Publications by Vassily Hatzimanikatis

Metabolic network reconstruction as a resource for analyzing Salmonella Typhimurium SL1344 growth in the mouse intestine

Vassily Hatzimanikatis, Homa Mohammadi Peyhani, Evangelia Vagena

Nontyphoidal Salmonella strains (NTS) are among the most common foodborne enteropathogens and constitute a major cause of global morbidity and mortality, imposing a substantial burden on global health. The increasing antibiotic resistance of NTS bacteria h ...

PUBLIC LIBRARY SCIENCE2025

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

Ljubisa Miskovic, Vassily Hatzimanikatis

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

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

Vassily Hatzimanikatis, Mohammadomid Oftadeh, Anastasia Sveshnikova

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

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

Ljubisa Miskovic, Vassily Hatzimanikatis, Francisco Javier Perez Saez, Maria Masid Barcon, 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

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

Ljubisa Miskovic, Vassily Hatzimanikatis

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

Rational strain design with minimal phenotype perturbation

Ljubisa Miskovic, Vassily Hatzimanikatis, Daniel Robert Weilandt

Devising genetic interventions for desired cellular phenotypes remains challenging regarding time and resources. Kinetic models can accelerate this task by simulating metabolic responses to genetic perturbations. However, exhaustive design evaluations with ...

Nature Portfolio2024

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

Ljubisa Miskovic, Vassily Hatzimanikatis

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

Pseudomonas aeruginosa faces a fitness trade-off between mucosal colonization and antibiotic tolerance during airway infection

Vassily Hatzimanikatis, Tamara Rossy, Alexandre Louis André Persat, Evangelia Vagena

Pseudomonas aeruginosa frequently causes antibiotic-recalcitrant pneumonia, but the mechanisms driving its adaptation during human infections remain unclear. To reveal the selective pressures and adaptation strategies at the mucosal surface, here we invest ...

2024

Host cell CRISPR genomics and modelling reveal shared metabolic vulnerabilities in the intracellular development of Plasmodium falciparum and related hemoparasites

Vassily Hatzimanikatis

Parasitic diseases, particularly malaria (caused by Plasmodium falciparum) and theileriosis (caused by Theileria spp.), profoundly impact global health and the socioeconomic well-being of lower-income countries. Despite recent advances, identifying host me ...

Nature Research2024

Computer-aided design and implementation of efficient biosynthetic pathways to produce high added-value products derived from tyrosine in Escherichia coli

Vassily Hatzimanikatis, Anastasia Sveshnikova

Developing efficient bioprocesses requires selecting the best biosynthetic pathways, which can be challenging and time-consuming due to the vast amount of data available in databases and literature. The extension of the shikimate pathway for the biosynthes ...

2024

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

Ljubisa Miskovic, Vassily Hatzimanikatis, 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

Ljubisa Miskovic, Vassily Hatzimanikatis, 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 (https://doi.org/10.1101/2023. ...

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

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

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

Ljubisa Miskovic, Vassily Hatzimanikatis, 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