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Genomic surveillance of respiratory syncytial virus (RSV) enables detecting and monitoring of circulating lineages and the emergence of amino acid substitutions affecting transmission, severity, and treatment. We present a comprehensive workflow for RSV whole-genome sequencing, …
Read PDFSynthetic combinatorial DNA libraries are widely used to produce protein variants, optimize binders, and for high-throughput studies of protein-DNA interactions. The libraries can be made by researchers or vendors, and high-throughput sequencing is used for …
Read PDFWhole-genome sequencing (WGS) is a comprehensive approach for the genomic evaluation of acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS). We recently described a streamlined tumor-only WGS assay (ChromoSeq) that uses Illumina short-read sequencing with …
Read PDFTrichogramma ostriniae (Hymenoptera: Trichogrammatidae) is an important biological control agent that is effective against the Asian corn borer Ostrinia furnacalis. In this study, we present a chromosome-scale genome assembly of T. ostriniae. By integrating PacBio …
Read PDFThird-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies …
Read PDF<h4>Motivation</h4>Untargeted, also known as metagenomic, nanopore sequencing is a powerful tool for virus genomic surveillance, particularly in resource-limited settings and when paired with the portability of the MinION device (Oxford Nanopore Technologies, ONT). However, a …
Read PDF<h4>Introduction</h4>Early and accurate diagnosis of drug-resistant tuberculosis (DR-TB) is essential for improving treatment outcomes. Phenotypic drug susceptibility testing (pDST) is comprehensive but slow, while rapid molecular assays provide resistance information for a limited number of …
Read PDFBloodstream infections (BSIs) pose a significant global health challenge, particularly due to the increasing prevalence of antimicrobial resistance (AMR). Timely and accurate identification of pathogens and resistance determinants is critical for guiding appropriate therapy and …
Read PDF<h4>Background</h4>Endometrial cancer (EC) is the most common gynaecological malignancy globally, with rising incidence and notable disparities in outcomes. In New Zealand, EC rates have increased significantly, particularly among Māori and Pacific women, who face higher …
Read PDFWe present the genome sequence of <i>Ceratocystis huliohia</i>, one of two fungal pathogens causing the Rapid 'Ōhi'a Death disease of the native 'ōhi'a tree in Hawai'i. This assembly was generated using long-read Nanopore sequencing of …
Read PDFTick-borne encephalitis virus (TBEV) is primarily transmitted by <i>Ixodes</i> spp. and poses significant health risks, leading to morbidity and mortality in humans. Two of the five subtypes, Siberian and Far Eastern are known to circulate …
Read PDFHighly pathogenic avian influenza (HPAI) poses a major threat to the world economy and human health; hence, rapid and accurate identification of avian influenza virus (AIV) subtypes is required for effective surveillance and outbreak prevention, …
Read PDFWe present the complete genome sequence of Sphingomonas sp. gentR, a strain exhibiting high-level resistance to gentamicin (MIC = 40 mg/mL). The genome was assembled from hybrid Illumina and Nanopore sequencing data into a gap-free …
Read PDFTicks pose substantial threats to public health. Blacklegged ticks (Ixodes scapularis) are responsible for most tick-borne diseases in the US, transmitting seven human pathogens, including the etiological agent of Lyme disease, Borrelia burgdorferi. Molecular surveillance …
Read PDF<h4>Motivation</h4>Long-read sequencing (LRS) is increasingly used for human medical research and clinical diagnostics due to its capacity to generate complete genome information. However, there is a lack of robust and easy-to-use pipelines for comprehensive LRS …
Read PDFThe bumble bee wax moth, Aphomia sociella, is an important lepidopteran pest impacting bee colonies essential for pollination and apiculture. Like other moths, this species has been reported to ingest plastics. Although specific enzymes have …
Read PDFModern genetics increasingly relies on genomic data sets to address medical, ecological, and evolutionary questions. Investigating these questions requires a diverse set of core competencies in wet-lab techniques, data analysis, and bioinformatics. We describe the …
Read PDFHalisarca dujardinii is a marine sponge known for its ability to completely regenerate via cell reaggregation. Here we present the first chromosome-level genome assembly of H. dujardinii, generated using Oxford Nanopore long reads, Illumina short …
Read PDFDiagnostic testing of foot-and-mouth disease virus (FMDV) currently utilizes reverse transcription quantitative PCR (RT-qPCR) to detect the presence of viral RNA and double antibody sandwich ELISAs (DAS-ELISAs) to determine viral serotype. Serotype identification is critical …
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