James Rodney Brister

First community challenge for automated virus taxonomy

This paper organizes a community challenge to develop automated virus taxonomy classification tools and evaluates their performance on a combined dataset of expert-curated and metagenomic sequences.

Towards increased accuracy and reproducibility in SARS-CoV-2 next generation sequence analysis for public health surveillance

This study evaluates the impact of sequencing technologies and bioinformatic protocols on SARS-CoV-2 variant calling and introduces standardized parameters to improve pipeline consistency.

A fast, scalable, MinHash-based k-mer tool to assess Sequence Read Archive next generation sequence submissions.

The paper introduces a MinHash-based k-mer tool to assess taxonomic diversity in Sequence Read Archive submissions, improving metadata quality and data utility.

VADR: validation and annotation of virus sequence submissions to GenBank

VADR validates and annotates viral sequences submitted to GenBank, improving submission speed and annotation quality by using curated RefSeq models and providing deterministic alerts.

Gene sharing networks to automate genome-based prokaryotic viral taxonomy

This paper introduces vConTACT 2.0, a network-based tool for prokaryotic virus taxonomy that scales to large datasets and achieves high accuracy in taxonomic assignments.