Publications de Ljubisa Miskovic

Engineering improved productivity of 1,4-butanediol in E. coli – a kinetic modeling approach

Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh, Anirikh Chakrabarti, Stefano Andreozzi

Microbial cell factories are becoming a norm for commercially viable production of chemicals for pharmaceutical, biotechnology, food and beverage industries. However, engineering of microbial cell factories requires a simultaneous optimization of several c ...

2014

Implications of the Assumptions on Intracellular Metabolic Operational States in Metabolic Control Analysis

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

Modeling and analysis of metabolic networks is inherently biased by assumptions regarding the intracellular metabolite and flux states. Despite the advanced metabolomics and fluxomics methods at our disposal, the sheer complexity of metabolic networks prev ...

2014

Unraveling the inhibitory effects of acetate on ethanol production in CEN.PK

Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh, Anirikh Chakrabarti

In this study, we used the ORACLE (Optimization and Risk Analysis of Complex Living Entities)[1] framework to study the impact of extracellular acetic acid on the S. cerevisiae metabolism with the aim to improve ethanol production in the presence of this i ...

2014

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

Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh, Anirikh Chakrabarti

Mathematical modeling is an essential tool for a comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the construction and analysis of stoichiometric models made it possib ...

2013

Identification of Feasible Metabolic Fluxes and Metabolite Concentrations using Large-scale Kinetic Models

Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh, Anirikh Chakrabarti

The constraints imposed during modeling must satisfy biologically representative phenotypes of the studied organism. Simultaneously, identification and analysis of these constraints enhances our understanding of the evolution/operational paradigms of the o ...

2013

In silico analysis of the interplay between P/O ratio and physiological states of the optimally grown Escherichia coli

Ljubisa Miskovic, Meriç Ataman, Keng Cher Soh, Stefano Andreozzi

The bioenergetics efficiency of aerobic respiration of an organism is expressed through P/O ratio, which represents the ATP production per oxygen atom reduced in Electron Transport Chains (ETC). P/O ratio, to date, has not been extensively used in the cont ...

2013

Data, Parameters & Nonlinearities: Development and Applications of Large-scale Dynamic Models of Metabolism

Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh, Anirikh Chakrabarti

Dynamic nonlinear models of metabolism offer a significant advantage as compared to constraint-based stoichiometric descriptions. However, progress in the development of large-scale nonlinear models has been hindered by both structural and quantitative unc ...

2013

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