Chunyu Zhao

EukDetect2 improves eukaryote detection in metagenomes with a larger database and quantitative metrics, revealing Blastocystis and Dientamoeba as prevalent gut eukaryotes.

The paper examines genomic diversity in gut bacteria, finding that accessory genes show faster linkage decay compared to core SNPs, with mobile genetic elements showing minimal linkage to core SNPs.

microSLAM identifies microbiome-disease associations by analyzing gene presence/absence across strains, revealing 49 species and 83 genes linked to IBD.

This study constructs pangenomes of 728 human gut prokaryotic species, revealing genetic diversity linked to stress response, antibiotic resistance, and host characteristics.

The paper introduces StrainPGC and MIDAS v3 to accurately estimate intraspecific microbial gene content variation in metagenomic data, outperforming existing methods and revealing functional diversity in gut microbiomes.

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

MIDAS2 improves metagenomic analysis by enhancing SNV and CNV detection with custom databases and paired-end reads, enabling efficient genotyping of large sample sets.

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.

Sunbeam is a modular pipeline for metagenomic analysis that standardizes preprocessing and removes low-complexity reads, enabling reproducible and extensible workflows.