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Cytomegalovirus (CMV) infections occur in 10%-40% of organ or stem cell transplant patients. Despite the low prevalence, CMV antiviral resistance has an important impact on patient outcomes. Guidelines for transplant recipients recommend that resistance should …
Read PDFDespite the complementary strengths of short- and long-read sequencing approaches, variant-calling methods still rely on a single data type. In this study, we collected and harmonized Nanopore datasets of the seven healthy individuals in the …
Read PDF<h4>Objective</h4>The pathogenic fungus Diplodia sapinea is of significant importance due to its primary role inducing tip dieback on various Pinus species which are widely distributed throughout the world. The objective of this study is to …
Read PDFImprovements in sequencing technology make the development of new tools for detection of structural variance more and more common. However, since the tools available for the long-read Oxford Nanopore sequencing are limited, and the selection …
Read PDF<h4>Background</h4>India has made substantial progress in reducing <i>Plasmodium falciparum</i> malaria cases and has set a target to eliminate malaria by 2030. Although artemisinin-based combination therapy (ACT) treatment remains effective, tracking regional differences in genetic variants …
Read PDF<h4>Background and objectives</h4>Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is caused by contraction of the D4Z4 repeat array at 4q35. Genetic diagnosis is particularly difficult in somatic mosaic cases, where conventional short-read sequencing cannot directly resolve …
Read PDF<h4>Introduction</h4>Phenylketonuria (PKU) is an inherited metabolic disorder caused by biallelic variants in the <i>PAH</i> gene, leading to phenylalanine accumulation and progressive neuronal damage. Over 3,000 variants have been described worldwide; however, a previously unreported exon …
Read PDF<h4>Background</h4>Nanopore technology enables the direct sequencing of intact RNA molecules allowing for the detection of native chemical modifications. In 2024, Oxford Nanopore Technologies updated direct RNA sequencing from RNA002 to RNA004 platform as well as …
Read PDFTelomere-to-telomere (T2T) assembly is the ultimate goal for de novo genome assembly. Existing algorithms<sup>1,2</sup> capable of near-T2T assembly all require Oxford Nanopore Technologies (ONT) ultra-long reads, which are costly and experimentally challenging to obtain and …
Read PDFThis study examined the tracheal and cecal microbiome composition across three broiler chicken genotypes including a heritage New Hampshire × Columbian cross (NHC) and modern Ross × Ross 308 (R308) and Ross YP × Ross …
Read PDFMultiple displacement amplification (MDA) outperforms conventional PCR in long fragment and whole-genome amplification, making it attractive to couple MDA with long-read sequencing of samples with limited quantities of DNA to obtain improved genome assemblies. Here, …
Read PDFPangenome projects have enhanced our understanding of human genomic and genetic diversity, but repetitive regions are still challenging to assemble and yet medically important. Here we generate 20 near-complete haplotypes from 10 Japanese male individuals …
Read PDFCharting the eukaryotic epitranscriptome by direct RNA sequencing is promising but still very challenging, as current bioinformatics tools are based on modification-unaware software and require multiple modification-specific learning steps. Here, we introduce NanoSpeech, a modification-aware …
Read PDFGoats play a significant role in global livestock production and are highly valued for their meat, which is both nutritious and easily digestible. The longissimus dorsi and biceps femoris muscles are not only critical for …
Read PDF<h4>Background</h4>Progressive myoclonic epilepsy is a heterogeneous neurodegenerative disorder characterized by early-onset myoclonus, epilepsy, generalized tonic-clonic seizures, and progressive neurological deterioration. Recently, a CGG repeat expansion and increased CSNK1E DNA methylation have been shown to be …
Read PDFAn isolate of the multidrug-resistant yeast <i>Candida auris</i> (Pal1) was identified in the urine of a patient with sepsis and sequenced using both Oxford Nanopore and Illumina sequencing technologies. Phylogenetic analysis placed <i>C. auris</i> Pal1 …
Read PDFMobile elements, particularly long terminal repeat retrotransposons (LTR-RTEs), are abundant and dynamic components of plant genomes. Although viral infections are known to transcriptionally activate retrotransposons, it remains unclear whether such virus-induced activation leads to their …
Read PDF<h4>Objective</h4>This study aimed to investigate the metagenomic and microbial diversity of dadih in Kampar District, Riau, Indonesia.<h4>Materials and methods</h4>The dadih samples were collected from dadih producers in three villages, namely Limau Manis (LM), Rumbio (RB), …
Read PDFTwo near-complete genomes of genotype II African swine fever viruses (ASFV) recovered from domestic pigs in Mbozi district, Tanzania, in 2017 were generated using tiled amplicon Oxford nanopore sequencing. These two ASFV genomes described in …
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