Samuel Horsfield

ALLCAPS: a scalable and accurate deep-learning method for in silico pneumococcal serotyping

ALLCAPS is a deep-learning tool for in silico pneumococcal serotyping that outperforms existing methods and identifies novel serotypes.

Bayesian bacterial GWAS model reveals threshold-dependent genetic changes in antimicrobial resistance phenotypes

This paper introduces a Bayesian ordered logistic regression GWAS model for bacterial antimicrobial resistance phenotypes, showing improved variant discovery and MIC prediction by accounting for threshold-dependent effects.

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions

The paper develops a mathematical model to predict vaccine replacement dynamics in Streptococcus pneumoniae and identifies optimal genomic surveillance strategies.

Rapid and consistent clustering of millions of genomes highlights the diversity of prokaryotic life

The paper introduces a fast clustering tool for bacterial genomes, enabling efficient analysis of millions of genomes and revealing taxonomic insights.

Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks

This paper trains species-specific transformer models for bacterial genomic surveillance, showing they can cluster genomes, identify emerging lineages, and predict antibiotic resistance gene uptake.

Global population structure and phase variation of serotype 12F Streptococcus pneumoniae following the introduction of pneumococcal conjugate vaccine

This study characterizes the global population structure and genetic diversity of serotype 12F Streptococcus pneumoniae, identifying strand-slippage mutations as a mechanism for capsule variation and vaccine evasion.

Rapid gene exchange explains differences in bacterial pangenome structure

The paper develops a model to analyze pangenome dynamics and finds that differences in bacterial pangenomes are mainly due to variation in the number of rapidly exchanged genes.

Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variants

The paper uses Hi-C and Pore-C sequencing to compare chromosomal conformation in pneumococcal variants, finding that episomal elements drive differential contact patterns through stochastic replication and excision.

A contextualised protein language model reveals the functional syntax of bacterial evolution

Trained on over 1.3 million bacterial genomes represented as ordered protein sequences, the transformer foundation model Bacformer predicts protein interactions, operons, essentiality, and phenotypes while generating trait-conditioned synthetic proteomes.

Integrated population clustering and genomic epidemiology with PopPIPE

PopPIPE clusters bacterial populations and detects transmission events using reference-free methods, outperforming traditional approaches in nosocomial outbreak analysis.

Selection-free CRISPR-Cas9 editing protocol for distant Dictyostelid species

This paper introduces a selection-free CRISPR-Cas9 editing protocol effective across multiple Dictyostelid species, enabling efficient knock-out and knock-in mutations without antibiotic selection.

A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flow cell

The paper evaluates nanopore sequencing and assembly improvements for Arabidopsis genome assembly and methylation analysis using a single MinION flow cell.

PAN-GWES: Pangenome-spanning epistasis and co-selection analysis via de Bruijn graphs

PAN-GWES identifies co-selected and epistatic genomic variations in bacterial genomes using de Bruijn graphs to analyze drug resistance and adaptation traits.

CELEBRIMBOR: Pangenomes from metagenomes

CELEBRIMBOR improves core gene identification in metagenome-assembled genomes by adjusting frequency thresholds based on genome completeness.

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

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.

Graph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples

GNASTy improves pneumococcal serotyping by using a pangenome graph algorithm with Nanopore Adaptive Sampling, enhancing sensitivity for novel serotypes in complex samples.

Accurate and fast graph-based pangenome annotation and clustering with ggCaller

ggCaller provides a fast and accurate method for pangenome annotation and clustering by integrating gene prediction, annotation, and clustering using de Bruijn Graphs, outperforming existing tools in speed and accuracy.

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

This paper demonstrates how adaptive sampling in nanopore sequencing can enrich low-abundance species in metagenomic samples, with efficiency improving with longer read lengths and a mathematical model to predict outcomes.