Orkun S. Soyer

This study shows filamentous cyanobacteria use gliding motility to collect particles and form macrostructures, with aggregate formation dependent on filament length and flexibility.

This study shows microbial communities converge on similar metabolic functions under controlled environmental conditions, revealing the role of both imposed and emergent environmental filters.

The paper identifies asymmetric co-substrate usage at a metabolic branch point as a mechanism that enables flux switching and drives overflow metabolism, validated through modeling and experimental data in yeast.

This study observes synchronized growth oscillations in Serendipita indica fungi during sporulation using a microfluidic setup and links it to cell-cell communication.

This study investigates gliding motility in filamentous cyanobacteria, finding that cellular coordination enables rapid reversals, while loss of coordination leads to plectoneme formation.

The paper shows that ammonia leakage from bacteria enables nitrogen sharing with fungi in soil, highlighting a previously underappreciated mechanism of microbial interaction.

The paper develops a mathematical framework to show co-substrate cycling imposes flux limits in metabolic pathways and demonstrates this using simulations and existing metabolic data.

The paper analyzes how multi-site enzymes can generate bistable dynamics in reaction networks through mathematical modeling and derives conditions for bistability.

ChemChaste extends the Chaste library to simulate spatially inhomogeneous biochemical reaction-diffusion systems, enabling coupling of bulk and intracellular reactions.

STRONG identifies strains de novo from metagenome samples using coassembly, binning, and a Bayesian algorithm to resolve haplotypes and abundances.

The paper develops a host-virus metabolic model to predict antiviral targets for Chikungunya, Dengue, and Zika viruses by integrating human macrophage metabolism with viral biochemical demands.

The paper uses machine learning to predict functional and metabolic traits of microbes from their genomes, finding that lasso logistic regression on gene ortholog frequencies performs best.

The paper studies how sulfate perturbations affect aceto- and hydrogeno-trophic methanogens in synthetic communities, finding differential impacts on their stability and productivity.

This study shows that manganese oxide biomineralization by Roseobacter sp. AzwK-3b mitigates nitrite toxicity, improving microbial fitness through community-level stress resistance.

The paper identifies a thiamine auxotrophy in Serendipita indica and shows that co-culturing with Bacillus subtilis restores growth, but only under specific spatial and temporal conditions.