Search the literature by keyword, topic, or author. Filter to articles with full text available.
1062 results
Whole-genome sequencing (WGS) is emerging as a valuable tool for antimicrobial resistance (AMR) surveillance, yet implementation in low-resource settings remains limited by prohibitory costs and infrastructure constraints. Oxford Nanopore Technologies (ONT) offers portable sequencing platforms …
Read PDF<h4>Background</h4>Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that has caused multiple widespread outbreaks and poses a significant public health threat. Recently, CHIKV outbreaks were reported in Guangdong Province, China. However, genomic data and information on …
Read PDFWater quality assessment is critical for determining the suitability of water resources for human consumption. In Santa Marta, northern Colombia, limited access to potable water and sewage systems, along with poor treatment infrastructure, poses a …
Read PDFFast and accurate genetic subtyping of pathogens is required to respond appropriately to biological events caused by natural outbreaks or bioattacks involving anthrax. In this study, we developed and validated a culture-free genotyping method that …
Read PDF<i>Leifsonia</i> sp. McL0608, isolated from <i>Pinus radiata</i> forest soil in New Zealand, has a complete 4.2 Mb circular genome assembled from Nanopore reads. Genome annotations identified 3,942 coding sequences and predicted biosynthetic pathways for alkanes, …
Read PDFRiver ecosystems are vital for supporting biodiversity and supplying freshwater, but are increasingly impacted by microbial pollution, including the spread of antibiotic resistance genes (ARGs), which poses growing public health concerns. While high-throughput sequencing technologies …
Read PDFBACKGROUND: Toxoplasma gondii is an important pathogen and model organism for studying mechanisms of immune evasion and defense. Within the same strain, model organisms are typically assumed to be isogenic; for T. gondii, within-strain genetic …
Read PDFAlternative lengthening of telomeres (ALT) is a recombination-based pathway enabling cancer cells to maintain telomeres. ALT establishment remains poorly understood due to difficulties identifying its molecular steps. Here, using Oxford Nanopore sequencing and computational modeling, …
Read PDF<h4>Background</h4>The RNA virosphere's extensive diversity and its role in emerging infectious diseases underscore the importance of non-targeted sequencing for identifying unknown or rare pathogens, including co-infections. However, enriching low-abundance viral sequences in RNA metaviromics, particularly …
Read PDF<i>Burkholderia pseudomallei</i> is a saprophytic environmental bacterium and the causative agent of melioidosis, a serious opportunistic infection in tropical regions, including northern Australia. Infection occurs following environmental exposure via percutaneous inoculation, ingestion, or inhalation; however, …
Read PDFClinical pharmacogenomics (PGx) testing strategies are mainly based on targeted PCR, microarrays, or short-read sequencing. These methods perform well for detecting known single-nucleotide variants (SNVs), small insertions/deletions (indels), and certain copy number variants (CNVs), but …
Read PDFWhole genome amplification (WGA), and in particular multiple displacement amplification (MDA), has become a key technique for genomic sequencing of microscopic organisms, yet it introduces artefacts such as palindromic (inverted chimeric) reads that may compromise …
Read PDFOBJECTIVES: The gaur (Bos gaurus) is one of the largest wild cattle species in the Bovidae family and is among the most threatened mammals in Vietnam. Listed as vulnerable on the IUCN Red List since …
Read PDF<i>Pediococcus pentosaceus</i> TOKAI 10 m, isolated from Japanese Takuan pickle, shows potential as a soy milk yogurt starter. Its genome comprises a 1,788,781 bp chromosome and four plasmids (56,333, 13,649, 10,458, and 10,048 bp), with …
Read PDFDNA has been proposed as an alternative to magnetic and solid-state devices for storing digital data. In DNA data storage, writing data is performed through DNA synthesis, and reading is done via sequencing. Nanopore devices …
Read PDFThe gold standard for bloodstream infection (BSI) diagnostics involves culturing positive blood cultures (BCs) using phenotypic methods for organism identification and antimicrobial resistance (AMR) testing, which can take up to five days. However, it is …
Read PDF<h4>Background</h4><i>Pasteurella multocida</i> is a Gram-negative bacterium responsible for various diseases in animals, including hemorrhagic septicemia (HS). Oxford Nanopore Technologies' (ONT) platform streams the sequencing data immediately, allowing for on-the-fly analysis. This capability enables researchers to …
Read PDFViral non-structural proteins are key mediators of host-virus interplay, including RNA modification dynamics. The function of the transmissible gastroenteritis virus (TGEV) gene 7, which encodes a non-structural protein, remains poorly understood. Using Oxford Nanopore direct …
Read PDFWe present a genome of Echinomermella matsi (Nematoda: Plectida: Benthimermithidae), a body cavity parasite of the green sea urchin Strongylocentrotus spp. commonly found along the coast of Central and Northern Norway. Three assemblies were generated, …
Read PDFWe report a chromosome-level assembly of a male red coachwhip snake (<i>Masticophis flagellum piceus</i>) generated exclusively with nanopore sequencing. Using Hifiasm-ONT for assembly and RagTag for scaffold polishing, we produced a 1.61 Gb nuclear genome …
Read PDF