Liam P. Shaw

This study analyzes 1501 global genomes of multi-carbapenemase Enterobacterales, identifying common allelic combinations, plasmid distributions, and evolutionary mechanisms.

The paper examines the leading region of conjugative plasmids and finds evidence of sequence adaptation for translational efficiency in anti-defense genes.

The paper examines the relationship between plasmid copy numbers and size, arguing for two evolutionary strategies rather than a single scaling law.

This study benchmarks six tools for strain-level profiling of E. coli in short-read gut metagenomes, showing significant variation in performance and highlighting StrainR2's high accuracy and PathoScope 2.0/StrainGE's robustness in unknown strain scenarios.

The paper analyzes genome evolution in closely related E. coli ST131 strains, finding more accessory genome structural changes than core genome mutations, with most structural changes being short-lived and deleterious.

The paper analyzes the global genomic diversity of blaGES-5 integrons using a pangenome graph-based workflow, revealing differences between chromosomal and plasmid-associated integrons.

This study examines how Pseudomonas aeruginosa adapts to repeated invasion of Staphylococcus epidermidis, showing divergent evolutionary responses between monoculture and coculture conditions.

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

The paper introduces a method to visualize and quantify structural diversity around mobile resistance genes using pangraph, applied to beta-lactamase genes to show correlations between mutational and structural evolution.

PanGraph constructs a scalable pan-genome graph from whole-genome assemblies to capture structural and nucleotide polymorphisms across bacterial populations.

The paper investigates plasmid sharing among Enterobacterales in human infections, livestock, wastewater, and waterways in Oxfordshire, finding shared plasmid backbones and rapid accessory gene changes across niches.

Flanker clusters gene flanking sequences to identify mobile genetic element patterns associated with antimicrobial resistance genes.

The paper estimates changes in SARS-CoV-2 transmissibility using a phylogeny-based metric, finding that Delta is the most transmissible clade and transmissibility within clades slightly decreases over time.

This study tests if recurrent mutations in SARS-CoV-2 are linked to increased transmissibility and finds no significant association.

The paper analyzes IncF plasmid diversity across environmental and livestock settings using network community analysis, revealing niche-driven partitioning and core gene-defined communities.

This study evaluates SNP calling pipelines' performance on bacterial data, finding that reference genome selection strongly impacts accuracy, with Snippy performing consistently well across diverse genomes.

This study compares hybrid assemblies of bacterial genomes using Illumina and long-read sequencing technologies, finding that combining ONT and Illumina reads provides high-quality, low-cost genome reconstruction.

This study compares whole genome sequencing of Mycobacterium tuberculosis directly from sputum to sequencing from culture, finding greater genetic diversity in sputum-derived samples.

The paper investigates how structural variations in yeast genomes affect gene expression and quantitative traits, finding that copy number variants significantly influence phenotypes and reproductive isolation.