m6aViewer: software for the detection, analysis, and visualization of N 6 -methyladenosine peaks from m 6 A-seq/ME-RIP sequencing data

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

(2016) Xiaodong Cui et al.   BIOINFORMATICS

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

(2016) Yuan Zhou et al.   NUCLEIC ACIDS RESEARCH

HEPeak: an HMM-based exome peak-finding package for RNA epigenome sequencing data

(2015) Xiaodong Cui et al.   BMC GENOMICS

m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency

(2015) Tong Chen et al.   Cell Stem Cell

An association study of the m6A genes with major depressive disorder in Chinese Han population

(2015) Tingfu Du et al.   JOURNAL OF AFFECTIVE DISORDERS

N6-methyladenosine marks primary microRNAs for processing

(2015) Claudio R. Alarcón et al.   NATURE

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

(2015) Bastian Linder et al.   NATURE METHODS

Identification and analysis of the N6-methyladenosine in the Saccharomyces cerevisiae transcriptome

(2015) Wei Chen et al.   Scientific Reports

FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis

(2014) Xu Zhao et al.   CELL RESEARCH

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

(2014) Jia Meng et al.   METHODS

The dynamic epitranscriptome: N6-methyladenosine and gene expression control

(2014) Kate D. Meyer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Perturbation of m6A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5′ Sites

(2014) Schraga Schwartz et al.   Cell Reports

Exome-based analysis for RNA epigenome sequencing data

(2013) Jia Meng et al.   BIOINFORMATICS

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

MeRIP-PF: An Easy-to-use Pipeline for High-resolution Peak-finding in MeRIP-Seq Data

(2013) Yuli Li et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Kate D. Meyer et al.   CELL

ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility

(2012) Guanqun Zheng et al.   MOLECULAR CELL

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

(2012) Dan Dominissini et al.   NATURE

One size does not fit all: On how Markov model order dictates performance of genomic sequence analyses

(2012) Leelavati Narlikar et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

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

Initializing the EM algorithm in Gaussian mixture models with an unknown number of components

(2011) Volodymyr Melnykov et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Initializing Partition-Optimization Algorithms

(2008) R. Maitra   IEEE-ACM Transactions on Computational Biology and Bioinformatics

What is the expectation maximization algorithm?

(2008) Chuong B Do et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY