Contents -- Preface -- Part I Introduction: Molecular and Cellular Biology -- Chapter 1 Molecular and Cellular Biology: An Engineering Perspective -- 1.1 Cellular Structures and Functions -- 1.2 Introduction to Information Handling in Cells -- 1.3 The Importance and Diversity of Proteins -- 1.4 DNA Replication: Copying the Code -- 1.5 Transcription: Sending a Messenger -- 1.6 Translation: Protein Synthesis -- 1.7 Control of Gene Expression -- 1.8 Genetic Engineering -- 1.9 Summary -- Acknowledgments -- References -- Chapter 2 Proteomics: From Genome to Proteome -- 2.1 Defining the Proteome -- 2.2 Building Gene Collections for Functional Proteomics Approaches -- 2.3 Use of Clones in Functional Proteomics Approaches -- References -- Part II Analysis: Signal Processing -- Chapter 3 Introduction to Biological Signal Processing at the Cell Level -- 3.1 Introduction to Fundamental Signal Processing Concepts -- 3.2 Signal Detection and Estimation -- 3.3 System Identification and Analysis -- 3.4 Conclusion -- Acknowledgments -- References -- Chapter 4 Signal Processing Methods for Mass Spectrometry -- 4.1 Introduction -- 4.2 Signal Resampling -- 4.3 Correcting the Background -- 4.4 Aligning Mass/Charge Values -- 4.5 Normalizing Relative Intensity -- 4.6 Smoothing Noise -- 4.7 Identifying Ion Peaks -- References -- Part III Analysis: Control and Systems -- Chapter 5 Control and Systems Fundamentals -- 5.1 Introduction -- 5.2 Review of Fundamental Concepts in Control and Systems Theory -- 5.3 Control Theory in Systems Biology -- 5.4 Reverse Engineering Cellular Networks -- 5.5 Gene Networks -- 5.6 Conclusion -- Acknowledgments -- References -- Chapter 6 Modeling Cellular Networks -- 6.1 Introduction -- 6.2 Construction and Analysis of Kinetic Models -- 6.3 Case Studies -- 6.4 Conclusion -- References.

Part IV Analysis: Probabilistic Data Networks and Communications -- Chapter 7 Topological Analysis of Biomolecular Networks -- 7.1 Cellular Networks -- 7.2 Topology of Cellular Networks -- 7.3 Gene Ontology and Functional Clustering of Essential Genes -- 7.4 Conclusion and Future Avenues -- References -- Chapter 8 Bayesian Networks for Genetic Analysis -- 8.1 Introduction -- 8.2 Elements of Population Genetics -- 8.3 Bayesian Networks -- 8.4 Two Applications -- 8.5 Conclusion -- Acknowledgments -- References -- Part V Design: Synthetic Biology -- Chapter 9 Fundamentals of Design for Synthetic Biology -- 9.1 Overview -- 9.2 Circuits -- 9.3 Multicellular Systems -- 9.4 Challenges -- 9.5 Conclusion -- References -- Chapter 10 BioJADE: Designing and Building Synthetic Biological Systems from Parts -- 10.1 Introduction -- 10.2 Fundamentals of BioJADE and BioBricks Construction -- 10.3 Representing Parts -- 10.4 BioJADE Architecture -- 10.5 Using BioJADE, an Example: The Repressilator -- 10.6 Simulations -- 10.7 The Reality Check -- 10.8 Next Steps -- Acknowledgments -- References -- Chapter 11 Applied Cellular Engineering -- 11.1 Introduction -- 11.2 Engineering Tools -- 11.3 Case Study: Production of 1,3-Propanediol in E. coli -- 11.4 Frontiers -- 11.5 Conclusion -- References -- Part VI Integration: Applying Biology's Designs and Principles in Engineering -- Chapter 12 The Three Faces of DNA/RNA Sequence Hybridization -- 12.1 Introduction -- 12.2 A Short Introduction to DNA/RNA Sequence Hybridization and Self-Hybridization -- 12.3 DNA/RNA Sequence Hybridization: A Biological Point of View -- 12.4 DNA/RNA Sequence Hybridization: A Technological Point of View -- 12.5 DNA/RNA Sequence Hybridization: A Coding-Theoretic Point of View -- 12.6 Conclusion -- References -- Chapter 13 Application of Biomolecular Computing to Breakthroughs in Cryptography.

13.1 Introduction -- 13.2 Introduction of DNA Background -- 13.3 Factoring the Product of Two Large Prime Numbers -- 13.4 Conclusion -- References -- Chapter 14 Chemotaxis: Learning Navigation and Source Localization Strategies from Biology's Engineered Designs -- 14.1 Introduction -- 14.2 Bacterial Chemotaxis Principles -- 14.3 Mathematical Description of a Random Walk -- 14.4 Chemotaxis-Based Algorithms for Diffusive Environments -- 14.5 Performance Comparison of the Chemotaxis Algorithms -- 14.6 Summary -- References -- Systems Bioinformatics: Trends and Conclusions -- Appendix Contributing Authors and Contact Information -- About the Editors -- Index.