William Hsiao

This study identifies an atypical BlaIR system, pvmSR, in Pseudomonas aeruginosa that regulates virulence but not β-lactam resistance, using C. elegans as a model.

VIRUS-MVP tracks viral mutations and their functional impacts across multiple viruses, providing tools for analysis and visualization.

GAME provides a standardized framework for benchmarking genomics models across tasks, enabling consistent evaluation and community contributions.

This study examines the relationship between morphology, glycopeptidolipids, and infectivity in Mycobacterium abscessus clinical isolates using macrophage models.

The paper introduces NGBO, an ontology for integrating omics metadata into biobanking, enabling semantic representation and querying of contextual data.

This paper analyzes 180,098 Salmonella genomes to refine genomic typing nomenclature by identifying polyphyletic serovars and proposing a stable population structure based on core genome MLST thresholds.

ProbeTools designs hybridization probes for viral sequencing, validated with a panel targeting influenza A virus HA and NA segments, showing high coverage and enrichment in silico and in vitro.

A decentralized open-source web platform lets public health labs run outbreak sequencing pipelines on local compute, keeping data under their own governance while still exchanging results between instances.

This study examines the spatiotemporal dynamics of riverine microbial communities, including viruses, bacteria, and microeukaryotes, revealing distinct patterns and highlighting the need for holistic analysis.

MentaLiST is a fast and accurate MLST caller designed for large MLST schemes, outperforming existing tools in speed while maintaining or improving accuracy.

SNVPhyl is a phylogenomics pipeline that identifies SNVs and constructs whole-genome phylogenies from WGS data, showing high sensitivity and specificity in outbreak detection.

This study identifies antibiotic resistance genes in agricultural and urban watersheds using metagenomics and qPCR, finding higher ARG abundance in impacted sites.