Systems Metabolic Engineering

Methods and Protocols

  • Hal S. Alper

Part of the Methods in Molecular Biology book series (MIMB, volume 985)

Table of contents

  1. Front Matter
    Pages i-xii
  2. Modeling and Simulation Tools

    1. Front Matter
      Pages 1-1
    2. Stephan Pabinger, Zlatko Trajanoski
      Pages 3-16
    3. Scott Devoid, Ross Overbeek, Matthew DeJongh, Veronika Vonstein, Aaron A. Best, Christopher Henry
      Pages 17-45
    4. Pratish Gawand, Laurence Yang, William R. Cluett, Radhakrishnan Mahadevan
      Pages 47-59
    5. Edik M. Blais, Arvind K. Chavali, Jason A. Papin
      Pages 61-83
    6. Kieran Smallbone, Natalie J. Stanford
      Pages 113-121
    7. Matthew Moura, Linda Broadbelt, Keith Tyo
      Pages 123-147
    8. Pablo Carbonell, Anne-Gaëlle Planson, Jean-Loup Faulon
      Pages 149-173
  3. Genome Engineering Tools

    1. Front Matter
      Pages 175-175
    2. James Winkler, Luis H. Reyes, Katy C. Kao
      Pages 211-222
    3. Thomas J. Mansell, Joseph R. Warner, Ryan T. Gill
      Pages 223-246
  4. Systems-Level ‘Omics Tools

    1. Front Matter
      Pages 247-247
    2. Liam Royce, Erin Boggess, Tao Jin, Julie Dickerson, Laura Jarboe
      Pages 249-267
    3. Shilpa Nargund, Max E. Joffe, Dennis Tran, Vitali Tugarinov, Ganesh Sriram
      Pages 335-351
    4. Maciek R. Antoniewicz
      Pages 353-365
    5. Lara J. Jazmin, Jamey D. Young
      Pages 367-390
    6. Hein Stam, Michiel Akeroyd, Hilly Menke, Renger H. Jellema, Fredoen Valianpour, Wilbert H. M. Heijne et al.
      Pages 391-406
  5. Integrating Large Datasets for Modeling and Engineering Applications

    1. Front Matter
      Pages 407-407
    2. D. B. R. K. Gupta Udatha, Simon Rasmussen, Thomas Sicheritz-Pontén, Gianni Panagiotou
      Pages 409-428
    3. Christopher M. Gowen, Stephen S. Fong
      Pages 429-445
    4. Shuobo Shi, Tao Chen, Xueming Zhao
      Pages 447-458
  6. Back Matter
    Pages 471-474

About this book


With the ultimate goal of systematically and robustly defining the specific perturbations necessary to alter a cellular phenotype, systems metabolic engineering has the potential to lead to a complete cell model capable of simulating cell and metabolic function as well as predicting phenotypic response to changes in media, gene knockouts/overexpressions, or the incorporation of heterologous pathways.  In Systems Metabolic Engineering: Methods and Protocols, experts in the field describe the methodologies and approaches in the area of systems metabolic engineering and provide a step-by-step guide for their implementation. Four major tenants of this approach are addressed, including modeling and simulation, multiplexed genome engineering, ‘omics technologies, and large data-set incorporation and synthesis, all elucidated through the use of model host organisms.  Written in the highly successful Methods in Molecular Biology™ series format, chapters include introductions on their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.


Comprehensive and cutting-edge, Systems Metabolic Engineering: Methods and Protocols serves as an ideal guide for metabolic engineers, molecular biologists, and microbiologists aiming to implement the most recent approaches available in the field.


Cellular phenotype alteration Large data-set synthesis Metabolic function simulation Modeling Multiplexed genome engineering Strain improvement Systems metabolic engineering ‘Omics technologies

Editors and affiliations

  • Hal S. Alper
    • 1
  1. 1.Cockrell School of Engineering, Dept. of Chemical EngineeringThe University of Texas at AustinAustinUSA

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC 2013
  • Publisher Name Humana Press, Totowa, NJ
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-62703-298-8
  • Online ISBN 978-1-62703-299-5
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site