SalmonAct infers transcription factor activities in Salmonella using prior knowledge, aiding in interpreting high-dimensional transcriptomic data and uncovering regulatory mechanisms.

mSystems · Mar 30, 2026Peer-reviewedSystems Biology

Genomic Epidemiology of SARS-CoV-2 in Norfolk, UK, March 2020 - December 2022

Eleanor H. Hayles, Andrew J. Page, Robert A. Kingsley, Javier Guitián, Gemma C. Langridge

This study analyzes SARS-CoV-2 genomic data from Norfolk, UK, revealing high diversity and dynamic emergence of VOCs over 2.5 years.

Microbial Genomics · Jul 15, 2025Peer-reviewedGenomics

The TyphiNET data visualisation dashboard: Unlocking Salmonella Typhi genomics data to support public health

Zoe A. Dyson, Louise Cerdeira, Vandana Sharma, Megan E. Carey, Kathryn E. Holt, David M. Aanensen, Ali H. Abbas, Antoine G. Abou Fayad, Ayorinde O. Afolayan, Niyaz Ahmed, Irshad Ahmed, Afreenish Amir, Saadia Andleeb, Silvia Argimón, Abraham Aseffa, , Jackie Wright

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

Genome Medicine · May 9, 2025Peer-reviewedMicrobiology

Reversible excision of the wzy locus in Salmonella Typhimurium may aid recovery following phage predation

Oliver J. Charity, Gaetan J. A. Thilliez, Haider Al-Khanaq, Luke Acton, Rafał Kolenda, Matt Bawn, Liljana Petrovska, Robert A. Kingsley

This study identifies a reversible genetic mechanism in Salmonella Typhimurium that confers phage resistance by deleting the wzy locus, enabling recovery after phage predation.

PLoS Genetics · May 2, 2025Peer-reviewedMicrobiology

Population structure and evolution of Salmonella enterica serotype Typhi in Zimbabwe before a typhoid conjugate vaccine immunization campaign

Gaetan J. A. Thilliez, Tapfumanei Mashe, Blessmore Vimbai Chaibva, Valerie J. Robertson, Matt Bawn, Andrew Tarupiwa, Faustinos Tatenda Takawira, Marleen Magdalena Kock, Stanley Munyaradzi Midzi, Lusubilo Witson Mwamakamba, Jorge Matheu, Robert A. Kingsley, Marthie Magdaleen Ehlers

The paper analyzes the population structure and evolution of Salmonella enterica serotype Typhi in Zimbabwe before a typhoid vaccine campaign, identifying dominant resistant genotypes and their AMR mechanisms.

bioRxiv · Sep 1, 2022 · PreprintGenomics

Multi-layered networks of SalmoNet2 enable strain comparisons of the Salmonella genus on a molecular level

Marton L. Olbei, Balázs Bohár, Dávid Fazekas, Matthew Madgwick, Padhmanand Sudhakar, Isabelle Hautefort, Aline Métris, József Baranyi, Robert A. Kingsley, Tamas Douglas Korcsmaros

SalmoNet2 provides an updated multi-layered network resource for 20 Salmonella strains, enhancing strain comparisons through protein-protein, transcriptional regulatory, and metabolic interactions.

bioRxiv · Dec 20, 2021 · PreprintSystems Biology

Bacterial single-cell genomics enables phylogenetic analysis and reveals population structures from in vitro evolutionary studies

Matt Bawn, Johana Hernández, Eleftheria Trampari, Gaetan J. A. Thilliez, Mark Alexander Webber, Robert A. Kingsley, Neil Hall, Iain C. Macaulay

The paper uses single-cell genomics to analyze bacterial population structures in antibiotic stress experiments, revealing sub-populations and resistance development not detectable with bulk sequencing.

bioRxiv · Aug 25, 2020 · PreprintGenomics

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation

Matt Bawn, Nabil-Fareed Alikhan, Gaetan J. A. Thilliez, Mark Kirkwood, Nicole E. Wheeler, Liljana Petrovska, Timothy J. Dallman, Evelien M. Adriaenssens, Neil Hall, Robert A. Kingsley

This study constructs a phylogenetic tree of 131 S. Typhimurium strains to reveal population structure and adaptation to domesticated and wild animal hosts.

PLoS Genetics · Jun 8, 2020Peer-reviewedGenomics