Jennifer Lu

Biome-specific genome catalogues reveal functional potential of shallow sequencing

The paper introduces BioSIFTR, a tool that uses shallow shotgun sequencing and biome-specific databases to generate accurate taxonomic and functional profiles, validated against deep sequencing data.

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project

The paper analyzes microbial content in 5,734 whole-genome sequencing samples from TCGA to provide a comprehensive reference dataset for future cancer microbiome studies.

Novel metagenomics analysis of stony coral tissue loss disease

The paper applies a novel metagenomics analysis to SCTLD lesions and healthy tissues to identify disease-associated microbiome members.

SkewIT: Skew Index Test for detecting mis-assembled bacterial genomes

SkewIT detects mis-assembled bacterial genomes by analyzing GC skew patterns in 15,000+ Refseq bacterial genomes.

Ultrafast and accurate 16S microbial community analysis using Kraken 2

This study compares Kraken 2 and Bracken to QIIME 2 for 16S rRNA metagenomic analysis, showing Kraken 2 and Bracken are faster and more accurate.

Improved metagenomic analysis with Kraken 2

Kraken 2's minimizer-keyed compact hash table cuts memory 85% versus Kraken 1 and classifies over 5 times faster with comparable accuracy; translated search boosts viral sensitivity.

Removing Contaminants from Metagenomic Databases

The paper develops a bioinformatics system to remove contaminants and low-complexity sequences from eukaryotic pathogen genomes, improving metagenomic analysis accuracy.