Zhou Jason Shi

Maast: genotyping thousands of microbial strains efficiently

Maast efficiently genotypes SNPs from thousands of microbial strains by reducing redundancy and improving speed and accuracy compared to existing methods.

Pitfalls of genotyping microbial communities with rapidly growing genome collections

The paper shows that closely related microbial species in genome databases reduce metagenotyping accuracy and power, and suggests strategies to mitigate these issues.

Scalable microbial strain inference in metagenomic data using StrainFacts

StrainFacts enables scalable strain inference in metagenomic data, showing comparable accuracy to intensive tools and revealing strain diversity patterns in human stool samples.

EcoFun-MAP: An Ecological Function Oriented Metagenomic Analysis Pipeline

EcoFun-MAP is a metagenomic analysis pipeline designed for ecological function annotation, offering multiple workflows and a web interface to analyze environmental samples.

Ultra-rapid metagenotyping of the human gut microbiome

This paper introduces GT-Pro, a tool for ultra-fast and accurate SNP calling in metagenomes, enabling strain-level analysis of the human gut microbiome.