Publications related to Flux balance analysis

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

Vassily Hatzimanikatis, Vikash Kumar Pandey

Nonalcoholic fatty liver disease (NAFLD) is associated with metabolic syndromes spanning a wide spectrum of diseases, from simple steatosis to the more complex nonalcoholic steatohepatitis. To identify the deregulation that occurs in metabolic processes at ...

2019

Computational analysis of Pseudomonas Putida metabolism Using Large-scale Kinetic Models

Vassily Hatzimanikatis, Ljubisa Miskovic, Milenko Tokic

P. putida is a highly adaptive, non-pathogenic, soil bacterium that can grow on a wide range of substrates, and it is tolerant to high toxicity compounds. For these reasons, it emerged recently as one of the most promising production hosts for a wide range ...

2018

In vivo (13)C MRS in the mouse brain at 14.1 Tesla and metabolic flux quantification under infusion of [1,6-(13)C2]glucose

Rolf Gruetter, Cristina Ramona Cudalbu, Bernard Lanz, Carole Poitry-Yamate, Marta Lai, Corina Mihaela Berset

In vivo (13)C magnetic resonance spectroscopy (MRS) enables the investigation of cerebral metabolic compartmentation while, e.g. infusing (13)C-labeled glucose. Metabolic flux analysis of (13)C turnover previously yielded quantitative information of glutam ...

2018

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

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

Feasibility of in vivo measurement of glucose metabolism in the mouse hypothalamus by (1) H-[(13) C] MRS at 14.1T

Rolf Gruetter, Hongxia Lei, Bernard Lanz, João Miguel das Neves Duarte, Antoine Timothée Cherix, Blanca Lizarbe Serra

PURPOSE: Determine the feasibility of (1) H-[(13) C] MRS in the mouse hypothalamus using a 14.1T magnet. METHODS: We optimized the design of a (1) H-[(13) C] surface coil to maximize the signal-to-noise ratio of (1) H-[(13) C] MRS in the mouse hypothalamus ...

2018

In silico tracing of the fate of single carbon atoms in different physiological states of E. coli

Jasmin Maria Hafner, Noushin Hadadi, Beatriz Lopes Pinto Basto Carreira

Many applications of systems biology such as the simulation of isotope labeling experiments and pathway inference in metabolic engineering rely on atom-level representation of metabolism. Because of its challenging complexity and the difficulty of obtainin ...

2018

Deciphering ambiguous control over fluxes through characterization and reduction of uncertainty

Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret

The development of kinetic models is still facing the challenges such as large uncertainties in available data. Uncertainty originating from various sources including metabolite concentration levels, flux values, thermodynamic and kinetic data propagates t ...

2017

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Flux balance analysis

Computational studies of industrial hosts for improved production of the 2nd generation of biofuels

Towards comprehensive and consistent kinetic models of metabolism under uncertainty

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

Computational analysis of Pseudomonas Putida metabolism Using Large-scale Kinetic Models

In vivo (13)C MRS in the mouse brain at 14.1 Tesla and metabolic flux quantification under infusion of [1,6-(13)C2]glucose

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

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

Feasibility of in vivo measurement of glucose metabolism in the mouse hypothalamus by (1) H-[(13) C] MRS at 14.1T

In silico tracing of the fate of single carbon atoms in different physiological states of E. coli

Deciphering ambiguous control over fluxes through characterization and reduction of uncertainty

Graph Chatbot

Chat with Graph Search

Deciphering ambiguous control over fluxes through characterization and reduction of uncertainty

Computational studies of industrial hosts for improved production of the 2nd generation of biofuels

Computational analysis of Pseudomonas Putida metabolism Using Large-scale Kinetic Models

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

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

Feasibility of in vivo measurement of glucose metabolism in the mouse hypothalamus by (1) H-[(13) C] MRS at 14.1T

Towards comprehensive and consistent kinetic models of metabolism under uncertainty

In vivo (13)C MRS in the mouse brain at 14.1 Tesla and metabolic flux quantification under infusion of [1,6-(13)C2]glucose

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

In silico tracing of the fate of single carbon atoms in different physiological states of E. coli