FASTdRNA: a workflow for the analysis of ONT direct RNA sequencing
Bioinformatics Advances, 2023 Abstract Motivation Direct RNA-seq (dRNA-seq) using Oxford Nanopore Technology (ONT) has revolutionized transcript mapping by offering enhanced precision due to its long-read length. Unlike traditional techniques, dRNA-seq eliminates the need for PCR amplification, reducing the impact of GC bias, and ...
Xiaofeng Chen +5 more
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Applications and potentials of nanopore sequencing in the (epi)genome and (epi)transcriptome era
The Innovation, 2021 Summary: The Human Genome Project opened an era of (epi)genomic research, and also provided a platform for the development of new sequencing technologies.
Shangqian Xie +7 more
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Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D [PDF]
, 2018 Completion of eukaryal genomes can be difficult task with the highly repetitive sequences along the chromosomes and short read lengths of secondgeneration sequencing. Saccharomyces cerevisiae strain CEN.
Jenjaroenpun, Piroon +6 more
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Systematic comparison of tools used for m6A mapping from nanopore direct RNA sequencing
Nature Communications, 2023 Direct RNA sequencing using nanopore platform can be used to detect N6-methyladenosine (m6A) modifications on mRNAs. Here the authors systematically compare tools used for m6A detection from nanopore direct sequencing.
Zhen-Dong Zhong +11 more
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The contribution of Alu exons to the human proteome. [PDF]
, 2016 BackgroundAlu elements are major contributors to lineage-specific new exons in primate and human genomes. Recent studies indicate that some Alu exons have high transcript inclusion levels or tissue-specific splicing profiles, and may play important ...
Jiang, Peng +7 more
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Detection and quantification of 5moU RNA modification from direct RNA sequencing data
Current Genomics, 2023 Abstract Background Chemically modified therapeutic mRNAs have gained its momentum recently. In addition to commonly used modifications (e.g., pseudouridine), 5moU is considered a promising substitution of uridine in therapeutic mRNAs. Accurate identification of 5-Methoxyuridine (5moU) would be crucial for the study and quality control of ...
Li, Jiayi +6 more
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Simultaneous profiling of transcriptome and DNA methylome from a single cell. [PDF]
, 2016 BackgroundSingle-cell transcriptome and single-cell methylome technologies have become powerful tools to study RNA and DNA methylation profiles of single cells at a genome-wide scale. A major challenge has been to understand the direct correlation of DNA
An, Qin +9 more
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Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens. [PDF]
, 2019 The burden of meningitis in low-and-middle-income countries remains significant, but the infectious causes remain largely unknown, impeding institution of evidence-based treatment and prevention decisions.
Crawford, Emily D. +25 more
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A Path to Implement Precision Child Health Cardiovascular Medicine. [PDF]
, 2017 Congenital heart defects (CHDs) affect approximately 1% of live births and are a major source of childhood morbidity and mortality even in countries with advanced healthcare systems. Along with phenotypic heterogeneity, the underlying etiology of CHDs is
Brian Reemtsen +8 more
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Direct chemical method for sequencing RNA. [PDF]
Proceedings of the National Academy of Sciences, 1979 Four different base-specific chemical reactions generate a means of directly sequencing RNA terminally labeled with 32P. After a partial, specific modification of each kind of RNA base, an amine-catalyzed strand scission generates labeled fragments whose lengths determine the position of each nucleotide in the sequence.
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