Nucleotide resolution profiling of m7G tRNA modification by TRAC-Seq

Cooperativity between different tRNA modifications and their modification pathways

(2018) Mikołaj Sokołowski et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Mettl1/Wdr4-Mediated m 7 G tRNA Methylome Is Required for Normal mRNA Translation and Embryonic Stem Cell Self-Renewal and Differentiation

(2018) Shuibin Lin et al.   MOLECULAR CELL

The role of RNA modifications in the regulation of tRNA cleavage

(2018) Shawn M. Lyons et al.   FEBS LETTERS

mRNA circularization by METTL3–eIF3h enhances translation and promotes oncogenesis

(2018) Junho Choe et al.   NATURE

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

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

Detecting RNA modifications in the epitranscriptome: predict and validate

(2017) Mark Helm et al.   NATURE REVIEWS GENETICS

ALKBH1 is an RNA dioxygenase responsible for cytoplasmic and mitochondrial tRNA modifications

(2017) Layla Kawarada et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

The m 6 A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells

(2016) Shuibin Lin et al.   MOLECULAR CELL

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Efficient and quantitative high-throughput tRNA sequencing

(2015) Guanqun Zheng et al.   NATURE METHODS

ARM-seq: AlkB-facilitated RNA methylation sequencing reveals a complex landscape of modified tRNA fragments

(2015) Aaron E Cozen et al.   NATURE METHODS

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

(2014) Schraga Schwartz et al.   CELL

Role of tRNA modifications in human diseases

(2014) Adrian Gabriel Torres et al.   TRENDS IN MOLECULAR MEDICINE

Transcriptome-wide mapping of N6-methyladenosine by m6A-seq based on immunocapturing and massively parallel sequencing

(2013) Dan Dominissini et al.   Nature Protocols

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Detection of RNA modifications

(2010) Stefanie Kellner et al.   RNA Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY