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Vassily Hatzimanikatis

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Publications associées (123)

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Constraint-based metabolic control analysis for rational strain engineering

Vassily Hatzimanikatis, Ljubisa Miskovic, Meriç Ataman, Tuure Eelis Hameri, Sofia Tsouka

The advancements in genome editing techniques over the past years have rekindled interest in rational metabolic engineering strategies. While Metabolic Control Analysis (MCA) is a well-established method for quantifying the effects of metabolic engineering ...

2021

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

Vassily Hatzimanikatis, Meriç Ataman

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

Dataset - Generative Approaches to Kinetic Parameter Inference in Metabolic Networks via Latent Space Exploration

Oussama Gabouj, Vassily Hatzimanikatis, Ljubisa Miskovic, Subham Choudhury, Ilias Toumpe

Dataset needed to reproduce the results in the manuscript by "Generative Approaches to Kinetic Parameter Inference in Metabolic Networks via Latent Space Exploration" by S. Choudhury et al. (under review, a preprint available at https://www.biorxiv.org/con ...

Zenodo2025

NICEpath: Finding metabolic pathways in large networks through atom-conserving substrate-product pairs

Vassily Hatzimanikatis, Jasmin Maria Hafner

Motivation: Finding biosynthetic pathways is essential for metabolic engineering of organisms to produce chemicals, biodegradation prediction of pollutants and drugs, and for the elucidation of bioproduction pathways of secondary metabolites. A key step in ...

Oxford University Press2021

Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power

Vassily Hatzimanikatis, Jasmin Maria Hafner, Anastasia Sveshnikova, Alan Scheidegger

The ATLAS of Biochemistry is a repository of both known and novel predicted biochemical reactions between biological compounds listed in the Kyoto Encyclopedia of Genes and Genomes (KEGG). ATLAS was originally compiled based on KEGG 2015, though the number ...

AMER CHEMICAL SOC2020

Quantitative modeling of human metabolism: A call for a community effort

Vassily Hatzimanikatis, Maria Masid Barcon

Metabolism is the process by which cells and organisms obtain nutrients and energy to perform their functions. In the last years, many human diseases, including cancer, diabetes, and cardiac diseases, have been associated with altered metabolism. Understan ...

2021

Computational Framework for Predictive Biodegradation

Vassily Hatzimanikatis

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

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

Vassily Hatzimanikatis, Bart Deplancke, Alina Isakova, Yves Berset

Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its i ...

American Society for Biochemistry and Molecular Biology2016

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

Rizlan Bernier-Latmani, Vassily Hatzimanikatis, Karin Lederballe Meibom, Zhaleh Hosseini, Cornelia List

Iron is essential for most living organisms. In addition, its biogeochemical cycling influences important processes in the geosphere (e.g., the mobilization or immobilization of trace elements and contaminants). The reduction of Fe(III) to Fe(II) can be ca ...

2019

Dynamics of CLIMP-63 S-acylation control ER morphology

Vassily Hatzimanikatis, Françoise Gisou van der Goot Grunberg, Graham Knott, Kathryn Hess Bellwald, Luciano Andres Abriata, Laurence Gouzi Abrami, Patrick Alain Sandoz, Catherine Maclachlan, Béatrice Kunz, Sylvia Ho, Gard Spreemann, Robin Alexander Denhardt-Eriksson

A key player in the formation of endoplasmic reticulum sheets is CLIMP-63, but mechanistic details remained elusive. Here authors combined cellular experiments and mathematical modelling to show that S-acylation of CLIMP-63 regulates its function by mediat ...

Nature Portfolio2023

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, Georgios Savoglidis, Antoine Philippe Van Muyden, Sviatlana Siankevich, Safak Bulut

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

Functional genomics of Plasmodium falciparum using metabolic modelling and analysis

Vassily Hatzimanikatis, Stepan Tymoshenko

Plasmodium falciparum is an obligate intracellular parasite and the leading cause of severe malaria responsible for tremendous morbidity and mortality particularly in sub-Saharan Africa. Successful completion of the P. falciparum genome sequencing project ...

Oxford Univ Press2013

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

Dataset - Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production

Vassily Hatzimanikatis, Ljubisa Miskovic, Francisco Javier Perez Saez, Maria Masid Barcon, Bharath Narayanan, Wei Jiang

Dataset supporting the results presented in the paper entitled "Kinetic-model-guided engineering of multiple S. cerevisiae strains improves p-coumaric acid production" by Narayanan, Jiang & Wang et al (https://doi.org/10.1016/j.ymben.2025.06.008). Dataset ...

Zenodo2025

A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics

Vassily Hatzimanikatis, Ljubisa Miskovic, Maria Masid Barcon, Pierre Guy Rémy Salvy, Mohammadomid Oftadeh

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of ...

Nature Portfolio2021

Tunable reporter signal production in feedback-uncoupled arsenic bioreporters

Vassily Hatzimanikatis

Escherichia coli-based bioreporters for arsenic detection are typically based on the natural feedback loop that controls ars operon transcription. Feedback loops are known to show a wide range linear response to the detriment of the overall amplification o ...

Wiley-Blackwell2013

Metabolic interaction models recapitulate leaf microbiota ecology

Vassily Hatzimanikatis, Evangelia Vagena

Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We ...

American Association for the Advancement of Science2023

Designing pathways for bioproducing complex chemicals by combining tools for pathway extraction and ranking

Vassily Hatzimanikatis, Anastasia Sveshnikova, Mohammadomid Oftadeh

The synthesis of many important biochemicals involves complex molecules and numerous reactions. The design and optimization of whole-cell biocatalysts for the production of these molecules requires metabolic modeling to extract production pathways from bio ...

Springer Science and Business Media LLC2025

Systems biology

Vassily Hatzimanikatis

Elsevier2011

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

Daniel Federico Hernandez Gardiol, Vassily Hatzimanikatis, Meriç Ataman, 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