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View article: Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance
Genome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance Open
Structural variants (SVs) are increasingly recognized as key drivers of bacterial evolution, yet their role has not been explored thoroughly. This is due to limitations in traditional short-read sequencing and linear reference-based analys…
View article: Characterising the Transcriptomic Response to Interferon and Infection in European Domestic Ferret Respiratory Tissues Using Long‐Read <scp>RNA</scp> Sequencing
Characterising the Transcriptomic Response to Interferon and Infection in European Domestic Ferret Respiratory Tissues Using Long‐Read <span>RNA</span> Sequencing Open
The European domestic ferret ( Mustela putorius furo ) is considered the gold standard small animal model for studying human and avian influenza virus infections. However, experimental characterisation of the transcriptomic response to int…
View article: Invasive Streptococcus dysgalactiae subspecies equisimilis compared with Streptococcus pyogenes in Australia, 2011–23, and the emergence of a multi-continent stG62647 lineage: a retrospective clinical and genomic epidemiology study
Invasive Streptococcus dysgalactiae subspecies equisimilis compared with Streptococcus pyogenes in Australia, 2011–23, and the emergence of a multi-continent stG62647 lineage: a retrospective clinical and genomic epidemiology study Open
Australian National Health and Medical Research Council.
View article: Finding the optimal regimen for <i>Mycobacteroides abscessus</i> treatment (FOR<i>Ma</i>T) in people with <i>Mycobacteroides abscessus</i> pulmonary disease: a multicentre, randomised, multi-arm, adaptive platform trial
Finding the optimal regimen for <i>Mycobacteroides abscessus</i> treatment (FOR<i>Ma</i>T) in people with <i>Mycobacteroides abscessus</i> pulmonary disease: a multicentre, randomised, multi-arm, adaptive platform trial Open
Introduction Mycobacteroides abscessus (MABS) is within the non-tuberculous mycobacteria family. It inhabits soil and water, exhibits multi-antibiotic resistance and causes opportunistic lung infections, which may progress to symptomatic M…
View article: Impact of human lifestyle on the pathogenic potential of urban wastewater
Impact of human lifestyle on the pathogenic potential of urban wastewater Open
Domestic wastewater has been known for its pathogenic potential including the presence of pathogenic bacteria, virulence factor genes (VFGs) and antibiotic resistance genes (ARGs). While previous studies have investigated regional differen…
View article: Characterizing the transcriptomic response to interferon and infection in European Domestic Ferret respiratory tissues using long-read RNA sequencing
Characterizing the transcriptomic response to interferon and infection in European Domestic Ferret respiratory tissues using long-read RNA sequencing Open
The European domestic ferret (Mustela putorius furo) is considered the gold-standard small animal model for studying human and avian influenza virus infections. However, experimental characterization of the transcriptomic response to inter…
View article: Development and verification of a novel tiling PCR method for long-range HIV-1 sequencing in a diagnostic setting
Development and verification of a novel tiling PCR method for long-range HIV-1 sequencing in a diagnostic setting Open
View article: Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers
Utilizing Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers Open
View article: Genome graphs reveal the importance of structural variation in <i>Mycobacterium tuberculosis</i> evolution and drug resistance
Genome graphs reveal the importance of structural variation in <i>Mycobacterium tuberculosis</i> evolution and drug resistance Open
Structural variants (SVs) are increasingly recognized as key drivers of bacterial evolution, yet their role has not been explored thoroughly. This is due to limitations in traditional short-read sequencing and linear reference-based analys…
View article: Characterisation of <i>in vitro</i> resistance selection against second-/last-line antibiotics in methicillin-resistant <i>Staphylococcus aureus</i> ATCC 43300 strain
Characterisation of <i>in vitro</i> resistance selection against second-/last-line antibiotics in methicillin-resistant <i>Staphylococcus aureus</i> ATCC 43300 strain Open
Background and objectives The increasing occurrence of MRSA clinical isolates harbouring reduced susceptibility to mainstay antibiotics has escalated the use of second and last line antibiotics. Hence, it is critical to evaluate the likeli…
View article: Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland populations
Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland populations Open
Copy number variants (CNVs) are an important class of genomic variation known to be important for human physiology and diseases. Here we present genome-wide metabolomic signatures for CNVs in two Finnish cohorts—The Northern Finland Birth …
View article: Dosage effect of Copy Number Variation in Epilepsy and ten regions of the human brain
Dosage effect of Copy Number Variation in Epilepsy and ten regions of the human brain Open
Epilepsy and seizures are one of the most common neurological conditions which often manifest with complex symptoms. Several studies including large scale GWAS and exome studies have reported a comprehensive catalog of genes related to Epi…
View article: Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for isoform discovery and validation
Customizable host and viral transcript enrichment using CRISPR-Cas9 long-read sequencing for isoform discovery and validation Open
Long-read RNA sequencing has been broadly utilized to examine the diversity of transcriptomes, understand differential expression and discover novel transcript isoforms. One of the major limitations of whole transcriptome sequencing is the…
View article: Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study
Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study Open
National Health and Medical Research Council, and Leducq Foundation.
View article: A flexible framework for minimal biomarker signature discovery from clinical omics studies without library size normalisation
A flexible framework for minimal biomarker signature discovery from clinical omics studies without library size normalisation Open
Application of transcriptomics, proteomics and metabolomics technologies to clinical cohorts has uncovered a variety of signatures for predicting disease. Many of these signatures require the full ‘omics data for evaluation on unseen sampl…
View article: Peptide selectivity of killer cell immunoglobulin-like receptors differs with allotypic variation in HLA class I
Peptide selectivity of killer cell immunoglobulin-like receptors differs with allotypic variation in HLA class I Open
Natural killer (NK) cell activation is regulated by killer cell immunoglobulin-like receptors (KIRs) that recognize human leukocyte antigen (HLA) class I molecules. While polymorphism in HLA can directly impact these interactions, the exte…
View article: Predicting trajectories of acute illness using RNA velocity of whole blood
Predicting trajectories of acute illness using RNA velocity of whole blood Open
Transcriptomic analyses reveal the status of cells, tissues, or organisms, across states of health and disease. RNA velocity adds a temporal dimension to single cell analyses, predicting future transcriptomic and phenotypic states, based o…
View article: Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing Open
Polyadenylation is a dynamic process that is important in cellular physiology, which has implications in messenger RNA decay rates, translation efficiency, and isoform-specific regulation. Oxford Nanopore Technologies direct RNA sequencing…
View article: Characterisation of <i>in vitro</i> resistance selection against second-/last-line antibiotics in methicillin-resistant <i>Staphylococcus aureus</i>
Characterisation of <i>in vitro</i> resistance selection against second-/last-line antibiotics in methicillin-resistant <i>Staphylococcus aureus</i> Open
SYNOPSIS Background The increasing occurrence of MRSA clinical isolates harbouring reduced susceptibility to mainstay antibiotics has escalated the use of second and last line antibiotics. Hence, it is critical to evaluate the likelihood o…
View article: Utilising Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers
Utilising Nanopore direct RNA sequencing of blood from patients with sepsis for discovery of co- and post-transcriptional disease biomarkers Open
Background RNA sequencing of whole blood has been increasingly employed to find transcriptomic signatures of disease states. These studies traditionally utilize short-read sequencing of cDNA, missing important aspects of RNA expression suc…
View article: Genome size estimation from long read overlaps
Genome size estimation from long read overlaps Open
Summary Accurate genome size estimation is an important component of genomic analyses, though existing tools are primarily optimised for short-read data. We present LRGE, a novel tool that uses read-to-read overlap information to estimate …
View article: Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing
Using synthetic RNA to benchmark poly(A) length inference from direct RNA sequencing Open
Polyadenylation is a dynamic process which is important in cellular physiology. Oxford Nanopore Technologies direct RNA-sequencing provides a strategy for sequencing the full-length RNA molecule and analysis of the transcriptome and epi-tr…
View article: Author response: Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data
Author response: Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data Open
View article: Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data
Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data Open
Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, the construction of phylogenetic trees, and antimicrobial resistance detection. This study presents a comprehensive ben…
View article: Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland Populations
Plasma metabolomic signatures for copy number variants and COVID-19 risk loci in Northern Finland Populations Open
Here, we present genome-wide metabolomic signatures for copy-number variants (CNV) and single nucleotide polymorphisms (SNP) in two Finnish cohorts - The Northern Finland Birth Cohort 1966 (NFBC 1966) and NFBC 1986. This work builds upon o…
View article: Author response: Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data
Author response: Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data Open
View article: Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data
Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data Open
Variant calling is fundamental in bacterial genomics, underpinning the identification of disease transmission clusters, the construction of phylogenetic trees, and antimicrobial resistance prediction. This study presents a comprehensive be…
View article: Wastewater Microbiome Analysis for Population Alcohol Abuse
Wastewater Microbiome Analysis for Population Alcohol Abuse Open
This study aims to unveil correlations between wastewater microbiota and the catchment-specific population health risk, specifically alcohol abuse, with smoking and obesity as confounding factors. Our study highlights the importance of ext…
View article: A flexible framework for minimal biomarker signature discovery from clinical omics studies without library size normalisation
A flexible framework for minimal biomarker signature discovery from clinical omics studies without library size normalisation Open
Application of transcriptomics, proteomics and metabolomics technologies to clinical cohorts has uncovered a variety of signatures for predicting disease. Many of these signatures require the full ‘omics data for evaluation on unseen sampl…
View article: Sustained transmission over two decades of a previously unrecognised MPT64 negative Mycobacterium tuberculosis strain in Queensland, Australia: a whole genome sequencing study
Sustained transmission over two decades of a previously unrecognised MPT64 negative Mycobacterium tuberculosis strain in Queensland, Australia: a whole genome sequencing study Open