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Ljubisa Miskovic

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Systematic analysis for the redirection of carbon flux in metabolite-producing microorganisms requires the comprehensive understanding of their complex metabolic processes. The use of large-scale dynamic models of metabolism plays key role in the understan ...

2016

iSCHRUNK – In Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Vassily Hatzimanikatis, Ljubisa Miskovic, Stefano Andreozzi

Information about kinetics and enzyme activities while essential for quantitative understanding of metabolic dynamics remains rarely available and always involves uncertainty. In this work, we introduce the first computational methodology capable of determ ...

2016

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2016

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In recent years, constraint-based approaches have been widely used for analyzing cellular metabolism. These approaches use stoichiometric models for the characterization of the intracellular fluxes at steady state. Nonetheless, the stoichiometric models la ...

2015

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Engineering of microbial cell factories requires a simultaneous optimization of several criteria such as productivity, yield, titer, stress tolerance, all the while retaining the efficient, cost-effective and robust process. One of the most prominent examp ...

2015

iSCHRUNK – in Silico Approach to Characterization and Reduction of Uncertainty in the Kinetic Models of Genome-scale Metabolic Networks

Vassily Hatzimanikatis, Ljubisa Miskovic, Stefano Andreozzi

Accurate determination of physiological states of cellular metabolism requires detailed information about metabolic fluxes, metabolite concentrations and distribution of enzyme states. Integration of fluxomics and metabolomics data, and thermodynamics-base ...

2015

Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes

Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Fengos, Milenko Tokic

The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico. The lack of kinetic data hampers the development of ki ...

Elsevier2015

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Large-scale kinetic models of metabolism are essential for understanding and predicting the behavior of cellular systems when subject to perturbations. Despite the advances in experimental measurement technologies, the numerous parameters that are required ...

2015

Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches

Vassily Hatzimanikatis, Ljubisa Miskovic, Aikaterini Zisaki

Drug discovery and development is a high-risk enterprise that requires significant investments in capital, time and scientific expertise. The studies of xenobiotic metabolism remain as one of the main topics in the research and development of drugs, cosmet ...

Bentham Science Publishers2015

A Novel Approach to Design of Metabolic Engineering Strategiesa

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Georgios Fengos, Keng Cher Soh, Anirikh Chakrabarti

Dynamic nonlinear models of metabolism offer significant advantages as compared to traditional steady-state counterparts for the analysis of metabolic networks and identification of metabolic engineering strategies. Uncertainties in the metabolic network s ...

2014