Publications by authors named "Timothy Peto"

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Evaluating 12 automated, whole-genome sequencing analysis pipelines for Mycobacterium tuberculosis complex: a comparative study.
Ruan Spies, Derrick W Crook, Timothy E A Peto, Philip W Fowler, Robert Turner

Lancet Microbe· December 2025

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The impact of different antimicrobial exposures on the gut microbiome in the ARMORD observational study.
Leon Peto, Nicola Fawcett, Musaiwale M Kamfose, Claire Scarborough, Andy Peniket, Timothy E A Peto

Elife· December 2025

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Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663 samples.
Jeremy Westhead, Catriona S Baker, Marc Brouard, Matthew Colpus, Bede Constantinides, Timothy E A Peto

Microb Genom· December 2025

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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
Martin Hunt, Angie S Hinrichs, Daniel Anderson, Lily Karim, Bethany L Dearlove, Timothy Ea Peto

bioRxiv· November 2024

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Rapid antigen testing for SARS-CoV-2 by lateral flow assay: A field evaluation of self- and professional testing at UK community testing sites.
Matthias E Futschik, Samuel Johnson, Elena Turek, David Chapman, Simon Carr, Timothy Peto

J Clin Virol· April 2024

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Prediction of pyrazinamide resistance in using structure-based machine-learning approaches.
Joshua J Carter, Timothy M Walker, A Sarah Walker, Michael G Whitfield, Glenn P Morlock, Timothy E A Peto

JAC Antimicrob Resist· April 2024

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Author Correction: The plasmidome associated with Gram-negative bloodstream infections: a large-scale observational study using complete plasmid assemblies.
Samuel Lipworth, William Matlock, Liam Shaw, Karina-Doris Vihta, Gillian Rodger, Timothy Peto

Nat Commun· April 2024

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The plasmidome associated with Gram-negative bloodstream infections: A large-scale observational study using complete plasmid assemblies.
Samuel Lipworth, William Matlock, Liam Shaw, Karina-Doris Vihta, Gillian Rodger, Timothy Peto

Nat Commun· February 2024

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Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on .
Timothy J Davies, Jeremy Swann, Anna E Sheppard, Hayleigh Pickford, Samuel Lipworth, Timothy E A Peto

Microb Genom· December 2023

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Erratum: Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction.
Nicholas D Sanderson, Natalia Kapel, Gillian Rodger, Hermione Webster, Samuel Lipworth, Timothy Peto

Microb Genom· November 2023

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Swab pooling enables rapid expansion of high-throughput capacity for SARS-CoV-2 community testing.
Jamie Fagg, Rupert Beale, Matthias E Futschik, Elena Turek, David Chapman, Timothy Ea Peto

J Clin Virol· October 2023

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Antibiotic review kit for hospitals (ARK-Hospital): a stepped-wedge cluster-randomised controlled trial.
Martin J Llewelyn, Eric P Budgell, Magda Laskawiec-Szkonter, Elizabeth L A Cross, Rebecca Alexander, Timothy E A Peto

Lancet Infect Dis· February 2023

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Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction.
Nicholas D Sanderson, Natalia Kapel, Gillian Rodger, Hermione Webster, Samuel Lipworth, Timothy Peto

Microb Genom· January 2023

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transmission in Birmingham, UK, 2009-19: An observational study.
Timothy M Walker, Marc Choisy, Martin Dedicoat, Philip G Drennan, David Wyllie, Timothy E A Peto

Lancet Reg Health Eur· June 2022

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A crowd of BashTheBug volunteers reproducibly and accurately measure the minimum inhibitory concentrations of 13 antitubercular drugs from photographs of 96-well broth microdilution plates.
Philip W Fowler, Carla Wright, Helen Spiers, Tingting Zhu, Elisabeth M L Baeten, Timothy E A Peto

Elife· May 2022

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The 2021 WHO catalogue of complex mutations associated with drug resistance: A genotypic analysis.
Timothy M Walker, Paolo Miotto, Claudio U Köser, Philip W Fowler, Jeff Knaggs, Timothy Ea Peto

Lancet Microbe· April 2022

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An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction.
Yang Yang, Timothy M Walker, Samaneh Kouchaki, Chenyang Wang, Timothy E A Peto

Brief Bioinform· November 2021

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Antimicrobial resistance determinants are associated with bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study.
Bernadette C Young, Chieh-Hsi Wu, Jane Charlesworth, Sarah Earle, James R Price, Timothy E Peto

Microb Genom· November 2021

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Antimicrobial resistance genes and clonal success in Escherichia coli isolates causing bloodstream infection.
Sam Lipworth, Timothy Ea Peto, Derrick W Crook, A Sarah Walker, Nicole Stoesser

Lancet Microbe· October 2021

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Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK.
Samuel Lipworth, Karina-Doris Vihta, Kevin Chau, Leanne Barker, Sophie George, Timothy E A Peto

Genome Med· September 2021

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Flanker: a tool for comparative genomics of gene flanking regions.
William Matlock, Samuel Lipworth, Bede Constantinides, Timothy E A Peto, A Sarah Walker

Microb Genom· September 2021

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Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season.
Yifei Xu, Kuiama Lewandowski, Louise O Downs, James Kavanagh, Thomas Hender, Timothy Peto

Euro Surveill· July 2021

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Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time.
A Sarah Walker, Emma Pritchard, Thomas House, Julie V Robotham, Paul J Birrell, Timothy Ea Peto

Elife· July 2021

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Diagnosis of SARS-CoV-2 Infection with LamPORE, a High-Throughput Platform Combining Loop-Mediated Isothermal Amplification and Nanopore Sequencing.
Leon Peto, Gillian Rodger, Daniel P Carter, Karen L Osman, Mehmet Yavuz, Timothy E A Peto

J Clin Microbiol· May 2021

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Antibody testing for COVID-19: A report from the National COVID Scientific Advisory Panel.
Emily R Adams, Mark Ainsworth, Rekha Anand, Monique I Andersson, Kathryn Auckland, Timothy Peto

Wellcome Open Res· June 2020

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