David Wayne Ussery

The paper benchmarks 16S rRNA, FastANI, Mash, and FastAAI on 30,495 prokaryotic genomes to evaluate their taxonomic resolution across ranks, finding no single method is optimal across all levels.

This study introduces long-range PCR primers for SARS-CoV-2 sequencing to reduce amplicon dropout and coverage bias, improving genome quality and lineage accuracy.

This study analyzes over 100,000 E. coli genomes to identify 14 phylogroups, revealing population structure and genomic adaptations in virulence and antibiotic resistance.

The paper applies unsupervised clustering to analyze population structure in thousands of bacterial genomes, showing improved identification of mixed genomes and inter-related groups.

This paper demonstrates a method using long-read nanopore sequencing to directly sequence native RNA viruses, achieving high accuracy and enabling real-time detection of complex viral transcriptomes.

The paper develops ELIGOS, a bioinformatic tool to detect RNA modifications and secondary structures using native RNA sequencing data from E. coli, yeast, and human cells.

The paper creates a database of bacterial genome quality scores to help users filter high-quality genomes for bioinformatics analysis.