Dan Knights

The paper links sugar-rich foods to microbiome disruption during antibiotic treatment in patients and mice.

XTree aligns sequencing reads to large genome databases efficiently and accurately, outperforming existing tools in precision and recall.

The paper identifies genetic loci influencing milk gene expression and links these to infant gut microbiome composition in breastfeeding mothers.

The paper investigates the association between human cytomegalovirus in breast milk and milk composition, infant gut microbiome, and infant growth.

This study identifies shared and disease-specific host-microbiome interactions in colorectal cancer, inflammatory bowel disease, and irritable bowel syndrome using machine learning.

Exhaustive gapped short-read aligner BURST returns all optimal matches above an identity cutoff, with tie-breaking or LCA taxonomy, at 1,000,000 reads/minute against 5,500 prokaryotic genomes (32 cores).

This study evaluates shallow shotgun sequencing as an alternative to 16S for affordable, high-resolution human microbiome analysis, finding it provides accurate taxonomic and functional profiles.

HOMINID identifies host SNPs correlated with microbiome taxa abundances using Lasso regression, showing improved accuracy over existing methods and identifying 13 SNPs across body sites.

BugBase assigns pathway coverage and traits (Gram stain, oxygen tolerance, pathogenicity) to individual taxa in 16S or shotgun microbiome data, detecting some functional differences bag-of-genes profiles miss.

The paper identifies virulence genes as a signature of the microbiome in the colorectal tumor microenvironment, highlighting novel bacterial taxa and their potential role in cancer development.