RNAmod: an integrated system for the annotation of mRNA modifications

WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach

(2019) Kunqi Chen et al.   NUCLEIC ACIDS RESEARCH

Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers

(2019) Hailing Shi et al.   MOLECULAR CELL

SnapShot: Messenger RNA Modifications

(2018) Veronica Davalos et al.   CELL

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

Recognition of RNA N6-methyladenosine by IGF2BP proteins enhances mRNA stability and translation

(2018) Huilin Huang et al.   NATURE CELL BIOLOGY

mRNA circularization by METTL3–eIF3h enhances translation and promotes oncogenesis

(2018) Junho Choe et al.   NATURE

POSTAR2: deciphering the post-transcriptional regulatory logics

(2018) Yumin Zhu et al.   NUCLEIC ACIDS RESEARCH

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning

(2018) Yiqian Zhang et al.   BMC BIOINFORMATICS

Acetylation of Cytidine in mRNA Promotes Translation Efficiency

(2018) Daniel Arango et al.   CELL

RNAm5Cfinder: A Web-server for Predicting RNA 5-methylcytosine (m5C) Sites Based on Random Forest

(2018) Jianwei Li et al.   Scientific Reports

M6AMRFS: Robust Prediction of N6-Methyladenosine Sites With Sequence-Based Features in Multiple Species

(2018) Xiaoli Qiang et al.   Frontiers in Genetics

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

The N6-methyladenosine (m6A)-forming enzyme METTL3 controls myeloid differentiation of normal hematopoietic and leukemia cells

(2017) Ly P Vu et al.   NATURE MEDICINE

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest

(2017) Bora Uyar et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Jia-Jia Xuan et al.   NUCLEIC ACIDS RESEARCH

MeT-DB V2.0: elucidating context-specific functions of N6-methyl-adenosine methyltranscriptome

(2017) Hui Liu et al.   NUCLEIC ACIDS RESEARCH

Detecting N6-methyladenosine sites from RNA transcriptomes using ensemble Support Vector Machines

(2017) Wei Chen et al.   Scientific Reports

A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data

(2016) Xiaodong Cui et al.   BIOINFORMATICS

Post-transcriptional modifications in development and stem cells

(2016) Michaela Frye et al.   DEVELOPMENT

ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization

(2016) Guangchuang Yu et al.   Molecular BioSystems

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

(2016) Shuibin Lin et al.   MOLECULAR CELL

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

(2016) Irmgard U. Haussmann et al.   NATURE

Transcriptome-wide mapping reveals reversible and dynamic N1-methyladenosine methylome

(2016) Xiaoyu Li et al.   Nature Chemical Biology

SRAMP: prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features

(2016) Yuan Zhou et al.   NUCLEIC ACIDS RESEARCH

Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features

(2016) Xiaodong Cui et al.   Biomed Research International

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

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

(2015) Bastian Linder et al.   NATURE METHODS

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis

(2014) Guangchuang Yu et al.   BIOINFORMATICS

A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package

(2014) Jia Meng et al.   METHODS

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

(2014) Thomas M. Carlile et al.   NATURE

HAMR: high-throughput annotation of modified ribonucleotides

(2013) P. Ryvkin et al.   RNA

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

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

(2012) Dan Dominissini et al.   NATURE

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

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

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

BayesPeak: Bayesian analysis of ChIP-seq data

(2009) Christiana Spyrou et al.   BMC BIOINFORMATICS

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY