Results 1 to 10 of about 1,335,933 (257)

From bulk, single-cell to spatial RNA sequencing

International Journal of Oral Science, 2021
RNA sequencing (RNAseq) can reveal gene fusions, splicing variants, mutations/indels in addition to differential gene expression, thus providing a more complete genetic picture than DNA sequencing.
Xinmin Li, Cun-Yu Wang
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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
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HCC: RNA-Sequencing in Cirrhosis

Biomolecules, 2023
Hepatocellular carcinoma (HCC) ranks the most common types of cancer worldwide. As the fourth leading cause of cancer-related deaths, its prognosis remains poor. Most patients developed HCC on the basis of chronic liver disease. Cirrhosis is an important
Haoyu Wang, Wenjie Shi, Jing Lu, Yuan Liu, Wei Zhou, Zekun Yu, Shengying Qin, Junwei Fan   +7 more
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Quantification of substoichiometric modification reveals global tsRNA hypomodification, preferences for angiogenin-mediated tRNA cleavage, and idiosyncratic epitranscriptomes of human neuronal cell-lines

Computational and Structural Biotechnology Journal, 2023
Modification of tRNA is an integral part of the epitranscriptome with a particularly pronounced potential to generate diversity in RNA expression. Eukaryotic tRNA contains modifications in up to 20% of their nucleotides, but not all sites are always ...
Florian Pichot, Marion C. Hogg, Virginie Marchand, Valérie Bourguignon, Elisabeth Jirström, Cliona Farrell, Hesham A. Gibriel, Jochen H.M. Prehn, Yuri Motorin, Mark Helm   +9 more
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Advances in Non-Coding RNA Sequencing

Non-Coding RNA, 2021
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology.
Julia Micheel, Aram Safrastyan, Damian Wollny   +2 more
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Holistic Optimization of Bioinformatic Analysis Pipeline for Detection and Quantification of 2′-O-Methylations in RNA by RiboMethSeq

Frontiers in Genetics, 2020
A major trend in the epitranscriptomics field over the last 5 years has been the high-throughput analysis of RNA modifications by a combination of specific chemical treatment(s), followed by library preparation and deep sequencing.
Florian Pichot, Florian Pichot, Florian Pichot, Virginie Marchand, Lilia Ayadi, Lilia Ayadi, Valérie Bourguignon-Igel, Valérie Bourguignon-Igel, Mark Helm, Yuri Motorin, Yuri Motorin   +10 more
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Utility of nanopore sequencing for detecting pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

Journal of Clinical Virology Plus, 2023
RNA viruses are the most frequent pathogens responsible for respiratory infections, particularly in pediatric patients. Next-generation sequencing, represented by Illumina sequencing, is one of the most comprehensive methods for identifying pathogens ...
Makoto Yamaguchi, Kazuhiro Horiba, Kazunori Haruta, Suguru Takeuchi, Takako Suzuki, Yuka Torii, Shinji Kawabe, Sho Wada, Takanari Ikeyama, Yoshinori Ito, Tomoo Ogi, Jun-ichi Kawada   +11 more
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Advances in application of single-cell RNA sequencing in cardiovascular research

Frontiers in Cardiovascular Medicine, 2022
Single-cell RNA sequencing (scRNA-seq) provides high-resolution information on transcriptomic changes at the single-cell level, which is of great significance for distinguishing cell subtypes, identifying stem cell differentiation processes, and ...
Yue Hu, Ying Zhang, Yutong Liu, Yan Gao, Tiantian San, Xiaoying Li, Xiaoying Li, Sensen Song, Binglong Yan, Zhuo Zhao, Zhuo Zhao   +10 more
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Dual RNA-Seq of Mtb-Infected Macrophages In Vivo Reveals Ontologically Distinct Host-Pathogen Interactions

Cell Reports, 2020
Summary: Dissecting the in vivo host-pathogen interplay is crucial to understanding the molecular mechanisms governing control or progression of intracellular infections.
Davide Pisu, Lu Huang, Jennifer K. Grenier, David G. Russell   +3 more
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MultiEditR: The first tool for the detection and quantification of RNA editing from Sanger sequencing demonstrates comparable fidelity to RNA-seq

Molecular Therapy: Nucleic Acids, 2021
We present MultiEditR (Multiple Edit Deconvolution by Inference of Traces in R), the first algorithm specifically designed to detect and quantify RNA editing from Sanger sequencing (z.umn.edu/multieditr).
Mitchell G. Kluesner, Rafail Nikolaos Tasakis, Taga Lerner, Annette Arnold, Sandra Wüst, Marco Binder, Beau R. Webber, Branden S. Moriarity, Riccardo Pecori   +8 more
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