Stephen C. Watts

Bactabolize generates strain-specific bacterial metabolic models and growth predictions, outperforming existing tools for Klebsiella pneumoniae.

The paper introduces a web-based tool for identifying Klebsiella isolates at species complex and phylogroup levels using MALDI-TOF mass spectrometry data.

The paper introduces Kleborate, a tool for analyzing K. pneumoniae genomes, demonstrating its use in genomic surveillance and metagenomic analysis of gut samples.

The paper shows improved metagenomic reference databases increase read classification rates and affect downstream microbiome analysis.

hicap predicts H. influenzae serotypes from genome sequences, identifying cap locus diversity and recombination in 691 genomes.

FastSpar rapidly infers correlation networks and calculates p-values for microbiome compositional data, significantly reducing computation time compared to SparCC.

The paper tracks the upper airway microbiome changes in preschool children and links them to asthma-associated persistent wheeze, showing that bacterial shifts precede viral infections and symptoms in sensitized children.