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Metabolic control analysis of the central carbon pathway in optimally grown E. coli

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Computational Analysis of Xylose-Utilizing Saccharomyces cerevisiae

Vassily Hatzimanikatis, Ljubisa Miskovic

Xylose fermentation from lignocellulosic material using recombinant yeast cells is a promising resource for efficient ethanol production as a future sustainable energy supply. Experimental approaches emphasize the engineering of xylose-utilizing recombinan ...

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

Quantification of uncertainty in metabolic networks through the sampling of kinetic data space

Vassily Hatzimanikatis, Ljubisa Miskovic

Study of a metabolic network with respect to the sensitivity of the metabolite concentrations and the metabolic fluxes to genetic, biochemical, and environmental variations requires knowledge of the kinetic properties of the enzymes in the network. Experim ...

2009

Computational Framework for Predictive Biodegradation

Vassily Hatzimanikatis, Stacey Deleria Finley

As increasing amounts of anthropogenic chemicals are released into the environment, it is vital to human health and the preservation of ecosystems to evaluate the fate of these chemicals in the environment. It is useful to predict whether a particular comp ...

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

Can microbial growth yield be estimated using simple thermodynamic analogies to technical processes?

Urs von Stockar

In view of the prime importance of the biomass yield in microbial growth for research, for environmental and for industrial applications some thermodynamic concepts are reviewed that were developed over the years in order to understand the large variations ...

2008

How reliable are thermodynamic feasibility statements of biochemical pathways?

Urs von Stockar

The driving force for organo- or lithotrophic growth as well as for each step in the metabolic network is the Gibbs reaction energy. For each enzymic step it must be neg. Thermodn. contributes therefore to the in-silico description of living systems. It ma ...

2005

Astaxanthin production by Phaffia rhodozyma

Urs von Stockar, Ian William Marison, Christopher Cannizzaro

Astaxanthin is primarily used as a food supplement in the aquaculture industry, which over the past twenty years has experienced tremendous growth. A complex synthetic process produces almost all of the astaxanthin sold, and consequently, the selling price ...

2000

Using MycDB on the World-Wide Web

Stewart Cole

MycDB is an integrated mycobacterial database. This means that it contains information on all aspects of mycobacteria, whether immunology, metabolism, or the researchers working on mycobacteria. For historical reasons, the starting point has been molecular ...

Humana Press1999