Concept
Flux balance analysis
Related publications (103)
Generative 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 ...
2023Constraint-based metabolic control analysis for rational strain engineering
Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka
The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...
2021The 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 ...
BMC2021Spatio-temporal modeling of the crowding conditions and metabolic variability in microbial communities
Vassily Hatzimanikatis, Liliana Angeles Martinez
The metabolic capabilities of the species and the local environment shape the microbial interactions in a community either through the exchange of metabolic products or the competition for the resources. Cells are often arranged in close proximity to each ...
PUBLIC LIBRARY SCIENCE2021Heat stress destabilizes symbiotic nutrient cycling in corals
Anders Meibom, Nils Rädecker, Claudia Isabella Pogoreutz
Recurrent mass bleaching events are pushing coral reefs worldwide to the brink of ecological collapse. While the symptoms and consequences of this breakdown of the coral–algal symbiosis have been extensively characterized, our understanding of the underlyi ...
2021Optimization methods and objective functions for analysis of metabolic network models
Computational studies of metabolism aim to systematically analyze the metabolic behaviour of biological systems in different conditions. Genome-scale metabolic network models (GEMs) capture the connection between elements of the network by applying stoichi ...
EPFL2020Modeling the coupled dynamics of stream metabolism and microbial biomass
Tom Ian Battin, Enrico Bertuzzo, Pier Luigi Segatto
Estimating and interpreting ecosystem metabolism remains an important challenge in stream ecology. Here, we propose a novel approach to model, estimate, and predict multiseasonal patterns of stream metabolism (gross primary production [GPP] and ecosystem r ...
2020Development of novel tools for imaging of metabolic fluxes in vivo
Bioluminescent imaging is a powerful technique that enables imaging in living organisms with high sensitivity, low background signal, low cost and without the need for radioactivity. The emitted photons are produced in the oxidation reaction of luciferin c ...
EPFL2020Magnetic resonance spectroscopy in the rodent brain: Experts' consensus recommendations
Rolf Gruetter, Lijing Xin, Cristina Ramona Cudalbu, Bernard Lanz
In vivo MRS is a non-invasive measurement technique used not only in humans, but also in animal models using high-field magnets. MRS enables the measurement of metabolite concentrations as well as metabolic rates and their modifications in healthy animals ...
WILEY2020Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Georgios Fengos, Tuure Eelis Hameri
Large-scale kinetic models are used for designing, predicting, and understanding the metabolic responses of living cells. Kinetic models are particularly attractive for the biosynthesis of target molecules in cells as they are typically better than other t ...
2019