Dr. Samuel T. Horsfield PhD SNSF Postdoctoral Fellow

Publications

2026

Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks
Species-specific transformer models of bacterial gene order and content for genomic surveillance tasks
Samuel T. Horsfield, Maciej Wiatrak, James O. McInerney, Stephen D. Bentley, Caroline Colijn, John A. Lees
openRxiv  ·  30 Apr 2026  ·  doi:10.64898/2026.04.28.721069
Global population structure and phase variation of serotype 12F i Streptococcus pneumoniae i following the introduction of pneumococcal conjugate vaccine
Global population structure and phase variation of serotype 12F Streptococcus pneumoniae following the introduction of pneumococcal conjugate vaccine
Thi N M Huynh, Alannah C King, Jason Chen Qixiang, Kathryn M Mulvihill, Hayley Demetriou, …, Lesley McGee, Chris Lok To Sham, David Goldblatt, Stephen D Bentley, Stephanie W Lo
openRxiv  ·  03 Apr 2026  ·  doi:10.64898/2026.04.03.714713
Rapid gene exchange explains differences in bacterial pangenome structure
Rapid gene exchange explains differences in bacterial pangenome structure
Samuel T. Horsfield, Anlei Peng, Matthew J. Russell, Johanna von Wachsmann, Jacqueline Toussaint, …, Henri Pesonen, Gerry Tonkin-Hill, Jukka Corander, Nicholas J. Croucher, John A. Lees
openRxiv  ·  06 Feb 2026  ·  doi:10.64898/2026.02.04.703695
Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species
Unlocking CRISPR-Cas9 editing for widely diverse Dictyostelid species
Mireia Garriga-Canut, Nikki Cannon, Matthew Benton, Andrea Zanon, Samuel T Horsfield, Jacob Scheurich, Kim Remans, John Lees, Alexandre Paix, Jordi van Gestel
Molecular Systems Biology  ·  12 Jan 2026  ·  doi:10.1101/2025.03.23.644600

2025

Rapid and consistent clustering of millions of genomes highlights the diversity of prokaryotic life
Rapid and consistent clustering of millions of genomes highlights the diversity of prokaryotic life
Johanna von Wachsmann, Leonie J. Lorenz, Matthew J. Russell, Tatiana A. Gurbich, Víctor Rodríguez-Bouza, Samuel T. Horsfield, John A. Lees, Robert D. Finn
openRxiv  ·  30 Dec 2025  ·  doi:10.64898/2025.12.30.695181
A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions
A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions
Leonie J. Lorenz, Joel Hellewell, Samuel T. Horsfield, Matthew J. Russell, Shrijana Shrestha, …, Stephen D. Bentley, Stephanie W. Lo, Caroline Colijn, Nicholas J. Croucher, John A. Lees
openRxiv  ·  21 Dec 2025  ·  doi:10.64898/2025.12.18.695090
Evolution of the accessory genome
Evolution of the accessory genome
Samuel T. Horsfield
EMBL-EBI  ·  05 Nov 2025  ·  doi:10.6019/TOL.pangenome-graphs-w.2025.00001.1
Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variants
Pore-C sequencing identifies episome-driven chromosome conformation perturbations differentiating pneumococcal epigenetic variants
Tze Yee Lim, Samuel T. Horsfield, Catherine M. Troman, Stephen D. Bentley, Min Jung Kwun, Nicholas J. Croucher
PLOS Pathogens  ·  14 Aug 2025  ·  doi:10.1371/journal.ppat.1013392
Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing
Determining genotype and antimicrobial resistance of Salmonella Typhi in environmental samples by amplicon sequencing
Catherine Troman, Samuel T. Horsfield, Dilip Abraham, Venkata Raghava Mohan, Sidhartha Giri, Satheesh Nair, Alexander G. Shaw, Zoe Dyson, Kathryn E. Holt, Nicholas C. Grassly
PLOS Neglected Tropical Diseases  ·  08 Jul 2025  ·  doi:10.1371/journal.pntd.0013211
Integrated population clustering and genomic epidemiology with PopPIPE
Integrated population clustering and genomic epidemiology with PopPIPE
Martin P. McHugh, Samuel T. Horsfield, Johanna von Wachsmann, Jacqueline Toussaint, Kerry A. Pettigrew, …, Stephen H. Gillespie, Kate E. Templeton, Matthew T. G. Holden, Nicholas J. Croucher, John A. Lees
Microbial Genomics  ·  28 Apr 2025  ·  doi:10.1099/mgen.0.001404
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm
Samuel T. Horsfield, Basil C.T. Fok, Yuhan Fu, Paul Turner, John A. Lees, Nicholas J. Croucher
Genome Research  ·  04 Mar 2025  ·  doi:10.1101/gr.279435.124

2024

A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flow cell
A Comparison of Nanopore Data Types, Basecalling, and Assembly Algorithms: Whole Plant Genome Assembly and Methylation Analysis from a Single MinION Flow cell
Samuel Martin, Darren Heavens, Yuxuan Lan, Ned Peel, Naomi Irish, Samuel Horsfield, Michael Giolai, Matthew D. Clark, Richard M. Leggett
openRxiv  ·  14 Nov 2024  ·  doi:10.1101/2024.11.13.623402
CELEBRIMBOR: core and accessory genes from metagenomes
CELEBRIMBOR: core and accessory genes from metagenomes
Joel Hellewell, Samuel T Horsfield, Johanna von Wachsmann, Tatiana A Gurbich, Robert D Finn, Zamin Iqbal, Leah W Roberts, John A Lees
Bioinformatics  ·  01 Sep 2024  ·  doi:10.1093/bioinformatics/btae542
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
Juri Kuronen, Samuel T. Horsfield, Anna K. Pöntinen, Sudaraka Mallawaarachchi, Sergio Arredondo-Alonso, …, Nicholas J. Croucher, Johan Pensar, John A. Lees, Gerry Tonkin-Hill, Jukka Corander
Genome Research  ·  01 Jul 2024  ·  doi:10.1101/gr.278485.123
AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics
AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics
Martin Hunt, Marcelo D. T. Torres, Nabil-Fareed Alikhan, Daniel Anderson, Maria Luiza Andreani, …, Maciej Wiatrak, Ouli Xie, Cesar de la Fuente-Nunez, John A. Lees, Zamin Iqbal
openRxiv  ·  11 Mar 2024  ·  doi:10.1101/2024.03.08.584059

2023

Accurate and fast graph-based pangenome annotation and clustering with ggCaller
Accurate and fast graph-based pangenome annotation and clustering with ggCaller
Samuel T. Horsfield, Gerry Tonkin-Hill, Nicholas J. Croucher, John A. Lees
Genome Research  ·  24 Aug 2023  ·  doi:10.1101/gr.277733.123

2022

Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples
Samuel Martin, Darren Heavens, Yuxuan Lan, Samuel Horsfield, Matthew D. Clark, Richard M. Leggett
Genome Biology  ·  24 Jan 2022  ·  doi:10.1186/s13059-021-02582-x

2020

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions
Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions
John A. Lees, T. Tien Mai, Marco Galardini, Nicole E. Wheeler, Samuel T. Horsfield, Julian Parkhill, Jukka Corander
mBio  ·  25 Aug 2020  ·  doi:10.1128/mBio.01344-20

2019

Mixtures of Aluminum and Indium Induce More than Additive Phenotypic and Toxicogenomic Responses in i Daphnia magna i
Mixtures of Aluminum and Indium Induce More than Additive Phenotypic and Toxicogenomic Responses in Daphnia magna
Nadja R. Brun, Peter D. Fields, Samuel Horsfield, Leda Mirbahai, Dieter Ebert, John K. Colbourne, Karl Fent
Environmental Science & Technology  ·  04 Jan 2019  ·  doi:10.1021/acs.est.8b05457

2016

Adulteration and poor quality of Ginkgo biloba supplements
Adulteration and poor quality of Ginkgo biloba supplements
Anthony Booker, Debora Frommenwiler, Eike Reich, Samuel Horsfield, Michael Heinrich
Journal of Herbal Medicine  ·  01 Jun 2016  ·  doi:10.1016/j.hermed.2016.04.003