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<h4>Background</h4>Long-read sequencing technology, widely used in research, is proving useful in clinical diagnosis, especially for infectious diseases. Despite recent advances, it hasn't been routinely applied to constitutional human diseases. Long-read sequencing detects intronic variants and …
Read PDFAs important primary producers and key components of biogeochemical processes, phytoplankton communities are highly diverse and continually adapt to changes in the environment, impacting the entire marine ecosystem. Consequently, it remains important to isolate, culture …
Read PDFEpitranscriptomics has emerged as a rapidly evolving field that focused on studying post-transcriptional RNA modifications and their role in spatiotemporal regulation of gene expression. N6-methyladenosine (m<sup>6</sup>A) and 5-methylcytosine (m<sup>5</sup>C) represent the most extensively studied modifications …
Read PDFWe present a protocol to achieve a higher depth of long-read sequencing of region(s) of interest in potato cyst nematodes without amplification using a Cas9-based Nanopore enrichment approach. We describe steps for designing high-fidelity guide …
Read PDFOver the last decade CRISPR gene editing has been successfully used to streamline the generation of animal models for biomedical research purposes. However, one limitation to its use is the potential occurrence of on-target mutations …
Read PDFLong-read sequencing (LRS) technologies have the potential to revolutionize scientific discoveries in RNA biology through the comprehensive identification and quantification of full-length mRNA isoforms. Despite great promise, challenges remain in the widespread implementation of LRS …
Read PDF<h4>Background</h4>Fungi are talented producers of secondary metabolites with applications in the pharmaceutical and agrochemical sectors. Aspergillus wentii CBS 141173 has gathered research interest due to its ability to produce high-value norditerpenoid compounds, including anticancer molecules. …
Read PDFTandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization of TRs; however, the underlying bioinformatics perspectives remain challenging. We present <i>otter</i> and TREAT: …
Read PDFThe study of the genetic diversity and adaptation mechanisms of the Kazakh apricot (<i>Prunus armeniaca</i> L.) is essential for breeding programs and the conservation of plant genetic resources in arid environments. Despite this species' ecological …
Read PDFThe effect of periodical heatwaves and related thermal stratification in freshwater aquatic ecosystems has been a hot research issue. A large dataset of samples was generated from samples exposed to temporary thermal stratification in mesocosms …
Read PDFBiallelic variants in <i>USH2A</i> are associated with retinitis pigmentosa (RP) and Type 2 Usher Syndrome (USH2), leading to impaired vision and, additionally, hearing loss in the latter. Although the introduction of next-generation sequencing into clinical …
Read PDFThe CYP21A2 gene, mapped to the RCCX module in 6p21.3, is responsible for 21-hydroxylase deficiency (21-HD). In this work, we leveraged Oxford Nanopore Technology (ONT) Long Read sequencing (LRS) to analyze samples from an Argentinian …
Read PDFDinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Some dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. <i>Amphidinium …
Read PDFExtrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in ∼15% of early-stage cancers and ∼30% of late-stage cancers. ecDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating …
Read PDFCryptosporidium parvum is a zoonotic parasite of the intestine and poses a threat to human and animal health. However, it is difficult to obtain a large number of oocysts for genome sequencing using in vitro …
Read PDFUnveiling the potential application of psychrophilic polymerases as candidates for polymerase-nanopore long-read sequencing presents a departure from conventional choices such as thermophilic <i>Bacillus</i> stearothermophilus (Bst) renowned for its limitation in temperature and mesophilic <i>Bacillus subtilis</i> …
Read PDFSomatic structural variations (SVs) represent a critical category of genomic mutations in hepatocellular carcinoma (HCC). However, the accurate identification of somatic SVs using short-read high-throughput sequencing is challenging. Here, we applied long-read nanopore sequencing and …
Read PDFEstablishing the protein-protein interaction network sheds light on functional genomics studies by providing insights from known counterparts. However, the rice interactome has barely been studied due to the lack of massive, reliable, and cost-effective methodologies. …
Read PDF<h4>Background</h4>The clinical diagnosis of Fabry Disease (FD) can be challenging due to the clinical heterogeneity, especially in females. Patients with FD often experience a prolonged interval between the onset of symptoms and receiving a diagnosis. …
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