Qimin Zhang

The paper identifies six reproducible nasopharyngeal community state types (NPCSTs) that explain most microbiome variance and develop a health index to assess nasopharyngeal wellness.

Beaver improves transcriptome assembly at single-cell resolution by combining a fragment graph with random forest models, outperforming existing assemblers in precision.

The paper uses 16S rRNA gene sequencing to characterize vaginal microbiomes in BV-diagnosed samples, showing strong concordance with PCR-based tests and identifying BV-associated microbial and metabolic signatures.

The paper investigates how transcript annotations affect assembly results and develops a tool to reduce intron retention bias in transcript assembly.

Scallop2 improves transcript assembly accuracy for multiple-end RNA-seq data by efficiently bridging gaps and reducing false positives.