Synthetic biology encompasses several different approaches, methodologies and disciplines, and many different definitions exist. This volume of Methods in Enzymology has been split into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA sssembly and manipulation.
Voigt / MIE Vol
Table of Contents
Synthetic biology, Part B
Subtitle: Computer Aided Design and DNA Assembly
Section I. Mathematical and Computational Methods
DNA-binding specificity prediction with FoldX
Alejandro D. Nadra, Luis Serrano, Andreu Alibés
The Ribosome Binding Site Calculator
Howard M. Salis
Designing Genes for Successful Protein Expression
Mark Welch, Alan Villalobos, Claes Gustafsson and Jeremy
Minshull
Application of Metabolic Flux Analysis in Metabolic Engineering
Sang Yup Lee, Jong Myoung Park and Tae Yong Kim
Section II. Grammars, Languages, and Computer-Aided Design
Clotho: A Software Platform for the Creation of Synthetic
Biological Systems
Swapnil Bhatia, Bing Xia, Ben Bubenheim, Maisam Dadgar, Douglas
Densmore and J. Christopher Anderson
SynBioSS-Aided Design of Synthetic Biological Constructs
Yiannis N. Kaznessis
The Eugene Language for Synthetic Biology
Lesia Bilitchenko, Adam Liu, Douglas Densmore
A step by step introduction to rule-based design of synthetic
genetic constructs using GenoCAD
Mandy L. Wilson, Russell Hertzberg, Laura Adam, Jean Peccoud
Methods for open innovation on a genome-design platform associating
scientific, commercial, and educational communities in synthetic
biology
Tetsuro Toyoda
Section III. Next-Generation DNA Assembly and Manipulation
Recursive construction and error correction of DNA molecules and
libraries from synthetic and natural DNA
Tuval Ben Yehezkel and Ehud Shapiro
Industrial scale gene synthesis
Frank Notka, Michael Liss & Ralf Wagner
Chemical DNA Synthesis: Methods and Applications
Randall A. Hughes, Aleksandr E. Miklos, and Andrew D. Ellington
Assembly of BioBrick standard biological parts using three
antibiotic assembly
Reshma Shetty, Meagan Lizarazo, Randy Rettberg, and Thomas F.
Knight, Jr
Genetic Assembly Tools for Synthetic Biology
Billyana Tsvetanova, Lansha Peng, Xiquan Liang, Ke Li, Jian-Ping
Yang, Tony Ho, Josh Shirley, Liewei Xu, Jason Potter, Wieslaw
Kudlicki, Todd Peterson, and Federico Katzen
Enzymatic assembly of overlapping DNA fragments
Daniel G. Gibson
Automated assembly of standard biological parts
Mariana Leguia, Jennifer Brophy, Douglas Densmore and J.
Christopher Anderson
MEGAWHOP Cloning: A method of creating random mutagenesis libraries
via megaprimer PCR of whole plasmids
Kentaro Miyazaki
Section III. Genome-scale Engineering
Rapid and Multiplexed Genome Engineering and Genotyping Methods:
Applications for Synthetic Biology and Protein and Pathway
Engineering
Harris H. Wang and George M. Church
Construction and manipulation of giant DNA by a genome vector
Mitsuhiro ITAYA and Kenji TSUGE
Mapping E. coli RNA Polymerase and associated transcription factors
and identifying promoters genome-wide
Sarah E. Davis, Rachel A. Mooney, Elenita I. Kanin, Jeff Grass,
Robert Landick and Aseem Z. Ansari
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