Oxford Nanopore sequencing can be used to achieve complete bacterial genomes. However, the error rates of Oxford Nanopore long reads are greater compared to Illumina short reads. Long-read assemblers using a variety of assembly algorithms have been d...
Long-read sequencing technologies provide portable and flexible service, making them attractive for small-scale sequencing studies. However, many existing RNA-sequencing analysis frameworks are designed for transcriptome-wide analyses and require sub...
Emerging viral infectious diseases present a major threat to the global swine industry. Since 2015, Senecavirus A (SVA) has been identified as a cause of vesicular disease in different countries and is considered an emerging disease. Despite the grow...
With the advantages that long-read sequencing platforms such as Pacific Biosciences (Menlo Park, CA, USA) (PacBio) and Oxford Nanopore Technologies (Oxford, UK) (ONT) can offer, various research fields such as genomics and transcriptomics can exploit...
Oxford Nanopore Technologies (ONT) long-read sequencing (LRS) has emerged as a promising genomic analysis tool, yet comprehensive benchmarks with established platforms across diverse datasets remain limited. This study aimed to benchmark LRS performa...
Background/Objectives: Short-read-sequencing (SRS) is currently the standard for genetic testing in inherited human diseases. Intrinsic limitations include PCR dependency, restricted read length, and challenges in identifying structural variants (SVs...
DNA methylation is a critical epigenetic mechanism involved in numerous physiological processes. Alterations in DNA methylation patterns are associated with various brain disorders, including dementias such as Alzheimer’s disease (AD) and front...
The gut microbiome plays a major role in chronic diseases, of which several are characterized by an altered composition and diversity of bacterial communities. Large-scale sequencing projects allowed for characterizing the perturbations of these comm...
Background/Objectives: BrdU (5′-bromo-2′-deoxyuridine), a synthetic thymidine (T) analog, is widely used to study cell proliferation and DNA synthesis. To precisely identify where and when DNA replication starts and terminates, it is esse...
Background: Sanger sequencing remains the gold standard for characterizing genetic variants in short DNA fragments (<700 bp). However, the increasing demand for short TATs and high sensitivities in variant detection, particularly in oncohematology...
Bovine leukemia virus (BLV) causes Enzootic Bovine Leukosis (EBL), a persistent life-long disease resulting in immune dysfunction and shortened lifespan in infected cattle, severely impacting the profitability of the US dairy industry. Our group has...
The ocular surface represents a unique microbial ecosystem continuously exposed to environmental microorganisms; however, the fungal component of the healthy equine ocular microbiome remains poorly characterized. This study aimed to characterize the...
An optimized, well-tested and validated targeted genomic sequencing-based high-throughput assay is currently not available ready for routine biodefense and biosurveillance applications. Earlier, we addressed this gap by developing and establishing ba...
This study combines Oxford Nanopore (ONT) third-generation sequencing with targeted amino acid metabolomics to elucidate the mechanisms underlying the structural and metabolic responses of the microbial community in Golden Ear Mushroom (Naematelia si...
HCT116 is a colorectal cancer cell line frequently used in anti-tumor drug development experiments as well as in studies of the molecular machinery of eukaryotic cells. It is well characterized by the presence of several single-nucleotide and short m...
The goal of biomarker testing, in the field of personalized medicine, is to guide treatments to achieve the best possible results for each patient. The accurate and reliable identification of everyone’s genome variants is essential for the succ...
Kluyveromyces marxianus (K. marxianus) is an increasingly popular industrially relevant yeast. It is known to possess a highly efficient non-homologous end joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into i...
Wheat (Triticum aestivum L.) is one of the most important staple crops in the world, along with maize and rice. More than 50 plant viruses are known to infect wheat worldwide. To date, there are no studies on the identification of viruses infecting w...
Chronic Hepatitis B Virus (HBV) infection remains a significant public health concern, particularly in Africa, where the burden is substantial. HBV is an enveloped virus, classified into ten phylogenetically distinct genotypes (A–J). Tests to d...
As countries with endemic canine rabies progress towards elimination by 2030, it will become necessary to employ techniques to help plan, monitor, and confirm canine rabies elimination. Sequencing can provide critical information to inform control an...
Ricin is a toxin which enters cells and depurinates an adenine base in the sarcin-ricin loop in the large ribosomal subunit, leading to the inhibition of protein translation and cell death. We postulated that this depurination event could be detected...
Background: Drosophila suzukii is a worldwide invasive species with serious economic impacts. Herein, we are presenting the first project of sequencing and assembling the whole genomes of two lines of D. suzukii derived from Romanian local population...
Diagnostic testing of foot-and-mouth disease virus (FMDV) currently utilizes reverse transcription quantitative PCR (RT-qPCR) to detect the presence of viral RNA and double antibody sandwich ELISAs (DAS-ELISAs) to determine viral serotype. Serotype i...
Rooibos (Aspalathus linearis) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South Africa, is at risk...
Oxford Nanopore Technologies’ MinION has proven to be a valuable tool within human and microbial genetics. Its capacity to produce long reads in real time has opened up unique applications for portable sequencing. Examples include tracking the...
Current routine real-time PCR methods used for the point-of-care diagnosis of infectious meningitis do not allow for one-shot genotyping of the pathogen, as in the case of deadly Haemophilus influenzae meningitis. Real-time PCR diagnosed H. influenza...
Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurate...
Nanopore sequencing for forensic short tandem repeats (STR) genotyping comes with the advantages associated with massively parallel sequencing (MPS) without the need for a high up-front device cost, but genotyping is inaccurate, partially due to the...
Peste des petits ruminants virus (PPRV) causes a highly devastating disease of sheep and goats that threatens food security, small ruminant production and susceptible endangered wild ruminants. With policy directed towards achieving global PPR eradic...
The detection of high-consequence viral pathogens is essential for spillover prevention and reduction in transmission but is limited by the low sensitivity of next-generation sequencing technology. Low-titer field samples from a variety of hosts are...
Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use...
Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-...
Salivary microbiome profiling may represent a promising non-invasive approach for characterizing OSCC-associated microbial patterns and longitudinal microbiome dynamics during patient management. This exploratory pilot study aimed to longitudinally a...
Background: Large-scale mitochondrial DNA (mtDNA) rearrangement, including deletion or duplication, is one of the important causes of primary mitochondrial disease. In clinical practice, short-read sequencing (SRS)-based assays typically detect these...
Long-read sequencing methods allow a comprehensive analysis of transcriptomes in identifying full-length transcripts. This revolutionary method represents a considerable breakthrough for non-model species since it allows enhanced gene annotation and...
Due to substantial improvements in read accuracy, third-generation long-read sequencing holds great potential in blood group diagnostics, particularly in cases where traditional genotyping or sequencing techniques, primarily targeting exons, fail to...
Rapid, accurate bacterial identification in biological samples is an important task for microbiology laboratories, for which 16S rRNA gene Sanger sequencing of cultured isolates is frequently used. In contrast, next-generation sequencing does not req...
Wild migratory birds are the principal natural reservoir of influenza A viruses (IAVs) and play a central role in their evolution and global dissemination. Ukraine lies along the Black Sea–Mediterranean Flyway, making surveillance of avian infl...
The identification of structural variants (SVs) in genomic data represents an ongoing challenge because of difficulties in reliable SV calling leading to reduced sensitivity and specificity. We prepared high-quality DNA from 9 parent–child trio...
The swimming crab (Portunus trituberculatus) is an economically important species in China, and its growth traits show obvious sexual dimorphism. Thus, it is important to study the mechanism of sex determination and differentiation in this species. H...
Human embryonic stem cell (hESC) neural differentiation involves extensive APA; however, reliance on short-read sequencing in prior studies has offered only a limited view of its complexity and dynamic regulation. Here, we integrated Oxford Nanopore...
Blastocystis is a common food- and water-borne intestinal protist parasite of humans and many other animals. Blastocystis comprises multiple subtypes (STs) based on variability within the small subunit ribosomal (SSU rRNA) RNA gene. Though full-lengt...
Considerable attention has been given to the species Lactobacillus plantarum regarding its probiotic potential. L. plantarum strains have shown health benefits in several studies, and even nonstrain-specific claims are allowed in certain markets. L. ...
This study presents a comprehensive analysis of mitochondrial DNA (mtDNA) variations in dogs diagnosed with primary and recurrent tumours, employing Oxford Nanopore Technologies (ONT) for sequencing. Our investigation focused on mtDNA extracted from...
In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human ca...
Background/Objectives: Oxford Nanopore sequencing produces long reads quickly, but most functional profiling tools were developed for short reads or rely on assembly pipelines that are computationally costly and sensitive to long-read error rates. We...
Increasing evidence suggests that both coding and non-coding regions of sarcomeric protein genes can contribute to hypertrophic cardiomyopathy (HCM). Here, we introduce an experimental workflow (tested on four patients) for complete sequencing of the...
Long-read sequencing (LRS) has been adopted to meet a wide variety of research needs, ranging from the construction of novel transcriptome annotations to the rapid identification of emerging virus variants. Amongst other advantages, LRS preserves mor...
Outbreaks of furunculosis cause significant losses in salmonid aquaculture worldwide. With a recent rise in antimicrobial resistance, regulatory measures to minimize the use of antibiotics in animal husbandry, including aquaculture, have increased sc...
Viruses from Picornaviridae family are known pathogens of poultry, although the information on their occurrence and pathogenicity in pigeons is scarce. In this research, efforts are made to broaden the knowledge on Megrivirus B and Pigeon picornaviru...
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