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Microbes are omnipresent, thriving in a range of habitats, from oceans to soils, and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. …
Read PDFThe long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly from sequencing reads. In this study, we used long-range PCR with ONT and …
Read PDFInherited retinal diseases (IRDs) are a major cause of visual impairment worldwide, marked by extensive genetic and phenotypic heterogeneity. Recent estimates from the U.S. suggest a prevalence of nearly 1 in 1000 individuals, reflecting both …
Read PDF<i>Escherichia coli</i> ST131 is a clinical challenge due to its multidrug resistant profile and successful global spread. They are often associated with complicated infections, particularly urinary tract infections (UTIs). Bacteriocins play an important role to …
Read PDFNuclear-embedded mitochondrial DNA segments (NUMT) preserve a record of ongoing mitochondrial-to-nuclear DNA transfer during evolution, with important implications for disease mechanisms and genome organization. Here, we develop a pangenome graph-based NUMT detection approach, achieving a …
Read PDF<h4>Background</h4>The assembly of fragmented RNA-sequencing reads into complete transcripts is error-prone, particularly for genes with complex splicing, resulting in ambiguity in transcript discovery and quantification. PacBio long-read RNA sequencing resolves transcripts with greater clarity than …
Read PDF<h4>Background</h4>Nearly 80% of patients with High grade serous ovarian cancer (HGSOC) will experience recurrence within 5 years, but little is known about the mechanisms that drive this process.<h4>Methods</h4>In this study we used whole genome sequencing …
Read PDFZea mays is an important genetic model for elucidating transcriptional networks. Uncertainties about the complete structure of mRNA transcripts limit the progress of research in this system. Here, using single-molecule sequencing technology, we produce 111,151 …
Read PDFGut bacteriophages profoundly impact microbial ecology and health<sup>1-3</sup>; yet, they are understudied. Using deep long-read bulk metagenomic sequencing, we tracked prophage integration dynamics in stool samples from six healthy individuals, spanning a 2-year timescale. Although …
Read PDF<h4>Background</h4>Sugarcane is an important global food crop and energy resource. To facilitate the sugarcane improvement program, genome and gene information are important for studying traits at the molecular level. Most currently available transcriptome data for …
Read PDFWilson disease (WD) is an autosomal recessive disorder of copper transport caused by bi-allelic pathogenic variants in the ATPase copper transporting beta gene (<i>ATP7B</i>). Results of standard genetic diagnostics remain inconclusive in 3%-20% of WD …
Read PDFFreshwater ecosystems are under increasing pressure from pollution, habitat degradation and climate change, highlighting the need for reliable biomonitoring approaches to assess ecosystem health and identify the causes of biodiversity and ecosystem service loss. Characterisation …
Read PDFFreshwater Gammarus species represent important keystone organisms in aquatic ecosystems, and are sensitive to environmental changes. Here, we present the first pseudo-chromosome-level genome of Gammarus nekkensis, endemic to north China. We integrated PacBio HiFi long-read …
Read PDFAtypical frontotemporal lobar degeneration with ubiquitin-positive inclusions (aFTLD-U) is neuropathologically characterized by aggregation of the FET family of proteins and clinically manifests as sporadic young-onset frontotemporal dementia. Here we describe a major risk locus on …
Read PDFThe human cytomegalovirus (HCMV) is a ubiquitous, human pathogenic herpesvirus. The complete viral genome is transcriptionally active during infection; however, a large part of its transcriptome has yet to be annotated. In this work, we …
Read PDFIn this study, we validated recombinant adeno-associated viral integration analysis (RAAVioli), a previously published computational method for the comprehensive analysis of adeno-associated virus vector (AAV) integration sites (ISs) and vector rearrangements across both long- and …
Read PDFAvian metapneumovirus (aMPV) is an important respiratory pathogen of global concern in poultry. Until recently, the United States (U.S.) was considered free of aMPV following the eradication of subtype C in the early 2000s. However, …
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