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A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

Related publications (41)

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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 ...

2023

The 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

Cell-to-cell variability plays a key role in tissue patterning by setting initial asymmetry that primes cell fate decisions. Fluctuations in the activity of regulatory molecules can commit individual cells to divergent differentiation pathways, and cell-to ...

EPFL2021

Organohalides are a class of compounds often considered as persistent pollutants and harmful to environmental and human health. Some bacteria, among which are representatives from the Firmicutes phylum, are capable of using these compounds as terminal acce ...

EPFL2021

Living organisms can catalyze many thousands of biochemical reactions that they use to convert energy and matter, which provides them with the essentials for life. The sum of these chemical reactions happening in an organism is called metabo-lism. Understa ...

EPFL2020

Algorithms and flowchart for the design of synthetic biochemical networks

Homa Mohammadi Peyhani

New drugs are needed to assure effective therapies for previously untreated diseases, emerging diseases, and personalized medicine, but the process of drug development is complex, costly, and time-consuming. This is especially problematic considering that ...

EPFL2020

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Living single yeast cells show a specific cellular motion at the nanometer scale with a magnitude that is proportional to the cellular activity of the cell. We characterized this cellular nanomotion pattern of nonattached single yeast cells using classical ...

AMER ASSOC ADVANCEMENT SCIENCE2020

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

Systematic reduction of genome-scale models for the study of metabolic phenotypes of human cells

Vassily Hatzimanikatis, Meriç Ataman, Maria Masid Barcon

In the last years, the analysis of cellular metabolism has sparked new interest in systems biology and metabolic modelling. In particular, modelling the phenotypes of healthy and diseased cells will help to understand the main metabolic characteristics of ...

2018

Mapping the diverse phenotypic states of yeast lipid metabolism to enzymes using mechanistic kinetic models

Sofia Tsouka

Lipids carry a very important role in cell structure and function, as well as in the physiopathology of many diseases. Maintenance of the lipid profiles should be tightly regulated as it is very important for preserving membrane permeability, cell integrit ...

2018