Ilija Dukovski

This study uses dynamic flux balance analysis to model cancer cell metabolism, revealing dependencies on growth media and cell-line specificities, and identifying potential therapeutic targets.

This paper develops a dynamical maximum entropy framework to model single-cell metabolic states during E. coli diauxie, revealing co-consumption as a continuous rather than discrete phenomenon.

The paper integrates flux balance analysis with diffusion equations to simulate spatio-temporal microbial community metabolism, showing optimal interaction distances for metabolite production.

This study shows that transgenic rice genotypes overexpressing PSY genes reduce methane emissions by altering rhizosphere microbial hydrogen cycling through changes in gene activity and metabolic pathways.

The paper uses consumer-resource models parametrized from monoculture exometabolite data to predict and design synthetic microbial consortia, revealing the importance of cross-feeding interactions and nonlinear dynamics.

The paper develops a chemotaxis module for COMETS, a microbial ecosystem simulation tool, and applies it to Pseudomonas simiae to study chemotaxis and metabolism coupling.

The paper introduces SoilMicrobeDB, a genome-based database improving metagenomic classification of soil microorganisms, particularly fungi and uncultivated taxa, and shows it enhances classification accuracy and fungal abundance estimates.

The paper develops a computational framework to model ATP allocation during viral infection, revealing new metabolic pathways and resource competition dynamics between host and virus.

The paper models bacterial colony morphology by integrating metabolic reactions and biomass propagation, showing realistic colony shapes and metabolic ring formation.

This paper introduces a dynamic flux balance model to simulate extracellular enzyme secretion and activity in microbial communities, finding optimal secretion rates that maximize growth or biomass yield based on environmental conditions.

This paper investigates butyrate production by F. prausnitzii and B. thetaiotaomicron in monoculture and coculture using experiments and simulations, finding enhanced butyrate production in coculture and complex metabolic strategies.