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Vassily Hatzimanikatis

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Related publications (124)

Constraint-based metabolic control analysis for rational strain engineering

Ljubisa Miskovic, Vassily Hatzimanikatis, 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

Mapping and Analysis of the Complexity of Lipid Metabolism for Applications in Health and Sustainability

Vassily Hatzimanikatis, Sofia Tsouka

Metabolism is a network of biotransformations that sustain life in cells. Over the past decades, metabolism has been studied in multiple contexts, ranging from medicine to industrial manufacturing. In particular, lipid metabolism has been linked to various ...

EPFL2020

MEMOTE for standardized genome-scale metabolic model testing

Jens Nielsen, Vassily Hatzimanikatis, Cheng Zhang, Meriç Ataman, Georgios Fengos, Ali Kaafarani

NATURE PUBLISHING GROUP2020

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

Vassily Hatzimanikatis, Pierre Guy Rémy Salvy

Systems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flu ...

Nature Research2020

Large-scale kinetic metabolic models of Pseudomonas putida KT2440 for consistent design of metabolic engineering strategies

Ljubisa Miskovic, Vassily Hatzimanikatis, Milenko Tokic

Background: Pseudomonas putida is a promising candidate for the industrial production of biofuels and biochemicals because of its high tolerance to toxic compounds and its ability to grow on a wide variety of substrates. Engineering this organism for impro ...

2020

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

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

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

redLips: a comprehensive mechanistic model of the lipid metabolic network of yeast

Vassily Hatzimanikatis, Sofia Tsouka

Over the last decades, yeast has become a key model organism for the study of lipid biochemistry. Because the regulation of lipids has been closely linked to various physiopathologies, the study of these biomolecules could lead to new diagnostics and treat ...

2020

Analysis of human metabolism by reducing the complexity of the genome-scale models using redHUMAN

Vassily Hatzimanikatis, Meriç Ataman, Maria Masid Barcon

Altered metabolism is associated with many human diseases. Human genome-scale metabolic models (GEMs) were reconstructed within systems biology to study the biochemistry occurring in human cells. However, the complexity of these networks hinders a consiste ...

Nature Research2020

Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism

Vassily Hatzimanikatis, Damien Lionel Nicolas, Dominique Soldati-Favre, Anush Chiappino-Pepe, Aarti Krishnan, Matteo Lunghi

To survive and proliferate in diverse host environments with varying nutrient availability, the obligate intracellular parasite Toxoplasma gondii reprograms its metabolism. We have generated and curated a genome-scale metabolic model (iTgo) for the fast-re ...

CELL PRESS2020

Enhanced flux prediction by integrating relative expression and relative metabolite abundance into thermodynamically consistent metabolic models

Vassily Hatzimanikatis, Noushin Hadadi, Vikash Kumar Pandey

The ever-increasing availability of transcriptomic and metabolomic data can be used to deeply analyze and make ever-expanding predictions about biological processes, as changes in the reaction fluxes through genome-wide pathways can now be tracked. Current ...

2019

Control Theory Concepts for Modeling Uncertainty in Enzyme Kinetics of Biochemical Networks

Ljubisa Miskovic, Vassily Hatzimanikatis, Georgios Savoglidis, Milenko Tokic

Analysis of the dynamic and steady-state properties of biochemical networks hinges on information about the parameters of enzyme kinetics. The lack of experimental data characterizing enzyme activities and kinetics along with the associated uncertainties i ...

2019

Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites

Ljubisa Miskovic, Vassily Hatzimanikatis, Noushin Hadadi, Marianne Seijo

Thousands of biochemical reactions with characterized activities are “orphan,” meaning they cannot be assigned to a specific enzyme, leaving gaps in metabolic pathways. Novel reactions predicted by pathway-generation tools also lack associated sequences, l ...

National Academy of Sciences2019

Investigating the deregulation of metabolic tasks via Minimum Network Enrichment Analysis (MiNEA) as applied to nonalcoholic fatty liver disease using mouse and human omics data

Vassily Hatzimanikatis, Vikash Kumar Pandey

Nonalcoholic fatty liver disease (NAFLD) is associated with metabolic syndromes spanning a wide spectrum of diseases, from simple steatosis to the more complex nonalcoholic steatohepatitis. To identify the deregulation that occurs in metabolic processes at ...

2019

Impact of iron reduction on the metabolism of Clostridium acetobutylicum

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

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

Statistical inference in ensemble modeling of cellular metabolism

Marc-Olivier Boldi, Vassily Hatzimanikatis, Tuure Eelis Hameri

Kinetic models of metabolism can be constructed to predict cellular regulation and devise metabolic engineering strategies, and various promising computational workflows have been developed in recent years for this. Due to the uncertainty in the kinetic pa ...

2019

Modeling metabolic networks of individual bacterial agents in heterogeneous and dynamic soil habitats (IndiMeSH)

Dani Or, Vassily Hatzimanikatis, Meriç Ataman

Natural soil is characterized as a complex habitat with patchy hydrated islands and spatially variable nutrients that is in a constant state of change due to wetting-drying dynamics. Soil microbial activity is often concentrated in sparsely distributed hot ...

2019

Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations

Ljubisa Miskovic, Vassily Hatzimanikatis, Meriç Ataman, Georgios Fengos, Tuure Eelis Hameri

Large-scale kinetic models are used for designing, predicting, and understanding the metabolic responses of living cells. Kinetic models are particularly attractive for the biosynthesis of target molecules in cells as they are typically better than other t ...

2019

Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage

Vassily Hatzimanikatis, Dominique Soldati-Favre, Anush Chiappino-Pepe, Vikash Kumar Pandey

Plasmodium gene functions in mosquito and liver stages remain poorly characterized due to limitations in the throughput of phenotyping at these stages. To fill this gap, we followed more than 1,300 barcoded P. berghei mutants through the life cycle. We dis ...

2019

Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism

Vassily Hatzimanikatis, Daniel Robert Weilandt

Many computational models for analyzing and predicting cell physiology rely on in vitro data collected in dilute and controlled buffer solutions. However, this can mislead models because up to 40% of the intracellular volume-depending on the organism, the ...

2019

110th Anniversary: From Solubility Parameters to Predictive Equation-of-State Modeling

Vassily Hatzimanikatis

A simple predictive molecular thermodynamic model for bulk phases and interfaces is presented. The model combines features of the quantitative structure-property relationships (QSPR) approach, the equation-of-state approach, and quantum-chemical calculatio ...

AMER CHEMICAL SOC2019

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