Computational methods for RNA modification detection from nanopore direct RNA sequencing data

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

(2021) Oguzhan Begik et al.   NATURE BIOTECHNOLOGY

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

(2021) Ploy N. Pratanwanich et al.   NATURE BIOTECHNOLOGY

Molecular Mechanisms Driving mRNA Degradation by m6A Modification

(2020) Yujin Lee et al.   TRENDS IN GENETICS

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

(2020) Matthew T Parker et al.   eLife

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

(2020) Luca Cozzuto et al.   Frontiers in Genetics

Direct RNA Sequencing for the Study of Synthesis, Processing, and Degradation of Modified Transcripts

(2020) Mattia Furlan et al.   Frontiers in Genetics

Decoding the epitranscriptional landscape from native RNA sequences

(2020) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

New Twists in Detecting mRNA Modification Dynamics

(2020) Ina Anreiter et al.   TRENDS IN BIOTECHNOLOGY

Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms

(2020) Kerstin C. Maier et al.   GENOME RESEARCH

RNA N6-Methyladenosine and the Regulation of RNA Localization and Function in the Brain

(2020) Sachithrani U. Madugalle et al.   TRENDS IN NEUROSCIENCES

Dynamics of transcriptional and post-transcriptional regulation

(2020) Mattia Furlan et al.   BRIEFINGS IN BIOINFORMATICS

Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

(2020) Alexander M. Price et al.   Nature Communications

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

(2019) Yuri Motorin et al.   Genes

METTL1 Promotes let-7 MicroRNA Processing via m7G Methylation

(2019) Luca Pandolfini et al.   MOLECULAR CELL

Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing

(2019) Andrew M. Smith et al.   PLoS One

Nanopore native RNA sequencing of a human poly(A) transcriptome

(2019) Rachael E. Workman et al.   NATURE METHODS

Accurate detection of m6A RNA modifications in native RNA sequences

(2019) Huanle Liu et al.   Nature Communications

m6A in mRNA coding regions promotes translation via the RNA helicase-containing YTHDC2

(2019) Yuanhui Mao et al.   Nature Communications

Antibody cross-reactivity accounts for widespread appearance of m1A in 5’UTRs

(2019) Anya V. Grozhik et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

N 6 -Methyladenosines Modulate A-to-I RNA Editing

(2018) Jian-Feng Xiang et al.   MOLECULAR CELL

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

AlkAniline-Seq: Profiling of m7 G and m3 C RNA Modifications at Single Nucleotide Resolution

(2018) Virginie Marchand et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Base-Resolution Mapping Reveals Distinct m 1 A Methylome in Nuclear- and Mitochondrial-Encoded Transcripts

(2017) Xiaoyu Li et al.   MOLECULAR CELL

m6A-dependent maternal mRNA clearance facilitates zebrafish maternal-to-zygotic transition

(2017) Boxuan Simen Zhao et al.   NATURE

The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution

(2017) Modi Safra et al.   NATURE

Nm-seq maps 2′-O-methylation sites in human mRNA with base precision

(2017) Qing Dai et al.   NATURE METHODS

Charting the unknown epitranscriptome

(2017) Eva Maria Novoa et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic m6A modification regulates local translation of mRNA in axons

(2017) Jun Yu et al.   NUCLEIC ACIDS RESEARCH

m6A potentiates Sxl alternative pre-mRNA splicing for robust Drosophila sex determination

(2016) Irmgard U. Haussmann et al.   NATURE

m6A modulates neuronal functions and sex determination in Drosophila

(2016) Tina Lence et al.   NATURE

Transcriptome-wide distribution and function of RNA hydroxymethylcytosine

(2016) B. Delatte et al.   SCIENCE

Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome

(2015) Bastian Linder et al.   NATURE METHODS

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA

(2014) Schraga Schwartz et al.   CELL

m6A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells

(2014) Pedro J. Batista et al.   Cell Stem Cell

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae

(2014) Alexander F. Lovejoy et al.   PLoS One

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

(2013) L. Bazak et al.   GENOME RESEARCH

Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons

(2012) Kate D. Meyer et al.   CELL

Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

(2012) Dan Dominissini et al.   NATURE

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO

(2011) Guifang Jia et al.   Nature Chemical Biology