Results 1 to 10 of about 721,197 (148)

RNA modifications detection by comparative Nanopore direct RNA sequencing

Nature Communications, 2021
Nanopore direct RNA Sequencing data contain information about the presence of RNA modifications, but their detection poses substantial challenges. Here the authors introduce Nanocompore, a new methodology for modification detection from Nanopore data.
Adrien Leger, Paulo P. Amaral, Luca Pandolfini, Charlotte Capitanchik, Federica Capraro, Valentina Miano, Valentina Migliori, Patrick Toolan-Kerr, Theodora Sideri, Anton J. Enright, Konstantinos Tzelepis, Folkert J. van Werven, Nicholas M. Luscombe, Isaia Barbieri, Jernej Ule, Tomas Fitzgerald, Ewan Birney, Tommaso Leonardi, Tony Kouzarides   +18 more
doaj   +2 more sources

A gene-specific RNA enrichment protocol for nanopore direct-RNA sequencing. [PDF]

PLoS ONE
Oxford Nanopore direct-RNA sequencing, a third-generation sequencing technology, allows for the analysis of native RNA molecules in their natural cellular state.
Maja Bele Dyrendalsli, Cecilie Løkke, Christer Einvik   +2 more
doaj   +2 more sources

A dual context-aware basecaller for nanopore direct RNA sequencing [PDF]

Nature Communications
Nanopore direct RNA sequencing (DRS) offers distinct advantages for transcriptome analysis over the traditional high-throughput RNA sequencing methods by preserving native RNA modifications, eliminating polymerase chain reaction bias, and simplifying the
Shaohui Xie, Lulu Ding, Yang Yu, Ling Liu, Yiwen Sun, Jianqiang Li, Jue Ruan, Zexuan Zhu   +7 more
doaj   +2 more sources

Raw signal segmentation for estimating RNA modification from Nanopore direct RNA sequencing data [PDF]

eLife
Estimating RNA modifications from Nanopore direct RNA sequencing data is a critical task for the RNA research community. However, current computational methods often fail to deliver satisfactory results due to inaccurate segmentation of the raw signal ...
Guangzhao Cheng, Aki Vehtari, Lu Cheng
doaj   +2 more sources

Enhanced detection of RNA modifications in Escherichia coli utilizing direct RNA sequencing [PDF]

Cell Reports: Methods
Summary: RNA modifications play crucial roles in prokaryotic cellular processes. In this study, we found that the recent advances in direct RNA sequencing have improved yield, accuracy, and signal-to-noise ratio in bacterial samples.
Zhihao Guo, Yanwen Shao, Lu Tan, Beifang Lu, Xin Deng, Sheng Chen, Runsheng Li   +6 more
doaj   +2 more sources

Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing

Viruses, 2020
Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms.
Carole Grädel, Miguel A. Terrazos Miani, Christian Baumann, Maria Teresa Barbani, Stefan Neuenschwander, Stephen L. Leib, Franziska Suter-Riniker, Alban Ramette   +7 more
doaj   +3 more sources

Direct detection of RNA modifications and structure using single-molecule nanopore sequencing

Cell Genomics, 2022
Summary: Modifications are present on many classes of RNA, including tRNA, rRNA, and mRNA. These modifications modulate diverse biological processes such as genetic recoding and mRNA export and folding. In addition, modifications can be introduced to RNA
William Stephenson, Roham Razaghi, Steven Busan, Kevin M. Weeks, Winston Timp, Peter Smibert   +5 more
doaj   +3 more sources

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets

Frontiers in Genetics, 2020
The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification.
Luca Cozzuto, Huanle Liu, Leszek P. Pryszcz, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Anna Delgado-Tejedor, Julia Ponomarenko, Julia Ponomarenko, Eva Maria Novoa, Eva Maria Novoa, Eva Maria Novoa, Eva Maria Novoa   +12 more
doaj   +3 more sources

Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing [PDF]

Nature Communications
Chimera artifacts in nanopore direct RNA sequencing (dRNA-seq) introduce substantial inaccuracies, complicating downstream applications such as transcript annotation and gene fusion detection.
Yangyang Li, Ting-You Wang, Qingxiang Guo, Yanan Ren, Xiaotong Lu, Qi Cao, Rendong Yang   +6 more
doaj   +2 more sources

Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing [PDF]

Nature Communications
Nanopore direct RNA sequencing (dRNA-seq) enables unique insights into RNA biology. However, applications are currently limited by the lack of accurate and cost-effective sample multiplexing. Here we introduce WarpDemuX, an ultra-fast and highly accurate
Wiep van der Toorn, Patrick Bohn, Wang Liu-Wei, Marco Olguin-Nava, Anne-Sophie Gribling-Burrer, Redmond P. Smyth, Max von Kleist   +6 more
doaj   +2 more sources