Xinrun Yang

eBiota: Designing microbial communities from large seed pools with desired function using rapid optimization and deep learning

eBiota designs microbial communities from large strain pools to generate target products using optimization and deep learning, showing accurate predictions and experimental validation.

Long-read metagenomic sequencing reveals novel lineages and functional diversity in urban soil microbiome

The paper uses long-read metagenomic sequencing to analyze urban soil samples, revealing novel microbial lineages and extensive functional diversity.

LorMe: a streamlined and interoperable R framework for end-to-end microbiome analysis

LorMe provides a unified R framework for microbiome analysis, offering an end-to-end pipeline with reproducibility and interoperability across tools.

Substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion

This study uses genome-scale models and synthetic communities to show that substrate utilization and cross-feeding synergistically determine microbiome resistance to pathogen invasion.