RMBase v2. 0: deciphering the map of RNA modifications from epitranscriptome sequencing data

JJ Xuan, WJ Sun, PH Lin, KR Zhou, S Liu… - Nucleic acids …, 2018 - academic.oup.com
More than 100 distinct chemical modifications to RNA have been characterized so far.
However, the prevalence, mechanisms and functions of various RNA modifications remain …

RMBase: a resource for decoding the landscape of RNA modifications from high-throughput sequencing data

WJ Sun, JH Li, S Liu, J Wu, H Zhou, LH Qu… - Nucleic acids …, 2016 - academic.oup.com
Although more than 100 different types of RNA modifications have been characterized
across all living organisms, surprisingly little is known about the modified positions and their …

RMBase v3. 0: decode the landscape, mechanisms and functions of RNA modifications

J Xuan, L Chen, Z Chen, J Pang, J Huang… - Nucleic Acids …, 2024 - academic.oup.com
Although over 170 chemical modifications have been identified, their prevalence,
mechanism and function remain largely unknown. To enable integrated analysis of diverse …

[HTML][HTML] Epitranscriptome: review of top 25 most-studied RNA modifications

VA Arzumanian, GV Dolgalev, IY Kurbatov… - International Journal of …, 2022 - mdpi.com
The alphabet of building blocks for RNA molecules is much larger than the standard four
nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of …

RNAmod: an integrated system for the annotation of mRNA modifications

Q Liu, RI Gregory - Nucleic acids research, 2019 - academic.oup.com
Dynamic and reversible RNA modifications such as N 6-methyladenosine (m6A) can play
important roles in regulating messenger RNA (mRNA) splicing, export, stability and …

Guitar: an R/bioconductor package for gene annotation guided transcriptomic analysis of RNA‐related genomic features

X Cui, Z Wei, L Zhang, H Liu, L Sun… - BioMed research …, 2016 - Wiley Online Library
Biological features, such as genes and transcription factor binding sites, are often denoted
with genome‐based coordinates as the genomic features. While genome‐based …

RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis

K Chen, B Song, Y Tang, Z Wei, Q Xu, J Su… - Nucleic acids …, 2021 - academic.oup.com
Deciphering the biological impacts of millions of single nucleotide variants remains a major
challenge. Recent studies suggest that RNA modifications play versatile roles in essential …

DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology

Y Zhang, J Jiang, J Ma, Z Wei, Y Wang… - Nucleic Acids …, 2023 - academic.oup.com
With advanced technologies to map RNA modifications, our understanding of them has
been revolutionized, and they are seen to be far more widespread and important than …

[HTML][HTML] The epitranscriptome toolbox

S Moshitch-Moshkovitz, D Dominissini, G Rechavi - Cell, 2022 - cell.com
In the last decade, the notion that mRNA modifications are involved in regulation of gene
expression was demonstrated in thousands of studies. To date, new technologies and …

[HTML][HTML] Analysis of RNA modifications by second-and third-generation deep sequencing: 2020 update

Y Motorin, V Marchand - Genes, 2021 - mdpi.com
The precise mapping and quantification of the numerous RNA modifications that are present
in tRNAs, rRNAs, ncRNAs/miRNAs, and mRNAs remain a major challenge and a top priority …