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<h4>Background</h4>Intracranial infections are severe, life-threatening conditions often caused by diverse pathogens. Targeted nanopore sequencing (TNPseq) offers rapid and accurate pathogen identification, addressing the limitations of traditional diagnostic methods. Besides the pathogen types, factors like inflammation …
Read PDF<b>Background/Objectives:</b> Massively parallel sequencing technologies have advanced chronic lymphocytic leukemia (CLL) diagnostics and precision oncology. Illumina platforms, while offering robust performance, require substantial infrastructure investment and a large number of samples for cost-efficiency. Conversely, third-generation …
Read PDFThe Oxford Nanopore platform and nanopore sequencing are gaining increasing popularity in modern metagenomic research. However, there is a limited set of dedicated tools for analyzing this type of data. The tools used for nanopore …
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Read PDF<h4>Background</h4>Recent evidence suggests that human semen harbors a complex microbiome that may influence semen quality and male fertility. However, comprehensive characterization of bacterial and fungal communities in semen remains limited, particularly using long-read sequencing technologies.<h4>Methods</h4>In …
Read PDFFree-roaming cats may contribute to zoonotic risk via parasites and other eukaryotic taxa, yet surveillance in protected island settings is limited and conventional coprology can miss low-intensity or degraded signals. We conducted a cross-sectional 18S …
Read PDFThe identification of structural variant (SV) breakpoints plays a crucial role in understanding the genetic variants, mutagenic mechanisms, and functional consequences that drive various genetic diseases. While next-generation sequencing (NGS) has become a cornerstone in …
Read PDFBangladesh's aquaculture is currently faced with <i>Vibrio</i> contamination, which poses a threat to public health, exports, and product quality. This research provides a detailed molecular characterization of <i>Vibrio</i> sp. found in shrimp through the use …
Read PDFThe combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to complete …
Read PDFBACKGROUND: Bats are recognised as reservoirs for a wide range of microorganisms, including viruses, bacteria, fungi, and parasites, some of which are of zoonotic concern. The common vampire bat (Desmodus rotundus) is particularly important due …
Read PDFA cell's transcriptome is regulated through the integration of external and internal signals that activate intracellular signal pathways, epigenetic modifications and post-translational changes. Post-transcriptional regulation through RNA methylation has emerged as an important mechanism in …
Read PDFOur study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long <i>Klebsiella pneumoniae</i> outbreak with Illumina short-read sequencing data as the point of reference. We detect …
Read PDF<h4>Background</h4>Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite recent strides in achieving haplotype-phased gapless genome assemblies …
Read PDF<i>Wolbachia</i> are widespread insect endosymbionts known for manipulating host reproduction, aiding vector-borne disease control, and influencing host evolution. Here, we provide the complete genome sequence of the <i>Wolbachia</i> strain <i>w</i>Mel derived from the <i>Drosophila melanogaster</i> …
Read PDFAs nanopore sequencing has been widely adopted, data accumulation has surged, resulting in over 700,000 public datasets. While these data hold immense potential for advancing genomic research, their utility is compromised by the absence of …
Read PDFLocal protein synthesis in neurons is vital for synaptic maintenance and plasticity, yet the regulatory mechanisms, particularly cytoplasmic polyadenylation, are not fully understood. This study used nanopore sequencing to examine transcriptomic responses and 3'-end dynamics …
Read PDFA unique feature of Oxford Nanopore Technologies sequencers, adaptive sampling, allows precise DNA molecule selection from sequencing libraries. Here, we present enhancements to our tool, readfish, enabling all features for the industrial scale PromethION sequencer, …
Read PDF<h4>Background</h4>Culturing of fungi is labor-intensive and reveals limited diversity, while high-throughput sequencing of barcodes (i.e., metabarcoding) enables a simultaneous detection of fungi from multiple environmental samples. Metabarcoding using short-read sequencers, such as Illumina platforms, provides …
Read PDFMore than 60 human disorders are caused by unstable expansion of short tandem repeat (STR) tracts. These can exhibit cell-type-specific mosaicism in several repeat expansion disorders and remain difficult to characterize due to technical challenges …
Read PDF<h4>Background</h4>Mycena is a widespread genus of mushroom capable of decomposing various dead plant substrates. Gastrodia elata is a fully mycoheterotrophic orchid whose seed germination depends on specific Mycena strains. However, only a few Mycena species …
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