Publications by Evangelia Vagena

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

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

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

Evangelia Vagena

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

EPFL2024

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

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

A workflow for annotating the knowledge gaps in metabolic reconstructions using known and hypothetical reactions

Vassily Hatzimanikatis, Meriç Ataman, Jasmin Maria Hafner, Homa Mohammadi Peyhani, Evangelia Vagena, Noushin Hadadi, Anush Chiappino-Pepe

Advances in medicine and biotechnology rely on a deep understanding of biological processes. Despite the increasingly available types and amounts of omics data, significant knowledge gaps remain, with current approaches to identify and curate missing annot ...

National Academy of Sciences2022