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Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiology constraints

Publications associées (72)

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Accumulation of pollutants and plant wellness: bottleneck or key to a successful phytoremediation?

Jean-Paul Schwitzguebel

Plants have efficient mechanisms for detoxification and sequestration of xenobiotic chemicals and trace elements, basis of any efficient phytoremediation process. However the amount of pollutants that can be accumulated and detoxified without disrupting th ...

2012

The Golgi apparatus: an organelle with multiple complex functions

Giovanni D'Angelo

Remarkable advances have been made during the last few decades in defining the organizational principles of the secretory pathway. The Golgi complex in particular has attracted special attention due to its central position in the pathway, as well as for it ...

2011

Modeling of uncertainties in biochemical reactions

Vassily Hatzimanikatis, Ljubisa Miskovic

Mathematical modeling is an indispensable tool for research and development in biotechnology and bioengineering. The formulation of kinetic models of biochemical networks depends on knowledge of the kinetic properties of the enzymes of the individual react ...

Wiley-Blackwell2010

Quantitative Analysis of Metabolic Networks Through the Explicit Consideration of Kinetic Mechanisms

Vassily Hatzimanikatis, Ljubisa Miskovic

Engineering of large-scale metabolic pathways to maximize production of a certain substance or to minimize creation of undesired chemicals require explicit information about the underlying enzyme kinetics. Unfortunately, such information is frequently not ...

2010

DREAMS of metabolism

Vassily Hatzimanikatis, Keng Cher Soh

Metabolic networks have been studied for decades, and sophisticated computational frameworks are needed to augment experimental approaches to harness these complex networks. BNICE (Biochemical Network Integrated Computational Explorer), a computational app ...

Elsevier2010

Metabolic Networks of Longevity

Johan Auwerx, Richardus Houtkooper

Molecular and cellular networks implicated in aging depend on a multitude of proteins that collectively mount adaptive and contingent metabolic responses to environmental challenges. Here, we discuss the intimate links between metabolic regulation and long ...

2010

The enigmatic role of tafazzin in cardiolipin metabolism

Richardus Houtkooper

The mitochondrial phospholipid cardiolipin plays an important role in cellular metabolism as exemplified by its involvement in mitochondrial energy production and apoptosis. Following its biosynthesis, cardiolipin is actively remodeled to achieve its final ...

2009

Enzyme States Allow Identification of Rate-Limiting Steps

Vassily Hatzimanikatis, Ljubisa Miskovic

A precise quantification of the effect of perturbations in a metabolic network depends on explicit knowledge of the kinetic properties of the enzymes of the individual reactions. However, a comprehensive knowledge of enzymes kinetics in a metabolic network ...

2008

Analysis of yeast metabolism using metabolic control analysis under uncertainty

Vassily Hatzimanikatis

Advancement of genomic research and anal. techniques enables an in-depth understanding of individual components in the cellular metab. The crit. subject is the integration of massive exptl. details and the quantification of the contributions of individual ...

2005

Exploring the diversity of complex metabolic networks

Vassily Hatzimanikatis

Motivation: Metab., the network of chem. reactions that make life possible, is one of the most complex processes in nature. We describe here the development of a computational approach for the identification of every possible biochem. reaction from a given ...

2005