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Vassily Hatzimanikatis

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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

Vassily Hatzimanikatis, Ljubisa Miskovic

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, 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

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

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

Vassily Hatzimanikatis, Ljubisa Miskovic

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

Vassily Hatzimanikatis, Ljubisa Miskovic, 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

Vassily Hatzimanikatis, Ljubisa Miskovic

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, Alexandre Louis André Persat, Evangelia Vagena, Tamara Rossy

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

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

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

2024

Rational strain design with minimal phenotype perturbation

Vassily Hatzimanikatis, Ljubisa Miskovic, Daniel Robert Weilandt

Nature Portfolio2024

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

Vassily Hatzimanikatis, Ljubisa Miskovic

Springer Science and Business Media LLC2024

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

Vassily Hatzimanikatis

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

2024