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Publications

Browse publications attributed to Doherty Institute researchers

Overview

Research publications at the Doherty Institute

Our commitment to advancing knowledge in infectious diseases and immunology is reflected in a growing body of peer-reviewed research. This page provides access to published studies from our world-class scientists and collaborators, showcasing breakthroughs that inform policy, improve clinical practice, and drive innovation to improve health outcomes. Browse our collection to stay informed on the latest scientific insights shaping the future.

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Showing publications from Dr Ryan Wick (61)

A genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs

2025 · journal-article
Abstract Background Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC…

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes

2025 · journal-article
ABSTRACT As whole-genome sequencing becomes an established component of the microbiologist’s toolbox, it is imperative that researchers, clinical microbiologists, and…

Recovery of small plasmid sequences via Oxford Nanopore sequencing

2025 · journal-article
Oxford Nanopore Technologies (ONT) sequencing platforms currently offer two approaches to whole-genome native-DNA library preparation: ligation and rapid. In this…

Trycycler: consensus long-read assemblies for bacterial genomes

2025 · journal-article
AbstractWhile long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we…

Polypolish: Short-read polishing of long-read bacterial genome assemblies

2025 · journal-article
Long-read-only bacterial genome assemblies usually contain residual errors, most commonly homopolymer-length errors. Short-read polishing tools can use short reads to…

The complete genome sequence of the crayfish pathogen Candidatus Paracoxiella cheracis n.g. n.sp. provides insight into pathogenesis and the phylogeny of the Coxiellaceae family

2025 · journal-article
ABSTRACT The Coxiellaceae bacterial family, within the order Legionellales, is defined by a collection of poorly characterized obligate intracellular bacteria.…

Targeted sequencing of Enterobacterales bacteria using CRISPR-Cas9 enrichment and Oxford Nanopore Technologies

2025 · journal-article
ABSTRACT Sequencing DNA directly from patient samples enables faster pathogen characterization compared to traditional culture-based approaches, but often yields insufficient…

Exploring SNP filtering strategies: the influence of strict vs soft core

2025 · journal-article
Phylogenetic analyses are crucial for understanding microbial evolution and infectious disease transmission. Bacterial phylogenies are often inferred from SNP alignments,…

Genomic and functional analysis of rmp locus variants in Klebsiella pneumoniae

2025 · journal-article
Abstract Background Klebsiella pneumoniae is an opportunistic pathogen and a leading cause of healthcare-associated infections in hospitals, which are frequently…
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