Ben Vezina

This study maps metabolic diversity in Klebsiella pneumoniae sub-lineages using genomics and metabolic modeling, revealing lineage-specific metabolic profiles that support coexistence through cross-feeding.

The paper investigates the relationship between insertion sequences (IS) and metabolic capacity in four Klebsiella pneumoniae sub-lineages, finding higher IS loads correlate with reduced metabolic gene numbers and substrate utilisation.

The paper provides 15 genomically characterized Shigella sonnei isolates representing diverse sub-clades, with complete genome sequences and public availability for research.

This paper demonstrates that CRISPR-Cas9 enrichment combined with Oxford Nanopore sequencing improves detection of AMR genes and MLST in patient samples compared to unenriched sequencing.

The paper identifies hidden metabolic mutations in Klebsiella pneumoniae cultures grown in rich media, showing how these mutations can persist undetected and affect auxotrophy.

This paper constructs a comprehensive pangenome-scale metabolic model for the Klebsiella pneumoniae species complex, showing improved accuracy in growth predictions compared to previous models.

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

Trycycler improves bacterial genome assemblies by combining multiple long-read assemblies, reducing errors and improving accuracy when followed by polishing with Medaka and Pilon.

The paper predicts Burkholderia pseudomallei DsbA substrates to identify potential virulence factors and vaccine targets using genomic analysis and homology searches.