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Nucella lapillus is an important player in rocky shore food chains and has been a focal organism of ecological and evolutionary studies for decades. Despite poor dispersal, they have a broad geographic range, which makes …
Read PDFGenomics research is essential for understanding the transmission and evolution of bacterial antimicrobial resistance. The development of nanopore long-read sequencing has revolutionized our understanding of the prevalence, spread, and dynamic evolution of bacterial ARGs. This …
Read PDF<h4>Background</h4>Symptomatic apical periodontitis (SAP) is a painful inflammatory disease driven by root canal infection. A detailed understanding of its microbial ecology, compared to a noninfectious baseline, is needed.<h4>Aims</h4>This study aimed to characterize the microbial ecology …
Read PDF<h4>Motivation</h4>Oxford Nanopore Technologies' devices, such as MinION, permit affordable, real-time DNA sequencing, and come with targeted sequencing capabilities. Such capabilities create new challenges for metagenomic classifiers that must be computationally efficient yet robust enough to …
Read PDF<b>Background:</b> Structural variants (SVs) play a significant role in gene function and are implicated in numerous human diseases. With advances in sequencing technologies, identifying SVs through whole-genome sequencing (WGS) has become a key area of …
Read PDFRNA modifications are essential regulators of gene expression and cellular function, modulating RNA stability, splicing, translation, and localization. Dysregulation of these modifications has been linked to cancer, neurodegenerative disorders, viral infections, and other diseases. Precise …
Read PDFThe community of microorganisms occurring in the animal gut, known as the gut microbiota, is closely connected to host health. It is essential for metabolic processes, digestion, and defense against pathogens. Knowledge about the composition …
Read PDFRNA editing and maturation are critical regulatory mechanisms in plant organelles, yet their quantification remains technically challenging. Traditional Sanger sequencing lacks sensitivity and reproducibility, whereas advanced next-generation sequencing (NGS) approaches, such as rRNA-depleted long non-coding …
Read PDF<i>Streptococcus pneumoniae</i> (pneumococcus) is a leading cause of community-acquired pneumonia and invasive diseases, particularly among children and the elderly. The introduction of pneumococcal conjugate vaccines has significantly reduced invasive pneumococcal disease, but the prevalence of …
Read PDFThis dataset comprises raw signal data from a multicenter study evaluating the accuracy of bacterial whole-genome genotyping using Oxford Nanopore long-read sequencing. The raw data comprises 79 isolates across six bacterial species, including 12 triplicates …
Read PDFMortality in very-low birth-weight (VLBW) infants accounts for up to 50%-70% of the neonatal mortality and up to 25%-30% of infant mortality. Despite the global increase in survival rates, this population remains at heightened risk …
Read PDF<i>Pseudomonas</i> sp. CBR-F is a bacterial species isolated from a water treatment plant targeting for per- and poly-fluoroalkyl substances, a difficult-to-degrade family of anthropogenic compounds. Here, we report a complete genome for <i>Pseudomonas</i> sp. CBR-F, …
Read PDFRespiratory syncytial virus (RSV) is a globally circulating virus, causing severe respiratory infections in infants and the elderly. Two RSV vaccines were recently approved, and passive immunization is now recommended in several countries for all …
Read PDFThe genus Ormosia is in the Fabaceae family. China is one of its centers of origin, with almost all species being endemic, suggesting the need for genomic studies to understand its evolution, conservation, and use. …
Read PDFAccurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared to traditional read-based variant-calling methods, using seven closely related <i>Staphylococcus …
Read PDF<h4>Background</h4>Species-level resolution is essential to understand gastric microbiome recovery after Helicobacter pylori eradication, yet short-read 16 S rRNA approaches often obscure clinically relevant changes.<h4>Methods</h4>Gastric biopsies from 121 adults in Bayan-Ölgii, Mongolia (71 H. pylori-positive, 50 …
Read PDFIn this protocol, we detect pseudouridine using nanopore direct RNA sequencing (DRS 002/004) and analyze dynamic changes to mRNA modifications in response to perturbation. We cover RNA extraction, poly(A) selection, DRS, unmodified transcriptome (in vitro …
Read PDFProtein-DNA interactions can be manipulated in vitro by changing buffer conditions. Here, we develop a methodology to map the cleavage preferences of chimeric gene editors that are fusions of the I-TevI nuclease domain to CRIPSR …
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