Refined RIP-seq protocol for epitranscriptome analysis with low input materials

RNA m6A methylation regulates the ultraviolet-induced DNA damage response

(2017) Yang Xiang et al.   NATURE

RNA modifications and structures cooperate to guide RNA–protein interactions

(2017) Cole J.T. Lewis et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

MODOMICS: a database of RNA modification pathways. 2017 update

(2017) Pietro Boccaletto et al.   NUCLEIC ACIDS RESEARCH

m 6 A in mRNA: An Ancient Mechanism for Fine-Tuning Gene Expression

(2017) Jean-Yves Roignant et al.   TRENDS IN GENETICS

Emerging links between m6A and misregulated mRNA methylation in cancer

(2017) Samie R. Jaffrey et al.   Genome Medicine

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

(2016) Xiaodong Cui et al.   BIOINFORMATICS

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Wen Xiao et al.   MOLECULAR CELL

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

The dynamic N1-methyladenosine methylome in eukaryotic messenger RNA

(2016) Dan Dominissini et al.   NATURE

Post-transcriptional gene regulation by mRNA modifications

(2016) Boxuan Simen Zhao et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

N6-methyladenosine–encoded epitranscriptomics

(2016) Nian Liu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m6A-demethylation of NANOG mRNA

(2016) Chuanzhao Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

N6-methyladenosine–encoded epitranscriptomics

(2016) Nian Liu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2015) Xiaodong Cui et al.   BMC GENOMICS

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

RNAN6-methyladenosine methylation in post-transcriptional gene expression regulation

(2015) Yanan Yue et al.   GENES & DEVELOPMENT

N6-methyladenosine marks primary microRNAs for processing

(2015) Claudio R. Alarcón et al.   NATURE

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

Widespread occurrence ofN6-methyladenosine in bacterial mRNA

(2015) Xin Deng et al.   NUCLEIC ACIDS RESEARCH

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

(2014) N. Bonhoure et al.   GENOME RESEARCH

Methyltransferases modulate RNA stability in embryonic stem cells

(2014) Shuibin Lin et al.   NATURE CELL BIOLOGY

Proteomic profiles of human lung adeno and squamous cell carcinoma using super-SILAC and label-free quantification approaches

(2014) Wen Zhang et al.   PROTEOMICS

Integrated Omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact

(2014) Lei Li et al.   Nature Communications

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

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

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

(2013) Schraga Schwartz et al.   CELL

RNA-Methylation-Dependent RNA Processing Controls the Speed of the Circadian Clock

(2013) Jean-Michel Fustin et al.   CELL

N6-methyladenosine-dependent regulation of messenger RNA stability

(2013) Xiao Wang et al.   NATURE

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

(2013) Dan Dominissini et al.   Nature Protocols

Probing N6-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA

(2013) N. Liu et al.   RNA

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

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

(2012) Dan Dominissini et al.   NATURE

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Effect of 1-methyladenine on thermodynamic stabilities of double-helical DNA structures

(2009) Hao Yang et al.   FEBS LETTERS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY