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Vassily Hatzimanikatis

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Publications associées (123)

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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

Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states

Vassily Hatzimanikatis, Ljubisa Miskovic, Subham Choudhury, Bharath Narayanan, David Michael Moret

Generating large omics datasets has become routine for gaining insights into cellular processes, yet deciphering these datasets to determine metabolic states remains challenging. Kinetic models can help integrate omics data by explicitly linking metabolite ...

Springer Science and Business Media LLC2024

Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx

Vassily Hatzimanikatis, Jasmin Maria Hafner, Anastasia Sveshnikova

Metabolic "dark matter" describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark ...

Nature Portfolio2022

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

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

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

Solvation quantities from a COSMO-RS equation of state

Vassily Hatzimanikatis

This work focuses on the extension of the successful COSMO-RS model of mixtures into an equation-of-state model of fluids and its application for the estimation of solvation/hydration quantities of a variety of chemical substances. These quantities include ...

Elsevier2015

From microbiome composition to functional engineering, one step at a time

Vassily Hatzimanikatis, Evangelia Vagena, Mohammadomid Oftadeh, Asli Sahin

Communities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective envi ...

Amer Soc Microbiology2023

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

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

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

The influence of the crowding assumptions in biofilm simulations

Vassily Hatzimanikatis, Liliana Angeles Martinez

Author summary In nature, many organisms grow in crowded biofilms that protect against stressful conditions, making their control/eradication a challenge. Modeling these microbial systems is a valuable tool for studying the interactions among cells and exp ...

2021

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

Vassily Hatzimanikatis, Anush Chiappino-Pepe, Damien Lionel Nicolas

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

Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis

Vassily Hatzimanikatis, Stepan Tymoshenko

Toxoplasma gondii is a human pathogen prevalent worldwide that poses a challenging and unmet need for novel treatment of toxoplasmosis. Using a semi-automated reconstruction algorithm, we reconstructed a genome-scale metabolic model, ToxoNet1. The reconstr ...

Public Library Science2015

The Origins of Time-Delay in Template Biopolymerization Processes

Vassily Hatzimanikatis

Time-delays are common in many physical and biological systems and they give rise to complex dynamic phenomena. The elementary processes involved in template biopolymerization, such as mRNA and protein synthesis, introduce significant time delays. However, ...

Public Library of Science2010

Exploration of trade-offs between steady-state and dynamic properties in signaling cycles

Dominique Bonvin, Vassily Hatzimanikatis, Benoît Chachuat, Andrijana Radivojevic

In the intracellular signaling networks that regulate important cell processes, the base pattern comprises the cycle of reversible phosphorylation of a protein, catalyzed by kinases and opposing phosphatases. Mathematical modeling and analysis have been us ...

Iop Publishing Ltd2012

Effects of codon distributions and tRNA competition on protein translation

Vassily Hatzimanikatis

Translation is a central cellular process and the complexity of its mechanism necessitates mathematical frameworks to better understand system properties and make quantitative predictions. We have developed a gene sequence-specific mechanistic model for tr ...

2008

A Model for Protein Translation: Polysome Self-Organization Leads to Maximum Protein Synthesis Rates

Vassily Hatzimanikatis

The genetic information in DNA is transcribed to mRNA and then translated to proteins, which form the building blocks of life. Translation, or protein synthesis, is hence a central cellular process. We have developed a gene-sequence-specific mechanistic mo ...

2007

Discovery and Analysis of Novel Metabolic Pathways for the Biosynthesis of Industrial Chemicals: 3-Hydroxypropanoate

Vassily Hatzimanikatis

Sustainable microbial production of high-value organic compounds such as 3-hydroxypropanoate (3HP) is becoming an increasingly attractive alternative to organic syntheses that utilize petrochemical feedstocks. We applied the Biochemical Network Integrated ...

Wiley-Blackwell2010

A method for analysis and design of metabolism using metabolomics data and kinetic models: Application on lipidomics using a novel kinetic model of sphingolipid metabolism

Vassily Hatzimanikatis, Paolo Angelino, Georgios Savoglidis

We present a model-based method, designated Inverse Metabolic Control Analysis (IMCA), which can be used in conjunction with classical Metabolic Control Analysis for the analysis and design of cellular metabolism. We demonstrate the capabilities of the met ...

Academic Press Inc Elsevier Science2016

A Genome-Scale Integration and Analysis of Lactococcus lactis Translation Data

Vassily Hatzimanikatis, Julien Racle

Protein synthesis is a template polymerization process composed by three main steps: initiation, elongation, and termination. During translation, ribosomes are engaged into polysomes whose size is used for the quantitative characterization of translatome. ...

Public Library of Science2013

The Dawn of High-throughput and Genome-scale Kinetic Modeling: Recent Advances and Future Directions

Vassily Hatzimanikatis, Ljubisa Miskovic, Subham Choudhury, Ilias Toumpe

Researchers have invested much effort into developing kinetic models due to their ability to capture dynamic behaviors, transient states, and regulatory mechanisms of metabolism, providing a detailed and realistic representation of cellular processes. Hist ...

AMER CHEMICAL SOC2025

Quantification of uncertainty in metabolic networks through the sampling of kinetic data space

Vassily Hatzimanikatis, Ljubisa Miskovic

Study of a metabolic network with respect to the sensitivity of the metabolite concentrations and the metabolic fluxes to genetic, biochemical, and environmental variations requires knowledge of the kinetic properties of the enzymes in the network. Experim ...

2009