Concept
Metabolic network modelling
Publications associées (106)
Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities
Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...
EPFL2024Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics
Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...
EPFL2024Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states
Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret
Large omics datasets are nowadays routinely generated to provide insights into cellular processes. Nevertheless, making sense of omics data and determining intracellular metabolic states remains challenging. Kinetic models of metabolism are crucial for int ...
2023A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics
Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Mohammadomid Oftadeh, Pierre Guy Rémy Salvy
Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...
NATURE PORTFOLIO2021Modelling the Intracellular Environment under Uncertainty, from Post-translational Modification to Metabolic Networks
Robin Alexander Denhardt-Eriksson
Modelling and analysis of biological systems is crucial in order to quantitatively explain and predict their behaviour.
The importance of modelling in systems biology
becomes even more evident when tackling complex, large systems. Approaches
that rely on ...
EPFL2021The effects of model complexity and size on metabolic flux distribution and control: case study in Escherichia coli
Vassily Hatzimanikatis, Georgios Fengos, Tuure Eelis Hameri
Background Significant efforts have been made in building large-scale kinetic models of cellular metabolism in the past two decades. However, most kinetic models published to date, remain focused around central carbon pathways or are built around ad hoc re ...
BMC2021