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Synthetic Biology, Part B - 1st Edition - ISBN: 9780123851208, 9780123851215

Synthetic Biology, Part B, Volume 498

1st Edition

Computer Aided Design and DNA Assembly

Editor: Chris Voigt
Hardcover ISBN: 9780123851208
eBook ISBN: 9780123851215
Imprint: Academic Press
Published Date: 9th June 2011
Page Count: 550
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Table of Contents

Voigt / MIE Vol

Table of Contents



Synthetic biology, Part B

Subtitle: Computer Aided Design and DNA Assembly

Section I. Mathematical and Computational Methods

  1. DNA-binding specificity prediction with FoldX
  2. Alejandro D. Nadra, Luis Serrano, Andreu Alibés

  3. The Ribosome Binding Site Calculator
  4. Howard M. Salis

  5. Designing Genes for Successful Protein Expression
  6. Mark Welch, Alan Villalobos, Claes Gustafsson and Jeremy Minshull

  7. Application of Metabolic Flux Analysis in Metabolic Engineering
  8. Sang Yup Lee, Jong Myoung Park and Tae Yong Kim

    Section II. Grammars, Languages, and Computer-Aided Design

  9. Clotho: A Software Platform for the Creation of Synthetic Biological Systems
  10. Swapnil Bhatia, Bing Xia, Ben Bubenheim, Maisam Dadgar, Douglas Densmore and J. Christopher Anderson

  11. SynBioSS-Aided Design of Synthetic Biological Constructs
  12. Yiannis N. Kaznessis

  13. The Eugene Language for Synthetic Biology
  14. Lesia Bilitchenko, Adam Liu, Douglas Densmore

  15. A step by step introduction to rule-based design of synthetic genetic constructs using GenoCAD
  16. Mandy L. Wilson, Russell Hertzberg, Laura Adam, Jean Peccoud

  17. Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology
  18. Tetsuro Toyoda

    Section III. Next-Generation DNA Assembly and Manipulation

  19. Recursive construction and error correction of DNA molecules and libraries from synthetic and natural DNA
  20. Tuval Ben Yehezkel and Ehud Shapiro

  21. Industrial scale gene synthesis
  22. Frank Notka, Michael Liss & Ralf Wagner

  23. Chemical DNA Synthesis: Methods and Applications
  24. Randall A. Hughes, Aleksandr E. Miklos, and Andrew D. Ellington

  25. Assembly of BioBrick standard biological parts using three antibiotic assembly
  26. Reshma Shetty, Meagan Lizarazo, Randy Rettberg, and Thomas F. Knight, Jr

  27. Genetic Assembly Tools for Synthetic Biology
  28. 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

  29. Enzymatic assembly of overlapping DNA fragments
  30. Daniel G. Gibson

  31. Automated assembly of standard biological parts
  32. Mariana Leguia, Jennifer Brophy, Douglas Densmore and J. Christopher Anderson

  33. MEGAWHOP Cloning: A method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids
  34. Kentaro Miyazaki

    Section III. Genome-scale Engineering

  35. Rapid and Multiplexed Genome Engineering and Genotyping Methods: Applications for Synthetic Biology and Protein and Pathway Engineering
  36. Harris H. Wang and George M. Church

  37. Construction and manipulation of giant DNA by a genome vector
  38. Mitsuhiro ITAYA and Kenji TSUGE

  39. 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


Synthetic biology encompasses a variety of 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 Assembly and Manipulation.

Key Features

  • Encompasses a variety of different approaches, methodologies and disciplines
  • Split into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA assembly and manipulation


Researchers and students in cell, molecular and developmental biology


No. of pages:
© Academic Press 2011
9th June 2011
Academic Press
Hardcover ISBN:
eBook ISBN:

Ratings and Reviews

About the Editor

Chris Voigt