Andrew S. Warren

The paper identifies niche-specific metabolic targets in pathobionts by analyzing genome-scale metabolic networks and demonstrates their potential for targeted antimicrobial therapies.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

ProtTox is a deep learning method for toxin classification of protein sequences, achieving an F1-score 5% higher than existing baselines.

The paper introduces a pan-synteny graph method for analyzing multiple prokaryotic genomes, enabling the identification of genomic changes and conservation patterns without a reference genome.

RNA-Rocket provides RNA-Seq and ChIP-Seq analysis tools for infectious disease research, offering pre-indexed genomes, educational resources, and integration with bioinformatics platforms.