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review article

The Dawn of High-throughput and Genome-scale Kinetic Modeling: Recent Advances and Future Directions

Toumpe, Ilias  
•
Choudhury, Subham  
•
Hatzimanikatis, Vassily  
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April 22, 2025
ACS Synthetic Biology

Researchers have invested much effort into developing kinetic models due to their ability to capture dynamic behaviors, transient states, and regulatory mechanisms of metabolism, providing a detailed and realistic representation of cellular processes. Historically, the requirements for detailed parametrization and significant computational resources created barriers to their development and adoption for high-throughput studies. However, recent advancements, including the integration of machine learning with mechanistic metabolic models, the development of novel kinetic parameter databases, and the use of tailor-made parametrization strategies, are reshaping the field of kinetic modeling. In this Review, we discuss these developments and offer future directions, highlighting the potential of these advances to drive progress in systems and synthetic biology, metabolic engineering, and medical research at an unprecedented scale and pace.

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Type
review article
DOI
10.1021/acssynbio.4c00868
Web of Science ID

WOS:001472536700001

PubMed ID

40262025

Author(s)
Toumpe, Ilias  

École Polytechnique Fédérale de Lausanne

Choudhury, Subham  

École Polytechnique Fédérale de Lausanne

Hatzimanikatis, Vassily  

École Polytechnique Fédérale de Lausanne

Miskovic, Ljubisa  

École Polytechnique Fédérale de Lausanne

Date Issued

2025-04-22

Publisher

AMER CHEMICAL SOC

Published in
ACS Synthetic Biology
Subjects

Kinetic models of metabolism

•

Dynamical nonlinearsystems

•

Kinetic rate laws

•

Generative machine learning

•

Synthetic biology

•

Systems biology

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCSB  
FunderFunding(s)Grant NumberGrant URL

Ecole Polytechnique Federale de Lausanne (EPFL)

Available on Infoscience
May 6, 2025
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/249860
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