Aldert Zomer

The paper benchmarks pangenome graph construction methods using Escherichia coli O157:H7 genomes, showing that representation strategies and assembly completeness significantly affect graph topology and accuracy.

This paper analyzes STEC population structure and host-disease associations using whole genome sequencing of 3,418 isolates from 11 European countries, identifying distinct subpopulations linked to disease severity.

The paper identifies Lactococcus lactis strains that inhibit livestock-associated Staphylococcus aureus in pig nasal microbiomes through sequencing-guided isolation and in vitro testing.

MetaPointFinder detects antimicrobial resistance-conferring point mutations from metagenomic reads, outperforming existing methods in simulated data.

This study uses cfDNA sequencing in newborn foals to detect sepsis-causing bacteria and identifies host-related biomarkers associated with sepsis.

Barbell improves demultiplexing of Nanopore sequencing data by addressing barcode artifacts, reducing trimming errors and barcode bleeding.

The paper investigates whether flumequine selects for the same resistance mechanisms in E. coli as enrofloxacin, finding similar SNPs in gyrA and comparable resistance rates.

Graphite uses a colored De Bruijn graph to paint genomes, reducing matches and revealing new biological insights in microbial genomics.

This study examines the longitudinal development of the piglet nasal microbiome and identifies microbial interactions that could help control respiratory pathogens.

The paper determines the minimal selective concentrations of three antibiotics in broiler cecal fermentations to identify thresholds for antimicrobial resistance selection.

This study identifies P. timonensis as a BV-associated bacterium with high mucin-degrading enzyme activity that removes protective glycocalyx sugars from vaginal epithelium.

This study shows that persistent antimicrobials in broilers lead to prolonged antimicrobial resistance, while non-persistent ones have shorter effects.

Lapidary identifies and reports amino acid sequences in metagenomes using DNA-protein alignments, outperforming assembly methods in fragmented data but underperforming in complete assemblies.

RFPlasmid predicts whether contigs from draft genomes are plasmid or chromosomal using machine learning, improving accuracy over single-feature methods.

The paper sequences whole genomes of Giardia duodenalis assemblages C and D from dog feces, revealing host-associated gene differences.