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Chimera artifacts in nanopore direct RNA sequencing (dRNA-seq) introduce substantial inaccuracies, complicating downstream applications such as transcript annotation and gene fusion detection. Current basecalling models are unable to detect or mitigate these artifacts, limiting the …
Read PDFNanopore direct RNA sequencing holds promise for advancing our understanding of the epitranscriptome. Recently, Oxford Nanopore Technologies released basecalling models capable of detecting N6-methyladenosine (m6A), inosine (I), pseudouridine (Ψ), and 5-methylcytosine (m5C). However, their performance …
Read PDFViral non-structural proteins are key mediators of host-virus interplay, including RNA modification dynamics. The function of the transmissible gastroenteritis virus (TGEV) gene 7, which encodes a non-structural protein, remains poorly understood. Using Oxford Nanopore direct …
Read PDFAccurate identification of RNA 5-methylcytidine (m<sup>5</sup>C) at the single-nucleotide resolution remains a central challenge in nanopore direct RNA sequencing (DRS). Current global scanning and modification-aware basecalling methods enable transcriptome-wide profiling but often yield high false-positive …
Read PDF<h4>Background</h4>The RNA bacteriophage MS2 is an RNA phage that infects the bacterium E. coli and is one of the most studied and prototypical model phages in molecular biology and microbiology. Previous research revealed complex translational …
Read PDFLong-read single-cell RNA sequencing provides an opportunity to understand human health and disease at a level difficult to resolve with bulk or short-read methods. This approach enables isoform-level investigation of cellular diversity and disease mechanisms …
Read PDFThe methyltransferase-like 5 (METTL5) protein has been shown to catalyze m6A deposition on 18S ribosomal RNA. However, whether it also methylates mRNAs remains unclear. To address this, we employed direct RNA sequencing (ONT) for m6A …
Read PDFLong-read RNA sequencing (RNA-seq) technologies have revolutionized transcriptomic research by enabling the sequencing of full-length RNA molecules, thus providing a more accurate characterization of complex transcript isoforms than traditional short-read approaches. In this study, we …
Read PDFSevere Fever with Thrombocytopenia Syndrome (SFTS) is caused by the SFTS virus (SFTSV) and is associated with a high mortality rate. Although previous studies have reported RNA modifications such as m6A on SFTSV RNA, an …
Read PDFWe report a complete genome of chicharrita del maiz iflavirus 1 from the United States, determined by RNAseq, PCR, and RACE in RNA extracted from <i>Dalbulus maidis</i> (corn leafhopper). The genome encodes a 3,306-amino-acid polyprotein …
Read PDFLong-read sequencing (LRS) is rapidly advancing and demonstrates considerable promise in hematological malignancies. At the 2025 ASH meeting, numerous studies highlighted advances in applying LRS across diverse hematological malignancies. Rapid LRS-based whole-genome sequencing and adaptive …
Read PDF<h4>Abstract</h4>Mantle cell lymphoma (MCL) is a biologically heterogeneous B-cell malignancy. Although genomics and transcriptomics have delineated parts of the MCL disease spectrum, proteomics remains largely unexplored. Here, we conducted a comprehensive proteogenomic analysis integrating genomics, …
Read PDFAdvances in artificial intelligence (AI) have significantly improved medical diagnosis, with deep learning models achieving expert-level performance across unimodal tasks such as medical imaging, physiological signal analysis, electronic health record (EHR) modeling, and omics-based prediction. …
Read PDFSingle-nucleus RNA sequencing (snRNA-seq) enables resolving cellular heterogeneity in complex tissues by using nuclei instead of cells, overcoming limitations of single-cell RNA sequencing and enabling analysis of frozen and hard-to-isolate tissues. Despite advances in isolation …
Read PDFBACKGROUND: Venom cocktails of cone snails are characterized by their dynamic composition and the rapid evolution of toxin-encoding genes due to various selective pressures. The integration of comparative genomics, transcriptomics, and proteomics has emerged as …
Read PDFHigh-grade serous ovarian carcinoma (HGSOC) is characterised by profound genomic instability and limited durable responses to standard therapy, leading to poor prognosis. The use of next-generation sequencing technologies has improved understanding of its molecular landscape, …
Read PDFAbrothrix olivacea (Waterhouse, 1837), the olive grass mouse, is a widely distributed sigmodontine rodent that inhabits a broad range of environments, from the hyper arid deserts of southernmost Perú and northern Chile to the Patagonian …
Read PDFStress has been prevalent and has become an epidemic health burden, loaded with chronic disorders. The stress response is an adaptive mechanism that prepares an individual to respond to threats or other stressors in a …
Read PDFThe Hippo pathway effector YAP promotes spontaneous proliferation of Müller glia (MG), suggesting that bypassing Hippo signaling and activating YAP could enhance retinal regeneration. However, whether proliferative adult MGs retain meaningful neurogenic competence remains unclear. …
Read PDF<h4>Background and objective</h4>The cellular distribution characteristics and functional mechanisms of glutathione (GSH) metabolism within the tumor microenvironment (TME) of glioblastoma multiforme (GBM) remain poorly understood. This study aims to elucidate the cellular landscape and GSH …
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