Preface IX

Volume 1

1 Synthetic Biology: Implications and Uses 1
Sanjay Vashee, Mikkel A. Algire, Michael G. Montague, and Michele S. Garfýnkel

Part I Biological Basis 33

2 The Emergence of the First Cells 35
Antoine Danchin

3 Regulation of Gene Expression 61
Anil Kumar, Sarika Garg and Neha Garg

4 Interactome 121
Teresa M. Przytycka and Dong-Yeon Cho

5 Microbiomes 153
Ramana Madupu, Yu-Hui Rogers, Doug Rusch, Jason Miller, Konstantinos Krampis, and Karen E. Nelson

Part II Modeling 179

6 Dynamics of Biomolecular Networks 181
Emanuele Cozzo, Joaquín Sanz, and Yamir Moreno

7 E-Cell: Computer Simulation of the Cell 211
Pawan K. Dhar, Kouichi Takahashi, Yoichi Nakayama, and Masaru Tomita

8 SynBioSS Designer Modeling Suite 229
Konstantinos Biliouris, Emma Weeding, and Yiannis N. Kaznessis

Part III Modular Parts and Circuits 247

9 Synthetic Gene Circuits 249
Barbara Jusiak, Ramiz Daniel, Fahim Farzadfard, Lior Nissim, Oliver Purcell, Jacob Rubens and Timothy K. Lu

10 DNA Origami Nanorobots 305
Ido Bachelet

11 RNAi Synthetic Logic Circuits for Sensing, Information Processing, and Actuation 333
Zhen Xie, Liliana Wroblewska, and Ron Weiss

12 Synthetic Hybrid Biosensors 357
Apoorv Shanker, Kangwon Lee, and Jinsang Kim

13 Synthetic Biology in Metabolic Engineering: From Complex Biochemical Pathways to Compartmentalized Metabolic Processes–a Vitamin Connection 393
Evelyne Deery, Stefanie Frank, Andrew Lawrence, Simon Moore, Susanne Schroeder, and Martin J. Warren

Volume 2

Part IV Synthetic Genomes 441

14 The Minimal Gene-Set Machinery 443
Rosario Gil

15 Production of Mitochondrial Genome and Chromosomal DNA Segments Highly Engineered for Use in Mouse Genetics by a Bacillus subtilis-Based BGM Vector System 479
Mitsuhiro Itaya

16 Synthetic Genetic Polymers Functioning to Store and Propagate Information by Genetic Alphabet Expansion 505
Ichiro Hirao

Part V Diseases and Therapeutics 521

17 Synthetic Biology Approaches for Regenerative Medicine 523
Elise Cachat, Kim C. Martin, and Jamie A. Davies

18 The Synthetic Biology Approach to Stem Cells and Regenerative Medicine 541
Boon Chin Heng, and Martin Fussenegger

19 Synthetic Biology Approaches to Cell Therapy 559
Sung-Ho Paek and Warren C. Ruder

20 Synthetic Biology Approaches for Vaccine Development 589
Sam H. Shen, Bruce Futcher, Chen Yang, and Eckard Wimmer

Part VI Chemicals Production 617

21 Metabolic Engineering for the Production of Diols 619
Katarzyna Leja, Dorota Samul, Piotr Kubiak, Agnieszka Drozdzynska, Alicja Kósmider, Wojciech Juzwa, Mariusz Lesiecki, and Katarzyna Czaczyk

22 Synthetic Biology in Biofuels Production 665
Rahul Singh, Anu Jose Mattam, Pavan Jutur, and Syed Shams Yazdani

23 Synthetic Biology of Antibiotic Production 699
Eriko Takano and Rainer Breitling

Index 723

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