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Third-generation sequencing technologies have revolutionized the study of epigenetic characteristics in human diseases, with Oxford Nanopore Technologies (ONT) at the forefront of long-read sequencing. ONT has made rapid improvements in flow cell designs, which greatly …
Read PDFThe endangered mountain gorilla, Gorilla beringei beringei, faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for …
Read PDF<h4>Introduction</h4><i>Synchytrium endobioticum</i>, the biotrophic pathogen causing potato wart, poses persistent challenges due to its long-term soil survival and quarantine status. Biological control agents (BCAs) offer a promising avenue for sustainable management, yet the ecological context …
Read PDFInfluenza A virus (IAV) remains a major health concern in both humans and animals, with pigs serving as key reservoirs for generating novel reassortant viruses with pandemic potential. Respiratory microbiome alterations during infection may facilitate …
Read PDF<b>Background/Objectives</b>: Rapid and accurate pathogen identification and antimicrobial susceptibility testing (AST) are critical for the proper management of patients with bloodstream infection (BSI). Real-time whole-genome sequencing (WGS) represents an attractive opportunity for exhaustive pathogen identification …
Read PDFThe selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes …
Read PDF<b>Background:</b> Medulloblastoma is the childhood tumor with the highest morbidity and mortality worldwide. This type of cancer is characterized by a high degree of heterogeneity that gives rise to different molecular groups with disparities in …
Read PDFSomatic cell nuclear transfer (SCNT) holds promise for animal cloning but remains limited by low efficiency and phenotypic abnormalities, often attributed to incomplete nuclear reprogramming. This study presents an integrative genomic and epigenomic analysis of …
Read PDFSevere acute respiratory infection (SARI) remains one of the leading causes of morbidity and mortality worldwide. Multiple viruses can cause this infection. Sequencing technologies hold great promise for detecting viral pathogens. This proof-of-concept study aimed …
Read PDFAntimicrobial-resistant (AMR) <i>Klebsiella</i> spp., the common agents of nosocomial infections, are on the rise and becoming increasingly dangerous, with tigecycline-resistant strains posing a serious clinical threat. This study aimed to characterize isolated tigecycline-resistant strains from …
Read PDF<h4>Background</h4>Whole-genome sequencing (WGS) provides critical insights into the respiratory syncytial virus (RSV) transmission and any emerging mutations that could impair the efficacy of monoclonal antibodies or vaccines that have been recently licenced for clinical use …
Read PDF<b>Background/Objectives</b>: Advances in nanopore sequencing have opened new avenues for studying DNA methylation at single-base resolution, yet their application in epigenetic ageing research remains underdeveloped. <b>Methods</b>: We present a novel framework that leverages the unique …
Read PDFNile tilapia (<i>Oreochromis niloticus</i>) is an indispensable source of high-quality protein worldwide. Along with the exponential expansion of tilapia aquaculture, several novel pathogenic viruses have emerged, and some cause significant economic losses. Unfortunately, there is …
Read PDF<h4>Objectives</h4>Hygroryza aristata, an aquatic plant native to Southeast Asia, shows a high degree of adaptability to aquatic environments. H. aristata, which belongs to the Oryzeae tribe and is closely related to rice (Oryza sativa), holds …
Read PDFHuman adenovirus type 3 (HAdV-3) in the species <i>Mastadenovirus blackbeardi</i> is a frequent cause of hundreds of respiratory infections in Japan, with outbreaks varying in clinical severity. Such a high frequency of cases could be …
Read PDFThe data presented in this study are metagenomic profiles of human gut microbiome deduced from frozen fecal samples using two different sequencing chemistries namely, Illumina and Oxford Nanopore Technologies (ONT). The generated data is obtained …
Read PDF<h4>Background</h4>Timely and accurate identification of bloodstream pathogens is critical for targeted antimicrobial therapy in sepsis. Conventional blood cultures remain the Standard-of-Care (SoC) for pathogen identification but are limited by low sensitivity and prolonged turnaround times, …
Read PDF<i>Listeria monocytogenes</i> is a major foodborne pathogen, responsible for severe listeriosis outbreaks associated with contaminated foods. This study reports the comparative genomic analysis of three novel <i>L. monocytogenes</i> strains C5, A2D9 and A2D10, obtained from …
Read PDFNucleotide modifications deviate nanopore sequencing readouts, therefore generating artifacts during the basecalling of sequence backbones. Here, we present a reference-guided, iterative approach to polish modification-disturbed basecalling results. We show that such an approach is uniquely …
Read PDFSoil microbiome profiling is crucial for understanding microbial diversity and its roles in ecosystem functioning and agricultural productivity. Recent advancements in high-throughput sequencing, particularly Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), offer long-read sequencing …
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