction to Biological Signal Processing at the Cell Level

(52)

Introduction to Fundamental Signal Processing Concepts

(8)

Signals

(3)

Systems

(3)

Random Processes and Spectral Analysis

(2)

Signal Detection and Estimation

(15)

DNA Sequencing

(7)

Gene Identification

(4)

Protein Hotspots Identification

(3)

System Identification and Analysis

(19)

Gene Regulation Systems

(7)

Protein Signaling Systems

(9)

Conclusion

(8)

Signal Processing Methods for Mass Spectrometry

101

(24)

Introduction

101

(4)

Data Acquisition Methods

102

(1)

History of Ionization Techniques

102

(1)

Sample Preparation

103

(1)

Ionization

103

(1)

Separation of Ions by Mass and Charge

103

(1)

Detection of Ions and Recorded Data

104

(1)

Data Preprocessing

104

(1)

Example Data

105

(1)

Signal Resampling

105

(4)

Algorithm Explanation and Discussion

106

(1)

Example Demonstrating Down Sampling

107

(2)

Correcting the Background

109

(3)

Algorithm Explanation and Discussion

109

(2)

Example Demonstrating Baseline Subtraction

111

(1)

Aligning Mass/Charge Values

112

(4)

Algorithm Explanation and Discussion

113

(1)

Example Demonstrating Aligning Mass/Charge Values

114

(2)

Normalizing Relative Intensity

116

(3)

Example Demonstrating Intensity Normalization

116

(3)

Smoothing Noise

119

(3)

Lowess Filter Smoothing

120

(1)

Savitzky and Golay Filter Smoothing

121

(1)

Example Demonstrating Noise Smoothing

121

(1)

Identifying Ion Peaks

122

(3)

PART III Analysis: Control and Systems

125

(54)

Control and Systems Fundamentals

127

(24)

Introduction

127

(1)

Review of Fundamental Concepts in Control and Systems Theory

128

(5)

Discrete-Time Dynamical Systems

132

(1)

Control Theory in Systems Biology

133

(2)

Reverse Engineering Cellular Networks

135

(2)

Gene Networks

137

(10)

Boolean Networks

139

(4)

Dynamic Bayesian Networks

143

(4)

Conclusion

147

(4)

Modeling Cellular Networks

151

(28)

Introduction

151

(2)

Construction and Analysis of Kinetic Models

153

(11)

Parameter Estimation and Modeling Resources

153

(1)

A Modular Approach to Model Formulation

154

(2)

Basic Kinetics

156

(2)

Deterministic Models

158

(1)

Cellular Noise and Stochastic Methods

158

(3)

System Analysis Techniques

161

(3)

Case Studies

164

(8)

Expression of a Single Gene

164

(2)

A Phosphorylation-Dephosphorylation Cycle

166

(2)

A Synthetic Population Control Circuit

168

(4)

Conclusion

172

(7)

PART IV Analysis: Probabilistic Data Networks and Communications

179

(50)

Topological Analysis of Biomolecular Networks

181

(24)

Cellular Networks

181

(8)

Genetic Regulation Networks

182

(2)

Protein-Protein Interaction Networks

184

(1)

Metabolic Regulation Networks

185

(1)

The Scale-Free Property: A Network Characteristics

186

(3)

The Topology of Cellular Networks

189

(9)

Network Motifs in Genetic Regulation Networks

189

(2)

Topological Characterization of Protein Networks

191

(1)

Topology of Metabolic Networks

192

(4)

Adjacency Matrices

196

(1)

Hubs

196

(1)

Reachability

197

(1)

Gene Ontology and Functional Clustering of Essential Genes

198

(3)

Conclusion and Future Avenues

201

(4)

Bayesian Networks for Genetic Analysis

205

(24)

Introduction

205

(1)

Elements of Population Genetics

206

(4)

Bayesian Networks

210

(11)

Representation

210

(3)

Learning

213

(4)

Reasoning

217

(2)

Validation and Inference

219

(1)

Risk Prediction

219

(2)

Two Applications

221

(3)

Stroke Risk in Sickle Cell Anemia Subjects

221

(1)

Network Representation of a Complex Trait

221

(3)

Conclusion

224

(5)

PART V Design: Synthetic Biology

229

(54)

Fundamentals of Design for Synthetic Biology

231

(12)

Overview

231

(1)

Circuits

232

(4)

Riboregulators

234

(1)

Feedback Loops

235

(1)

Toggle Switches

236

(1)

Logic Gates

236

(1)

Oscillators

236

(1)

Multicellular Systems

236

(2)

Challenges

238

(2)

Standardization

238

(1)

Stochasticity

238

(1)

Directed Evolution

239

(1)

Random and Targeted Mutagenesis and Recombination

239

(1)

System Interface

240

(1)

Kinetics

240

(1)

Conclusion

240

(3)

BioJADE: Designing and Building Synthetic Biological Systems from Parts

243

(20)

Introduction

243

(1)

Fundamentals of BioJade and BioBricks Construction

243

(3)

Inspiration

243

(1)

The BioBricks Standard

244

(1)

BioBrick Definition

244

(1)

The Abstraction Barrier

245

(1)

Representing Parts

246

(2)

Parts Data Model

247

(1)

BioJade Architecture

248

(3)

Aspects

248

(1)

Schematic

249

(1)

Functional Network Aspect

250

(1)

DNA Aspect

250

(1)

Icon Aspect

251

(1)

Part Repositories

251

(1)

Using BioJade, an Example: The Repressilator

251

(3)

Simulations

254

(3)

D-Flux

254

(1)

Stochastirator

255

(1)

Tabasco

255

(1)

Generating the Simulation

256

(1)

The Reality Check

257

(1)

Biological Circuit Design Cannot Be as Easy as VLSI Design

257

(1)

Bugs Fight Back

257

(1)

Next Steps

258

(5)

Simulations

258

(1)

Parts

259

(1)

Designing Systems

259

(1)

Measurement

259

(4)

Applied Cellular Engineering

263

(20)

Introduction

263

(3)

Biological Systems Engineering

263

(2)

Cellular Catalytic Machinery

265

(1)

Early Engineering Successes

265

(1)

Engineering Tools

266

(11)

Network Models and Analysis

266

(5)

Experimental Methods

271

(6)

Case Study: Production of 1,3-Propanediol in E. coli

277

(1)

Frontiers

277

(1)

Conclusion

278

(5)

PART VI Integration: Applying Biology's Designs and Principles in Engineering

283

(82)

The Three Faces of DNA/RNA Sequence Hybridization

285

(34)

Introduction

285

(1)

A Short Introduction to DNA/RNA Sequence Hybridization and Self-Hybridization

286

(3)

DNA/RNA Sequence Hybridization: A Biological Point of View

289

(5)

Functional RNA Molecules

289

(2)

Gene Silencing and RNA Interference

291

(1)

RNA Editing and Re-encoding

291

(2)

Fragile DNA Regions and Secondary Structures

293

(1)

DNA/RNA Sequence Hybridization: A Technological Point of View

294

(7)

DNA Computers

294

(4)

DNA Microarrays

298

(1)

DNA Cryptography

299

(1)

DNA/RNA-Aided Nanoparticle Assembly

300

(1)

DNA/RNA Sequence Hybridization: A Coding-Theoretic Point of View

301

(12)

DNA Codes

301

(6)

DNA Microarrays

307

(3)

Enumerating RNA Motifs

310

(3)

Conclusion

313

(6)

Application of Biomolecular Computing to Breakthroughs in Cryptography

319

(22)

Introduction

319

(2)

Introduction of DNA Background

321

(2)

DNA Manipulations

321

(1)

Comparisons of Various Famous DNA Models

322

(1)

Factoring the Product of Two Large Prime Numbers

323

(13)

Introduction to the RSA Public-Key Cryptosystem

323

(1)

Solution Space of DNA Strands for Every Unsigned Integer

323

(1)

Construction of the Product for Two Large Prime Numbers

324

(1)

Construction of a Parallel Comparator

325

(2)

Construction of a Parallel One-Bit Subtractor

327

(3)

Construction of a Binary Parallel Subtractor

330

(1)

Construction of a Binary Parallel Divider

331

(3)

Finding Two Large Prime Numbers

334

(1)

Breaking the RSA Public--Key Cryptosystem

335

(1)

The Complexity of Algorithm 1

336

(1)

Conclusion

336

(5)

Chemotaxis: Learning Navigation and Source Localization Strategies from Biology's Engineered Designs

341

(24)

Introduction

341

(1)

Bacterial Chemotaxis Principles

342

(2)

Mathematical Description of a Random Walk

344

(1)

Chemotaxis-Based Algorithms for Diffusive Environments

345

(15)

Single-Node Biased Random Walk and Receptor Cooperation

346

(1)

Multinode Biased Random Walks for Source Tracking

347

(3)

Multichemoreceptor Cooperation for Gradient Tracking

350

(10)

Performance Comparison of the Chemotaxis Algorithms

360

(1)

Summary

361

(4)

Systems Bioinformatics: Trends and Conclusions

365

(2)

Appendix: Contributing Authors and Contact Information

367

(4)

About the Editors

371

(2)

Index

373

Gil Alterovitz is an NIH Biomedical Informatics Fellow in the Division of Health Sciences and Technology (HST) at Harvard and the Massachusetts Institute of Technology (MIT), and is a research affiliate at the Computer Science and Artificial Intelligence Laboratory (CSAIL) in the Department of Electrical Engineering and Computer Science at MIT. Marco F. Ramoni is an assistant professor of Pediatrics and Medicine at Harvard Medical School and an assistant professor of health sciences and technology at Harvard and the Massachusetts Institute of Technology (MIT).

Systems Bioinformatics: An Engineering Case-Based Approach Unabridged edition [Hardback]

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