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Vassily Hatzimanikatis

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Related publications (124)

Uncertainty reduction in biochemical kinetic models: Enforcing desired model properties

Ljubisa Miskovic, Vassily Hatzimanikatis, Michaël Roger Germain Moret

A persistent obstacle for constructing kinetic models of metabolism is uncertainty in the kinetic properties of enzymes. Currently, available methods for building kinetic models can cope indirectly with uncertainties by integrating data from different biol ...

2019

Discovery and Evaluation of Biosynthetic Pathways for the Production of Five Methyl Ethyl Ketone Precursors

Ljubisa Miskovic, Vassily Hatzimanikatis, Noushin Hadadi, Meriç Ataman, Milenko Tokic

The limited supply of fossil fuels and the establishment of new environmental policies shifted research in industry and academia towards sustainable production of the 2nd generation of biofuels, with Methyl Ethyl Ketone (MEK) being one promising fuel candi ...

2018

pyTFA and matTFA: a Python package and a Matlab toolbox for Thermodynamics-based Flux Analysis

Vassily Hatzimanikatis, Keng Cher Soh, Meriç Ataman, Georgios Fengos, Pierre Guy Rémy Salvy

Summary: pyTFA and matTFA are the first published implementations of the original TFA paper. Specifically, they include explicit formulation of Gibbs energies and metabolite concentrations, which enables straightforward integration of metabolite concentrat ...

2018

Efficient cleavage of aryl ether C–O linkages by Rh–Ni and Ru–Ni nanoscale catalysts operating in water

Paul Joseph Dyson, Vassily Hatzimanikatis, Duncan Thomas Lindsay Alexander, Ning Yan, Antoine Philippe Van Muyden, Safak Bulut, Georgios Savoglidis, Sviatlana Siankevich

Bimetallic Ru–Ni and Rh–Ni nanocatalysts coated with a phase transfer agent efficiently cleave aryl ether C–O linkages in water in the presence of hydrogen. For dimeric substrates with weaker C–O linkages, i.e. α-O-4 and β-O-4 bonds, low loadings of the pr ...

2018

Exploring biochemical pathways for mono-ethylene glycol (MEG) synthesis from synthesis gas

Vassily Hatzimanikatis, Noushin Hadadi, Meriç Ataman

Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hen ...

Academic Press Inc Elsevier Science2017

Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks

Vassily Hatzimanikatis, Stepan Tymoshenko, Dominique Soldati-Favre, Meriç Ataman, Anush Chiappino-Pepe

Novel antimalarial therapies are urgently needed for the fight against drug-resistant para- sites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this co ...

Public Library of Science2017

On Lewis acidity/basicity and hydrogen bonding in the equation-of-state approach

Vassily Hatzimanikatis

The central objective of this work is to revisit the development of the widely used Lewis acidity/basicity scales and seek possibilities for their eventual unification. The primary focus is on hydrogen bonding interactions which are dealt with the estimati ...

Academic Press Ltd- Elsevier Science Ltd2017

Thermodynamics-based Metabolite Sensitivity Analysis in metabolic networks

Vassily Hatzimanikatis

The increasing availability of large metabolomics datasets enhances the need for computational methodologies that can organize the data in a way that can lead to the inference of meaningful relationships. Knowledge of the metabolic state of a cell and how ...

Elsevier2017

Redefining solubility parameters: Bulk and surface properties from unified molecular descriptors

Vassily Hatzimanikatis

The central objective of this work is to revisit the development of the widely used solubility parameters and linear solvation energy relationships (LSER) and seek interconnections and possibilities for secure exchange of information. Partial solvation par ...

Academic Press Ltd- Elsevier Science Ltd2017

Mechanistic Modeling of Genetic Circuits for ArsR Arsenic Regulation

Vassily Hatzimanikatis, Yves Berset

Bioreporters are living cells that generate an easily measurable signal in the presence of a chemical compound. They acquire their functionality from synthetic gene circuits, the configuration of which defines the response signal and signal-to-noise ratio. ...

Amer Chemical Soc2017

Integration of Metabolic, Regulatory and Signaling Networks Towards Analysis of Perturbation and Dynamic Responses

Vassily Hatzimanikatis, Meriç Ataman, Anush Chiappino-Pepe, Vikash Kumar Pandey

The expanding generation of dynamic biological data requires approaches that integrate and analyze information from different types of cellular processes –metabolism, regulation, and signaling–, and ultimately increase our insights into the cell behavior u ...

2017

lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites

Vassily Hatzimanikatis, Meriç Ataman

In the post-genomic era, Genome-scale metabolic networks (GEMs) have emerged as invaluable tools to understand metabolic capabilities of organisms. Different parts of these metabolic networks are defined as subsystems/pathways, which are sets of functional ...

2017

Single-molecule kinetic analysis of HP1-chromatin binding reveals a dynamic network of histone modification and DNA interactions

Vassily Hatzimanikatis, Louise Catherine Bryan, Georg Fantner, Pascal Damian Odermatt, Oliver Hantschel, Sandrine Madeleine Suzanne Georgeon, Beat Fierz, Sinan Kilic, Carolin Christine Lechner, Andreas Linus Bachmann, Daniel Robert Weilandt

Chromatin recruitment of effector proteins involved in gene regulation depends on multivalent interaction with histone post-translational modifications (PTMs) and structural features of the chromatin fiber. Due to the complex interactions involved, it is c ...

Oxford University Press (OUP)2017

Reconstruction of biological pathways and metabolic networks from in silico labeled metabolites

Vassily Hatzimanikatis, Keng Cher Soh, Noushin Hadadi, Jasmin Maria Hafner

Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely avai ...

Wiley-V C H Verlag Gmbh2017

A Design-Build-Test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models

Ljubisa Miskovic, Vassily Hatzimanikatis, Keng Cher Soh

Recent advancements in omics measurement technologies have led to an ever-increasing amount of available experimental data that necessitate systems-oriented methodologies for efficient and systematic integration of data into consistent large-scale kinetic ...

2017

redGEM: Systematic reduction and analysis of genome-scale metabolic reconstructions for development of consistent core metabolic models

Vassily Hatzimanikatis, Meriç Ataman, Daniel Federico Hernandez Gardiol, Georgios Fengos

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 ...

2017

Sustainability assessment of succinic acid production technologies from biomass using metabolic engineering

Konrad Hungerbühler, Vassily Hatzimanikatis, Meriç Ataman, Merten Morales

Over the past few years, bio-succinic acid from renewable resources has gained increasing attention as a potential bio-derived platform chemical for the detergent/surfactant, ion chelator, food and pharmaceutical markets. Until now, much research was under ...

Royal Soc Chemistry2016

ATLAS of Biochemistry: A Repository of All Possible Biochemical Reactions for Synthetic Biology and Metabolic Engineering Studies

Vassily Hatzimanikatis, Noushin Hadadi, Adrian Shajkofci, Aikaterini Zisaki, Jasmin Maria Hafner

Because the complexity of metabolism cannot be intuitively understood or analyzed, computational methods are indispensable for studying biochemistry and deepening our understanding of cellular metabolism to promote new discoveries. We used the computationa ...

Amer Chemical Soc2016

Molecular thermodynamics of metabolism: hydration quantities and the equation-of-state approach

Vassily Hatzimanikatis, Noushin Hadadi, Meriç Ataman

The present work is part of a series of papers aiming at a thorough understanding of the thermodynamics of metabolism over a broad range of external conditions. The focus here is on the systematic study of solvation/hydration of a variety of fluids via an ...

Royal Soc Chemistry2016

Analysis of Translation Elongation Dynamics in the Context of an Escherichia coli Cell

Julien Racle, Vassily Hatzimanikatis, Joana Raquel Pinto Vieira

Understanding the mechanisms behind translation and its rate-limiting steps is crucial for both the development of drug targets and improvement of heterologous protein production with many biotechnological applications, such as in pharmaceutical and biofue ...

Elsevier2016

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