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<h4>Motivation</h4>5-Methylcytosine (5mC) plays an important role in gene regulation and development. Although nanopore sequencing has enabled direct detection of 5mC, existing methods still face several limitations, including poor generalization across species and sequence contexts (CpG/CHG/CHH), …
Read PDFPhytophthora capsici is a globally widespread oomycete pathogen that causes severe damage to diverse host plants, posing major agricultural challenges. Here, we present a high-quality, chromosome-level genome assembly of P. capsici isolate BYA5 using PacBio …
Read PDFDuck Plague Virus (DPV), an alphaherpesvirus, causes significant morbidity and mortality in waterfowl and remains a persistent threat to duck farming across Asia. This study reports the first complete genomic characterization of DPV isolates from …
Read PDFBreeding elite apple cultivars with scab resistance is a key global goal, as reliance on fungicides is unsustainable. The causal fungus, Venturia inaequalis, evolves rapidly, threatening cultivars with single-gene resistance. Since the 1980s, breeding programmes …
Read PDFCanine distemper virus (CDV) affects both domestic and wild carnivores and is associated with a high mortality rate. The virus can cross species barriers, infecting a wide range of mammals, which raises concerns for both …
Read PDF<h4>Motivation</h4>Changes in poly(A) tail length were identified as a key post-transcriptional mechanism that controls protein synthesis. The length of the poly(A) tail was shown to directly impact mRNA stability and translation, broadening its regulatory scope. …
Read PDFRecurrent chromosomal translocations are hallmarks of many hematological malignancies, including lymphomas and leukemias. Accurate breakpoint detection is essential for diagnostics, treatment optimization, and disease monitoring. Long-read sequencing (Oxford Nanopore Technologies) enables unambiguous mapping and translocation …
Read PDF<h4>Introduction</h4>Blood culture is the cornerstone of microbiological diagnostics for patients with acute undifferentiated fever and no obvious localization of infection; however, up to 50% of cases remain undiagnosed. Infections caused by arboviruses, fastidious or even …
Read PDFOxford Nanopore Sequencing Technology (ONT) has emerged as a scalable method for generating DNA barcode reference libraries, capable of sequencing hundreds of DNA barcodes simultaneously using the portable, benchtop MinION sequencing device. In this study, …
Read PDFNanopore sequencing enables the simultaneous detection of genetic sequences and DNA modifications, yet the development of accurate, open-source computational models for these tasks, particularly for non-ONT platforms, remains challenging. To address this, we developed Bream, …
Read PDFRNA methylation, notably m6A modification, is a predominant epitranscriptomic alteration in mRNA, yet its evolutionary properties and the selective constraints acting on it across mammals remain poorly understood. Here, we generated a single-base-resolution m6A modification …
Read PDFYellow wood sorrel (Oxalis stricta L.), also known as sourgrass, juicy fruit, or sheep weed, is a member of the Oxalidaceae family. Yellow wood sorrel is commonly considered a weed, and while native to North …
Read PDFMultiple primary cancers (MPC) refer to the occurrence of two or more independent primary malignant tumors in the same patient, either simultaneously or metachronously. Their clinical diagnosis and differential diagnosis are challenging, treatment strategies are …
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Read PDFNucleotide sequences in the FASTQ or BAM format are widely shared, yet derived from platform-specific raw data outputs that differ across sequencing platforms. In Oxford Nanopore Technologies (ONT) sequencing, raw signal data contain valuable biological …
Read PDFLablab purpureus (L.) Sweet, a resilient tropical legume critical for sustainable agriculture, is prized for its adaptability, nutritional richness, and drought tolerance. Here, we present the first telomere-to-telomere (T2T) genome assembly of Lablab purpureus (L.) …
Read PDF<h4>Background</h4>The genus <i>Betta</i> (family Osphronemidae) comprises over 70 species, many of which are endemic to Southeast Asia and highly vulnerable to habitat loss. While <i>Betta splendens</i> is well studied due to its importance in the …
Read PDF<h4>Introduction</h4>Whole genome sequencing (WGS) is a valuable tool in surveillance of antimicrobial resistance (AMR). However, the technology faces several implementation challenges in low-resource settings. While advances in Oxford Nanopore Technologies (ONT) field sequencing have enabled …
Read PDF<h4>Background and purpose</h4>Metabolic disorders, which are estimated to include approximately 1,500 distinct conditions such as urea cycle disorders, lysosomal storage diseases, and mitochondrial dysfunctions, pose a significant clinical challenge due to their genetic heterogeneity and …
Read PDFWhole-genome sequencing (WGS) is an invaluable tool that enables high-resolution genotyping to precisely identify bacterial strains. It is particularly significant for highly pathogenic bacteria such as <i>Streptococcus pneumoniae</i>, a worldwide leading cause of mortality and …
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