Computational Approaches on Stoichiometric and Kinetic Modeling for Efficient Strain Design

  • Mohammad Mazharul Islam
  • Rajib SahaEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1671)


Engineering biological systems that are capable of overproducing products of interest is the ultimate goal of any biotechnology application. To this end, stoichiometric (or steady state) and kinetic models are increasingly becoming available for a variety of organisms including prokaryotes, eukaryotes, and microbial communities. This ever-accelerating pace of such model reconstructions has also spurred the development of optimization-based strain design techniques. This chapter highlights a number of such frameworks developed in recent years in order to generate testable hypotheses (in terms of genetic interventions), thus addressing the challenges in metabolic engineering. In particular, three major methods are covered in detail including two methods for designing strains (i.e., one stoichiometric model-based and the other by integrating kinetic information into a stoichiometric model) and one method for analyzing microbial communities.

Key words

Computational strain design Stoichiometric metabolic models Kinetic models Metabolic modeling Ensemble modeling Microbial communities Whole plant model Multi-tissue model 



This work was supported by the University of Nebraska-Lincoln faculty start-up grant 21-1106-4308 to R.S.


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© Springer Science+Business Media, LLC 2018

Authors and Affiliations

  1. 1.Chemical and Biomolecular EngineeringUniversity of Nebraska-LincolnLincolnUSA

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