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

iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

PPUS: a web server to predict PUS-specific pseudouridine sites: Table 1.

(2015) Yan-Hui Li et al.   BIOINFORMATICS

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   CELL

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

(2015) Tong Chen et al.   Cell Stem Cell

A majority of m6A residues are in the last exons, allowing the potential for 3′ UTR regulation

(2015) Shengdong Ke et al.   GENES & DEVELOPMENT

Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification

(2015) Caroline Roost et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

N6-methyladenosine marks primary microRNAs for processing

(2015) Claudio R. Alarcón et al.   NATURE

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

N6-methyladenosine-dependent RNA structural switches regulate RNA–protein interactions

(2015) Nian Liu et al.   NATURE

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

(2015) Bastian Linder et al.   NATURE METHODS

m6A mRNA methylation facilitates resolution of naïve pluripotency toward differentiation

(2015) Shay Geula et al.   SCIENCE

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

(2015) Wei Chen et al.   Scientific Reports

High-ResolutionN6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing

(2014) Kai Chen et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Pivotal Regulatory Landscape of RNA Modifications

(2014) Sheng Li et al.   Annual Review of Genomics and Human Genetics

Gene expression regulation mediated through reversible m6A RNA methylation

(2014) Ye Fu et al.   NATURE REVIEWS GENETICS

The dynamic epitranscriptome: N6-methyladenosine and gene expression control

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

MeT-DB: a database of transcriptome methylation in mammalian cells

(2014) Hui Liu 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

hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties

(2013) Zhen Chen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Incorporating key position and amino acid residue features to identify general and species-specific Ubiquitin conjugation sites

(2013) Xiang Chen 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

A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation

(2013) Jianzhao Liu et al.   Nature Chemical Biology

ClinVar: public archive of relationships among sequence variation and human phenotype

(2013) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

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

(2013) N. Liu et al.   RNA

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

MODOMICS: a database of RNA modification pathways—2013 update

(2012) Magdalena A. Machnicka et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

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

Prediction of Ubiquitination Sites by Using the Composition of k-Spaced Amino Acid Pairs

(2011) Zhen Chen et al.   PLoS One

Cascleave: towards more accurate prediction of caspase substrate cleavage sites

(2010) Jiangning Song et al.   BIOINFORMATICS

TargetSpy: a supervised machine learning approach for microRNA target prediction

(2010) Martin Sturm et al.   BMC BIOINFORMATICS

Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites

(2010) Jianjiong Gao et al.   MOLECULAR & CELLULAR PROTEOMICS

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

Predictive learning via rule ensembles

(2008) Jerome H. Friedman et al.   Annals of Applied Statistics