Metabolic network modelling

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Related publications (26)

Towards comprehensive and consistent kinetic models of metabolism under uncertainty

Tuure Eelis Hameri

Metabolism is the sum of the chemical interactions occurring inside a cell that process nutrients into cellular constituents and energy. Research in the recent decades has enabled the characterization of metabolic reaction networks for multiple organisms. ...

EPFL2019

Kinetic 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

Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks

Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Savoglidis, Milenko Tokic

Analysis of the dynamic and steady-state properties of biochemical networks hinges on information about the parameters of enzyme kinetics. The lack of experimental data characterizing enzyme activities and kinetics along with the associated uncertainties i ...

2019

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Vassily Hatzimanikatis, Noushin Hadadi, Vikash Kumar Pandey

The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...

2019

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

Vassily Hatzimanikatis, Meriç Ataman, Dani Or

Natural soil is characterized as a complex habitat with patchy hydrated islands and spatially variable nutrients that is in a constant state of change due to wetting-drying dynamics. Soil microbial activity is often concentrated in sparsely distributed hot ...

2019

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Keng Cher Soh, Pierre Guy Rémy Salvy

Summary: pyTFA and matTFA are the first published implementations of the original TFA paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, which enables straightforward integration of metabolite concentrat ...

2018

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