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Publications

Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes.

Carey ME. et al, (2023), eLife, 12

Deep clustering of bacterial tree images.

Hayati M. et al, (2022), Philos Trans R Soc Lond B Biol Sci, 377

Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic

Attwood SW. et al, (2022), Nature Reviews Genetics, 23, 547 - 562

Europe-wide expansion and eradication of multidrug-resistant Neisseria gonorrhoeae lineages: a genomic surveillance study.

Sánchez-Busó L. et al, (2022), Lancet Microbe, 3, e452 - e463

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

Griffiths EJ. et al, (2022), GigaScience, 11

Conservation of vaccine antigen sequences encoded by sequenced strains of Streptococcus equi subsp. equi.

Frosth S. et al, (2022), Equine veterinary journal

Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

Kraemer MUG. et al, (2021), Science, 373, 889 - 895

Genomic Epidemiology of CC30 Methicillin-Resistant Staphylococcus aureus Strains from Argentina Reveals Four Major Clades with Distinctive Genetic Features.

Di Gregorio S. et al, (2021), mSphere, 6, e01297 - e01220

Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

du Plessis L. et al, (2021), Science, 371, 708 - 712

Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae.

David S. et al, (2020), Proceedings of the National Academy of Sciences of the United States of America, 117, 25043 - 25054

Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines.

Argimón S. et al, (2020), Nature communications, 11

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread

David S. et al, (2019), Nature Microbiology, 4, 1919 - 1929

Pneumococcal lineages associated with serotype replacement and antibiotic resistance in childhood invasive pneumococcal disease in the post-PCV13 era: an international whole-genome sequencing study

Lo SW. et al, (2019), The Lancet Infectious Diseases, 19, 759 - 769

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection.

McNally A. et al, (2019), mBio, 10

PANINI: Pangenome Neighbour Identification for Bacterial Populations

Abudahab K. et al, (2019), Microbial Genomics, 5

Author Correction: Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Rhodes J. et al, (2018), Emerging Microbes & Infections, 7, 1 - 2

Development and worldwide use of non-lethal, and minimal population-level impact, protocols for the isolation of amphibian chytrid fungi

Fisher MC. et al, (2018), Scientific Reports, 8

Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris

Rhodes J. et al, (2018), Emerging Microbes & Infections, 7, 1 - 12

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

Park SE. et al, (2018), Nature Communications, 9

Gene exchange drives the ecological success of a multi-host bacterial pathogen

Richardson EJ. et al, (2018), Nature Ecology & Evolution, 2, 1468 - 1478

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