John R. Lee

SurvBal identifies microbiome taxon balances associated with survival outcomes using survival models and step-wise selection.

The paper introduces Coffee-seq, a metagenomic DNA sequencing method that reduces environmental contamination, and applies it to detect infections and microbial signatures in clinical samples.

This study uses scRNA-seq to analyze kidney allograft biopsies and identifies recipient-derived fibroblasts and other cell states associated with fibrosis and rejection.

The paper introduces LBBC, a tool to reduce noise in metagenomic cfDNA sequencing, improving detection of urinary tract infection while minimizing false positives.

This paper introduces a cell-free DNA metagenomic sequencing assay that integrates host damage response to infection, showing it can accurately capture microbial composition and tissue damage in urinary tract infections.

This study uses urinary cell-free DNA to monitor host and pathogen dynamics in urinary tract infections, revealing insights into microbiome composition, antimicrobial susceptibility, and kidney injury.