Publications by authors named "Ryan Wick"

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Challenges and considerations for whole-genome-based antimicrobial resistance plasmid investigations.
Jia Qi Beh, Ryan R Wick, Benjamin P Howden, Christopher H Connor, Jessica R Webb

Antimicrob Agents Chemother· December 2025

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Microbiota and resistome dynamics in untreated and treated wastewater: A ten-month study leveraging RNA-probe capture and subspecies-level metagenomics.
Kenneth Lindstedt, Adriana Osińska, Ahmed Bargheet, Henning Sørum, Ryan R Wick

J Hazard Mater· December 2025

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Quantifying plasmid movement in drug-resistant Shigella species using phylodynamic inference.
Nicola F Müller, Ryan R Wick, Louise M Judd, Deborah A Williamson, Trevor Bedford

PLoS Pathog· December 2025

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Novel insights into the genome organization of : identification of linear plasmids.
Nemanja Kuzmanovic, Ryan R Wick, Michał Kalita, Joanna Puławska, George C diCenzo

Microb Genom· November 2025

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Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi.
Danielle J Ingle, Jane Hawkey, Martin Hunt, Zamin Iqbal, Jacqueline A Keane, Ryan R Wick

Genome Med· October 2025

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Autocycler: long-read consensus assembly for bacterial genomes.
Ryan R Wick, Benjamin P Howden, Timothy P Stinear

Bioinformatics· September 2025

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Comparative and functional genomic analysis of foreign DNA defense mechanisms in .
Alexandra L Krause, Louise M Judd, Ryan Wick, Timothy P Stinear, Andrew H Buultjens

Microbiol Spectr· August 2025

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Transposon-directed insertion-site sequencing (TraDIS) analysis of using nanopore sequencing and a WebAssembly analysis platform.
Alexandra L Krause, Wytamma Wirth, Adrianna M Turner, Louise Judd, Lucy Li, Ryan Wick

Microbiol Spectr· July 2025

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Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Typhi.
Danielle J Ingle, Jane Hawkey, Martin Hunt, Zamin Iqbal, Jacqueline A Keane, Ryan R Wick

bioRxiv· July 2025

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Complete genomes of 568 diverse species complex isolates from humans, animals, and marine sources in Norway from 2001 to 2020.
Marit A K Hetland, Mia A Winkler, Håkon Kaspersen, Fredrik Håkonsholm, Ragna-Johanne Bakksjø, Ryan R Wick

Microbiol Resour Announc· June 2025

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Genomics to understand the global landscape of linezolid resistance in and .
Jia Qi Beh, Diane S Daniel, Louise M Judd, Ryan R Wick, Peter Kelley

Microb Genom· June 2025

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Are reads required? High-precision variant calling from bacterial genome assemblies.
Ryan R Wick, Louise M Judd, Timothy P Stinear, Ian R Monk

Access Microbiol· May 2025

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The complete genome sequence of the crayfish pathogen Candidatus n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family.
Danielle J Ingle, Calum J Walsh, Genevieve R Samuel, Ryan R Wick, Nadav Davidovich

mSphere· April 2025

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Genomic and functional analysis of rmp locus variants in Klebsiella pneumoniae.
Margaret M C Lam, Stephen M Salisbury, Logan P Treat, Ryan R Wick, Louise M Judd

Genome Med· April 2025

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A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs.
Marit A K Hetland, Mia A Winkler, Håkon P Kaspersen, Fredrik Håkonsholm, Ragna-Johanne Bakksjø, Ryan R Wick

Genome Med· April 2025

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Targeted sequencing of bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies.
Hugh Cottingham, Louise M Judd, Jessica A Wisniewski, Ryan R Wick, Thomas D Stanton

mSystems· February 2025

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Exploring SNP filtering strategies: the influence of strict vs soft core.
Mona L Taouk, Leo A Featherstone, George Taiaroa, Torsten Seemann, Danielle J Ingle, Ryan R Wick

Microb Genom· January 2025

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Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data.
Michael B Hall, Ryan R Wick, Louise M Judd, An N Nguyen, Eike J Steinig

Elife· October 2024

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Diversity, functional classification and genotyping of SHV β-lactamases in .
Kara K Tsang, Margaret M C Lam, Ryan R Wick, Kelly L Wyres, Michael Bachman

Microb Genom· October 2024

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How low can you go? Short-read polishing of Oxford Nanopore bacterial genome assemblies.
George Bouras, Louise M Judd, Robert A Edwards, Sarah Vreugde, Timothy P Stinear, Ryan R Wick

Microb Genom· June 2024

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Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies.
George Bouras, Ghais Houtak, Ryan R Wick, Vijini Mallawaarachchi, Michael J Roach

Microb Genom· May 2024

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Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies.
George Bouras, Ghais Houtak, Ryan R Wick, Vijini Mallawaarachchi, Michael J Roach

bioRxiv· April 2024

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Corrigendum: 'Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, '.
Ebenezer Foster-Nyarko, Hugh Cottingham, Ryan R Wick, Louise M Judd, Margaret M C Lam

Microb Genom· August 2023

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Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing.
Ryan R Wick, Louise M Judd, Kathryn E Holt

PLoS Comput Biol· March 2023

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Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2.
Q X Charles Mak, Ryan R Wick, James Matthew Holt, Jeremy R Wang

Mol Biol Evol· March 2023

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