Computational methods in synthetic biology
Author(s)
Bibliographic Information
Computational methods in synthetic biology
（Methods in molecular biology / John M. Walker, series editor, 2189）（Springer protocols）
Humana Press, c2021
2nd ed
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
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 Barisic
3. Computational Methods For The Design Of Recombinase Logic Circuits
Sarah Guiziou and Jerome Bonnet
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
6. iGUIDE Method for CRISPR Off-target Detection Christopher L. Nobles
7. Web-based Base Editing Toolkits: BE-Designer and BE-Analyzer
Gue-Ho Hwang and Sangsu Bae
8. Synthetic Gene Circuit Analysis and Optimization
Irene Otero-Muras and Julio R. Banga
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 Drager
17. A Systems Bioinformatics Approach to Interconnect Biological Pathways
George Minadakis and George M. Spyrou
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