Vassily Hatzimanikatis

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Publications associées (124)

Genome-scale models of metabolism and expression predict the metabolic burden of recombinant protein expression

Vassily Hatzimanikatis, Mohammadomid Oftadeh

The production of recombinant proteins in a host using synthetic constructs such as plasmids comes at the cost of detrimental effects such as reduced growth, energetic inefficiencies, and other stress responses, collectively known as metabolic burden. Incr ...

2024

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations

Vassily Hatzimanikatis, Daniel Robert Weilandt, Asli Sahin

One of the main challenges hampering the development of kinetic models is the lack of kinetic parameters for many enzymatic reactions. Here, the authors introduce a framework to explore the catalytically optimal operating conditions of any complex enzyme m ...

Nature Portfolio2023

Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" -Part 2

Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret

Supplementary files containing datasets needed to reproduce the results of the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" by S. Choudhury et al. The code to use with these da ...

Zenodo2023

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

Supplementary datasets for the manuscript "Generative machine learning produces kinetic models that accurately characterize intracellular metabolic states" - Part 3

Vassily Hatzimanikatis, Ljubisa Miskovic, Michaël Roger Germain Moret

Zenodo2023

SYSTEMS BIOLOGY APPROACHES ALLOW INVESTIGATING THE SIGNALING AND METABOLIC REPROGRAMMING OF T CELLS

Vassily Hatzimanikatis, Maria Masid Barcon

Mary Ann Liebert, Inc2023

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

Vassily Hatzimanikatis, Asli Sahin, Mohammadomid Oftadeh, Evangelia Vagena

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

Dynamics of CLIMP-63 S-acylation control ER morphology

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

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

Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation

Vassily Hatzimanikatis, Ljubisa Miskovic, Homa Mohammadi Peyhani, Anastasia Sveshnikova

The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikati ...

Zenodo2023

Linear Solvation-energy Relationships (lser) and Equation-of-state Thermodynamics: on the Extraction of Thermodynamic Information From the Lser Database

Vassily Hatzimanikatis

There is a remarkable wealth of thermodynamic information in freely accessible databases, the LSER database being a classical example. The LSER, or Abraham solvation parameter model, is a very successful predictive tool in a variety of applications in the ...

MDPI2023

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