Computational Methods in Synthetic Biology

This second edition book provides complete coverage of the computational approaches currently used in Synthetic Biology.  New chapters detail computational methods and algorithms for the design of bio-components, insight on CAD programs, analysis techniques, and distributed systems. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, application details for both the expert and non-expert reader, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and practical, Computational Methods in Synthetic Biology, Second Edition aims to feature a broad overview of the research areas that can be met in the area of in silico Synthetic Biology.

1. Using a Design of Experiments Approach to Inform the Design of Hybrid Synthetic Yeast Promoters

James Gilman, Valentin Zulkower, and Filippo Menolascina

2. Computational Design of Multiplex Oligonucleotide-Based Assays

Michaela Hendling and Ivan Barišic

3. Computational Methods For The Design Of Recombinase Logic Circuits

4. Modular Modeling Of Genetic Circuits in SBML Level 3

Mario Andrea Marchisio

5. CRISPR-ERA: A Webserver for Guide RNA Design of Gene Editing and Regulation

Honglei Liu and Xiaowo Wang

Christopher L. Nobles

7. Web-based Base Editing Toolkits: BE-Designer and BE-Analyzer

8. Synthetic Gene Circuit Analysis and Optimization

9. Monitoring Single S. cerevisiae Cells with Multi-Frequency Electrical Impedance Spectroscopy in an Electrode-integrated Microfluidic Device

Zhen Zhu, Yangye Geng, and Yingying Wang

10. Construction of Protein Expression Network

Nor Afiqah-Aleng and Zeti-Azura Mohamed-Hussein

11. Systems-theoretic Approaches to Design Biological Networks with Desired Functionalities

Priyan Bhattacharya, Karthik Raman, and Arun K. Tangirala

12. A Deterministic Compartmental Modeling Framework for Disease Transmission

King James B. Villasin, Eva M. Rodriguez, and Angelyn R. Lao

13. Computer Aided Assembly and Verification of Synthetic Chromosomes

Giovanni Stracquadanio and Valentin Zulkower

14. Minimal Genome Design Algorithms using Whole-Cell Models

Joshua Rees-Garbutt, Oliver Chalkley, Claire Grierson, and Lucia Marucci

15. Tn-Core: Functionally Interpreting Transposon-Sequencing Data with Metabolic Network Analysis

George C diCenzo, Marco Galardini, and Marco Fondi

16. Genome-scale Metabolic Modeling of Escherichia coli and its Chassis Design for Synthetic Biology Applications

Bashir Sajo Mienda and Andreas Dräger

17. A Systems Bioinformatics Approach to Interconnect Biological Pathways