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Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies
Related publications (38)
Studying cancer cells phenotypes integrating omics data in human reduced genome-scale metabolic models.
Vassily Hatzimanikatis, Maria Masid Barcon, Vikash Kumar Pandey
Cancer is a leading cause of death in the world, and the mechanisms underlying this disease are still not completely understood. In the last decades, altered tumour metabolism has been recognized as a hallmark of cancer. This has created a resurgence of in ...
2018Predicted responses of a large-scale Pseudomonas putida KT2440 kinetic metabolic model to several single-gene knockouts are consistent with experimental observations
Vassily Hatzimanikatis, Ljubisa Miskovic, Milenko Tokic
P. putida emerged as one of the most promising production hosts for a wide range of chemicals, due to its fast growth with a low nutrient and cellular energy demand, considerable metabolic versatility, ability to grow in wide range of chemicals, suitabilit ...
2018Computational 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 ...
2018redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models
Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Daniel Federico Hernandez Gardiol
Genome-scale metabolic reconstructions have proven to be valuable resources in enhancing our understanding of metabolic networks as they encapsulate all known metabolic capabilities of the organisms from genes to proteins to their functions. However the co ...
2017Generation and Analysis of Large-Scale Dynamic Non-Linear Models of Metabolism
Vassily Hatzimanikatis, Ljubisa Miskovic, Georgios Fengos
Understanding complex responses of metabolic processes in biochemical systems requires the quantitative description of the dynamic interplay between metabolite levels, enzyme levels, and reaction rates. Generation and use of such models is hindered by the ...
2017Optimization of the production of methyl ethyl ketone in recombinant Pseudomonas putida using large-scale kinetic models
Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Milenko Tokic
The production of second generation of biofuels by conversion of inexpensive feedstocks is a basis for future bio-sustainable economy. Among many proposed molecules, methyl ethyl ketone (MEK) emerged as one of the most prominent fuel candidates due to its ...
2017Discovery and evaluation of novel pathways for production of methyl ethyl ketone
Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Noushin Hadadi, Milenko Tokic
The limited supply of fossil fuels and environmental reasons shifted research in industry and academia towards finding their replacements. An important part of these efforts is focused on a sustainable production of the 2nd generation of biofuels. Among ma ...
2017Navigating and Managing the Complexity of Genome Scale Metabolic Networks for Studies in Cellular Physiology and Industrial Biotechnology
Metabolism is a network of biochemical reactions that converts carbon sources to cellu-lar fuels and building blocks. Metabolism of many organisms has been studied for many decades. These studies define metabolism as a very large and complex network. Stoic ...
EPFL2016Discovery and Evaluation of Novel Pathways for Production of the Second Generation of Biofuels
Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Noushin Hadadi, Milenko Tokic
In an effort of overcoming the limited availability of fossil energy resources the focus of the research and development in the area of biofuels has moved towards developing the second generation of fuels that should be produced via microbial fermentation. ...
2016Exploring enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models
Vassily Hatzimanikatis, Ljubisa Miskovic, Keng Cher Soh, Anirikh Chakrabarti, Stefano Andreozzi
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