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RPGR (Retinitis Pigmentosa GTPase Regulator) is the main gene involved in X-linked retinitis pigmentosa (RP) and up to 28% of sporadic RP. Pathogenic variants are mostly located in its retina-specific transcript, RPGRorf15, especially in the …
Read PDFLong-read sequencing offers unprecedented opportunities for high-resolution bacterial genome reconstruction, yet fragmented bioinformatics workflows hinder biological insights. <i>StrainCascade</i> addresses this gap by providing a fully automated, modular pipeline that integrates genome assembly, accurate annotation, and …
Read PDF<h4>Motivation</h4>DNA methylation serves as a key biomarker in clinical diagnostics, especially in cancer detection. With methylation-specific PCR (MSP), a widely used approach, patient samples can be screened fast and efficiently for differential methylation. During MSP, …
Read PDF<h4>Background</h4>Advances in sequencing technologies continue to improve the resolution and completeness with which human genetic variation can be characterized. Short-read sequencing remains widely used due to its high base accuracy, throughput, and cost efficiency; however, …
Read PDF<h4>Background</h4>The litchi fruit borer, <i>Conopomorpha sinensis</i> (Lepidoptera: Gracillariidae), is a devastating pest affecting litchi and longan production across Asia. Although a reference mitochondrial genome (mitogenome) has been published, its utility is limited by the lack …
Read PDF<h4>Background</h4>In microbial diagnostics, whole-genome sequencing (WGS) is used to address key questions such as species identification, presence of antimicrobial resistance genes (ARGs), virulence genes, and outbreak detection. The choice of sequencing technology is crucial to …
Read PDF<h4>Motivation</h4>Unique molecular identifiers (UMIs) enable efficient error correction in amplicon sequencing but UMI-aware analysis workflows for long-read sequencing and particularly for nanopore data are still sparse. Existing approaches lack portability, real-time sequencing support, GPU acceleration, …
Read PDFAccess to genome sequences is crucial to investigate and engineer traits in plants, explore biodiversity, and support phylogenetic studies. Over the last decade, affordable sequencing devices have substantially increased the size of the genomics community …
Read PDF<i>Bacillus cereus</i> is a widely distributed gram-positive bacterium that exhibits several notable characteristics. Here, we report the complete genome sequence of <i>B. cereus</i> strain NBNT-070, which was isolated from the activated sludge of a wastewater …
Read PDFCell-free DNA (cfDNA) containing cancer information has become a key biomarker for cancer liquid biopsy. Current next-generation sequencing (NGS) technology for cfDNA detection often fail to capture multiomics information, such as fragmentomics, epigenetics, and genetics, …
Read PDF<h4>Background</h4>Although many individuals with dystonia present with features indicative of single-gene etiologies, obtaining definitive genetic diagnoses can be challenging.<h4>Objective</h4>We assessed the value of nanopore-based long-read sequencing (LRS) in achieving molecular clarification of dystonic syndromes.<h4>Methods</h4>From a …
Read PDFIn Europe, Maedi-Visna disease has high prevalence rates at the individual and flock levels, respectively, and is regarded as one of the most significant infectious disease in sheep. The lack of treatment or a commercial …
Read PDFAvian aspergillosis, caused by <i>Aspergillus fumigatus</i> (<i>Af</i>), lacks sensitive antemortem diagnostics. Existing microbial cell-free DNA (cfDNA) tests are prone to contamination and require a high pathogen load. We hypothesized that infection-induced tissue damage in chickens …
Read PDFBACKGROUND: This study provides an in-depth genomic and functional characterization of Lactiplantibacillus pentosus LP309, a strain isolated from table olive fermentations. The microorganism was sequenced using three next‑generation sequencing platforms—Illumina, PacBio, and Oxford Nanopore Technologies …
Read PDFAntimicrobial resistance (AMR) poses a significant threat to public health. Rapid and accurate antimicrobial sensitivity testing is essential to guide effective treatment. Here, we present "simplified 5PSeq" (s5PSeq), a streamlined protocol for profiling 5' monophosphorylated …
Read PDFThis study examined the relationships among seminal bacterial composition, oxidative status, and semen quality in Thai native, crossbred, and commercial roosters. Fresh ejaculates (<i>n</i> = 10 per group) were evaluated for semen quality parameters-mass motility, …
Read PDFThe respiratory microbiome plays a crucial role in health and disease, necessitating accurate characterization through high-throughput sequencing technologies. This study provides a comparative analysis of Illumina NextSeq and Oxford Nanopore Technologies (ONT) sequencing platforms for …
Read PDFGuyuan cattle, a transitional breed between northern and central Chinese cattle, are known for their climbing ability and disease resistance. However, the genomic resources of indigenous Chinese cattle breeds, including Guyuan cattle, remain largely unexplored. …
Read PDFSitobion avenae (Fabricius), a major pest of cereal crops worldwide, causes significant damage on agricultural production. However, the lack of high-quality genomes has limited in-depth studies on its biology and effective management strategies. Here, we …
Read PDFNanopore-based sequencing has emerged as a revolutionary tool for animal pathogen genomics, offering capabilities unattainable with Sanger and next-generation sequencing (NGS). Despite rapid technical progress, routine veterinary deployment still faces uncertainty in study design, sample …
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