Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

Current Opinion in Biotechnology
Ljubisa MiskovicVassily Hatzimanikatis

Abstract

The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico. The lack of kinetic data hampers the development of kinetic models, and most of the current models use ad hoc reduced stoichiometry or oversimplified kinetic rate expressions, which may limit their predictive strength. There is a need to introduce the community-level standards that will organize and accelerate the future developments in this area. We introduce here a set of requirements that will ensure the model quality, we examine the current kinetic models with respect to these requirements, and we propose a general workflow for constructing models that satisfy these requirements.

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Citations

Jan 19, 2016·Frontiers in Physiology·Cheng Zhang, Qiang Hua
Jan 31, 2019·Briefings in Bioinformatics·Basant K Tiwary
Jun 6, 2020·Nature Communications·Maria MasidVassily Hatzimanikatis
Aug 21, 2019·PLoS Computational Biology·Ljubisa MiskovicVassily Hatzimanikatis
Apr 26, 2021·Metabolic Engineering·Sophia TsoukaVassily Hatzimanikatis
Jul 20, 2018·ACS Synthetic Biology·Milenko TokicVassily Hatzimanikatis

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