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...
The high commercial value and the increasing demand for caviar make it susceptible to illegal trade and fraudulent activities, while mislabelling can occur both deliberately and unintentionally. Therefore, reliable methods are urgently needed to dist...
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...
Background/Objectives: Intra-abdominal infections (IAIs) constitute significant clinical challenges that can rapidly progress to life-threatening conditions if not promptly diagnosed and treated. Traditional pathogen identification methodologies, pre...
The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior...
Despite providing highly accurate results, the short reads generated by second generation sequencing have major limitations in mapping complex genomic regions. Longer reads can resolve these issues and additionally phase distant variants. The third g...
The increasing availability of massive omics data requires improving the quality of reference databases and their annotations. The combination of full-length isoform sequencing (Iso-Seq) with short-read transcriptomics and proteomics has been success...
Nanopore sequencing (ONT) is a new and rapidly developing method for determining nucleotide sequences in DNA and RNA. It serves the ability to obtain long reads of thousands of nucleotides without assembly and amplification during sequencing compared...
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...
The marine nematode Litoditis marina is widely distributed in intertidal zones around the globe, yet the mechanisms underlying its broad adaptation to salinity remain elusive. In this study, we applied ONT long-read sequencing technology to unravel t...
To date, different strategies of whole-genome sequencing (WGS) have been developed in order to understand the genome structure and functions. However, the analysis of genomic sequences obtained from natural populations is challenging and the biologic...
The genome-wide long hairpin RNA interference (lhRNAi) library is an important resource for plant gene function research. Molecularly characterizing lhRNAi mutant lines is crucial for identifying candidate genes associated with corresponding phenotyp...
Type I restriction-modification (RMI) systems play a crucial role in bacterial defense against mobile elements by distinguishing self and foreign DNA through sequence-specific methylation and cleavage. Here, we characterize BlihIA, a novel RMI system...
The green sea turtle (Chelonia mydas), a widely distributed species, plays a crucial role in maintaining the marine ecosystem. However, studies on C. mydas require accurate and comprehensive genome annotation information. Long-read direct transcripto...
Affordable, flexible surveillance tools are needed to detect SARS-CoV-2 and other pathogens in wildlife. Standard nucleic acid amplification tests (NAATs) are reliable but restricted to predefined targets, limiting their ability to detect co-infectio...
Reproductive efficiency determines the economic benefits of the sheep industry, yet the molecular mechanisms underlying prolificacy remain incompletely understood. To investigate transcriptomic differences associated with sheep prolificacy, we perfor...
Since the release of the MinION sequencer in 2014, it has been applied to great effect in the remotest and harshest of environments, and even in space. One of the most common applications of MinION is for nanopore-based DNA barcoding in situ for spec...
The advent of long-read sequencing offers a new assessment method of detecting genomic structural variation (SV) in numerous rare genetic diseases. For autism spectrum disorders (ASD) cases where pathogenic variants fail to be found in the protein-co...
Long-read sequencing (LRS) has transformed life science research by introducing third-generation sequencing (TGS) platforms applicable across various research fields, including environmental sciences. In the past decade, LRS platforms have been utili...
The long-read RNA sequencing developed by Oxford Nanopore Technology provides a direct quantification of transcript isoforms. That makes the number of transcript isoforms per gene an intrinsically suitable metric for alternative splicing (AS) profili...
Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from differen...
Burkholderia sp. SSG is a potent biological control agent. Even though its survival on the leaf surface declined rapidly, SSG provided extended, moderate plant protection from a broad spectrum of pathogens. This study used Arabidopsis Col-0 and its m...
Background: Since its first report in the country in 2013, NDM-producing Enterobacterales have been identified in all the Brazilian administrative regions. In this study, we characterized by antimicrobial susceptibility testing and by molecular typin...
Oxford Nanopore sequencing is an important sequencing technology, which reads the nucleotide sequence by detecting the electrical current signal changes when DNA molecule is forced to pass through a biological nanopore. The research on signal simulat...
Alternative lengthening of telomeres (ALT) is a homologous recombination-based pathway utilized by 10–15% of cancer cells that allows cells to maintain their telomeres in the absence of telomerase. This pathway was originally discovered in the...
Lactiplantibacillus plantarum stands out as a remarkably diverse species of lactic acid bacteria, occupying a myriad of ecological niches. Particularly noteworthy is its presence in human breast milk, which can serve as a reservoir of probiotic bacte...
Viruses are a major cause of acute gastroenteritis (AGE) in cats, chiefly in younger animals. Enteric specimens collected from 29 cats with acute enteritis and 33 non-diarrhoeic cats were screened in PCRs and reverse transcription (RT) PCR for a larg...
Long-read transcriptome sequencing provides us with a convenient tool for the thorough study of biological processes such as neuronal plasticity. Here, we aimed to perform transcriptional profiling of rat hippocampal primary neuron cultures after sti...
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...
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...
Overnutrition with a high-fat or high-sugar diet is widely considered to be the risk factor for various metabolic, chronic, or malignant diseases that are accompanied by alterations in gut microbiota, metabolites, and downstream pathways. In this stu...
Staphylococcus aureus biofilms represent a critical healthcare challenge, driving chronic infections and antimicrobial resistance. This study investigates the anti-staphylococcal efficacy of two Lactiplantibacillus strains isolated from traditional B...
Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the per...
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...
The reconstruction of individual haplotypes can facilitate the interpretation of disease risks; however, high costs and technical challenges still hinder their assessment in clinical settings. Second-generation sequencing is the gold standard for var...
The LDLR locus has clinical significance for lipid metabolism, Mendelian familial hypercholesterolemia (FH), and common lipid metabolism-related diseases (coronary artery disease and Alzheimer’s disease), but its intronic and structural variant...
Precision metagenomic approaches using Oxford Nanopore Technology (ONT) sequencing has been shown to allow recovery of complete genomes of foodborne bacteria from overnight enrichments of agricultural waters. This study tests the applicability of a s...
HIV-1 proviral single-genome sequencing by limiting-dilution polymerase chain reaction (PCR) amplification is important for differentiating the sequence-intact from defective proviruses that persist during antiretroviral therapy (ART). Intact proviru...
(1) Background: Short-read sequencing allows for the rapid and accurate analysis of the whole bacterial genome but does not usually enable complete genome assembly. Long-read sequencing greatly assists with the resolution of complex bacterial genomes...
The assembly of telomere-to-telomere (T2T) genomes is essential for understanding genomic architecture, especially in fungal pathogens with complex karyotypes, such as Colletotrichum lini, causing flax anthracnose disease. This study provides optimiz...
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...
Long-read direct RNA sequencing developed by Oxford Nanopore Technologies (ONT) is quickly gaining popularity for transcriptome studies, while fast turnaround time and low cost make it an attractive instrument for clinical applications. There is a gr...
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...
The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and microscopic examinations. Here, we demonstrate a ra...
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...
Leafy greens are a significant source of produce-related Shiga toxin-producing Escherichia coli (STEC) outbreaks in the United States, with agricultural water often implicated as a potential source. Current FDA outbreak detection protocols are time-c...
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...
Sweet orange (Citrus sinensis) is an economically important fruit crop worldwide. Mining for genes associated with ripening periods and fruit color traits is crucial for plant genetics and for the improvement of external fruit quality traits. The pre...
Long-read sequencing technologies, particularly those developed by Oxford Nanopore Technologies (ONT), have transformed genome sequencing by enabling high-resolution analysis of complex microbial communities. Among ONT devices, the MinION remains aff...
In 2014, Oxford Nanopore Technologies (ONT) introduced an affordable and portable sequencer called MinION. We reviewed emerging applications in water research and assessed progress made with this platform towards ubiquitous genetics. With >99% sav...
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