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The Arabidopsis Information Resource (TAIR) is the primary knowledgebase for Arabidopsis thaliana, providing curated genetics and genomics data, analysis tools, and community resources that support plant biology research worldwide. Since its establishment in 1999, TAIR …
Read PDF<h4>Summary</h4>Recent advances in long-read sequencing and genome assembly techniques have enabled the generation of high-quality assemblies, often comprising megabase-scale sequences that span entire chromosomes. This results in longer but fewer sequences per genome, which affects …
Read PDFThis response addresses the comments raised by Souichi Oka and colleagues in their Letter to the Editor titled "Addressing biases and limitations in feature attribution for circRNA modification profiling." We clarify that two independent XGBoost …
Read PDF<h4>Summary</h4>The rapid growth of genomic data and increasing adoption of long-read sequencing technologies have rendered variant calling one of the most computationally demanding tasks in genomic analysis. Although deep learning-based methods currently outperform conventional approaches …
Read PDF<h4>Motivation</h4>Allele typing for Human Leukocyte Antigen (HLA) genes has many important clinical applications. Popular short-read typing can only accurately distinguish alleles at the coding sequence level, which potentially limit our understanding of the effect of …
Read PDFH5 subtype high-pathogenicity avian influenza (HPAI) viruses continue to devastate the poultry industry and threaten food security and public health. The first outbreak of H5 HPAI in the Philippines was reported in 2017. Since then, …
Read PDFWe report two coding-complete genome sequences of porcine reproductive and respiratory syndrome virus 2 from field clinical samples obtained in 2021 (BA2021012A) and 2023 (ME20230008B-2) from the Philippines. BA2021012A (15,388 bp) is classified as a …
Read PDFWe report a coding-complete genome sequence of an African swine fever virus from an outbreak in 2021 among domestic pigs in Pangasinan, Philippines using Oxford Nanopore Technologies minION. The linear genome assembly is a single …
Read PDFAn African Swine Fever (ASF) outbreak was first recorded in the Philippines in July 2019. Since then, the disease has spread across provinces in Luzon, Visayas, and Mindanao, causing severe economic consequences for the country's …
Read PDF<h4>Motivation</h4>Oxford Nanopore sequencing enables long-read analysis for diverse applications, but artefacts introduced by Nanopore barcoding are poorly characterized and can compromise demultiplexing accuracy and downstream analyses.<h4>Results</h4>Using a rapid barcoding experiment on 66 diagnostic samples, we …
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 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 …
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