Orkun S. Soyer

Emergent particle collection by cyanobacteria through gliding motility and filament buckling

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

Enrichment of convergent metabolic functions in microbial communities through imposed and emergent environmental niches

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

Asymmetric co-substrate usage at a metabolic branch point as a minimal network motif that can drive overflow metabolism

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.

Ammonia leakage can underpin nitrogen-sharing among soil microbes

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

Co-substrate pools can constrain and regulate pathway fluxes in cell metabolism

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.

Multi-site enzymes as a mechanism for bistability in reaction networks

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

ChemChaste: Simulating spatially inhomogenous biochemical reaction-diffusion systems for modelling cell-environment feedbacks

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

Metagenomics Strain Resolution on Assembly Graphs

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

Integrated Human-Virus Metabolic Modelling Predicts Host-Based Antiviral Targets Against Chikungunya, Dengue and Zika Viruses

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.

Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes

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.

Synthetic methanogenic communities reveal differential impact of ecological perturbations on aceto- and hydrogeno-trophic methanogens

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

Manganese oxide biomineralization is a social trait protecting against nitrite toxicity

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

Impact of spatial organization on a novel auxotrophic interaction among soil microbes

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.