Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods

RNA N6-methyladenosine methyltransferase-like 3 promotes liver cancer progression through YTHDF2-dependent posttranscriptional silencing of SOCS2

(2018) Mengnuo Chen et al.   HEPATOLOGY

m6ASNP: a tool for annotating genetic variants by m6A function

(2018) Shuai Jiang et al.   GigaScience

Glucose is involved in the dynamic regulation of m6A in patients with type 2 diabetes

(2018) Ying Yang et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

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

(2017) Hui Liu et al.   NUCLEIC ACIDS RESEARCH

Reduced m6A mRNA methylation is correlated with the progression of human cervical cancer

(2017) Xiuli Wang et al.   Oncotarget

Emerging links between m6A and misregulated mRNA methylation in cancer

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

Viral and cellular N6-methyladenosine and N6,2′-O-dimethyladenosine epitranscriptomes in the KSHV life cycle

(2017) Brandon Tan et al.   Nature Microbiology

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

(2017) Wei Chen et al.   Scientific Reports

Identifying N6-methyladenosine sites using multi-interval nucleotide pair position specificity and support vector machine

(2017) Pengwei Xing et al.   Scientific Reports

pRNAm-PC: Predicting N6-methyladenosine sites in RNA sequences via physical–chemical properties

(2016) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

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

(2016) Xiaodong Cui et al.   BIOINFORMATICS

Gene expression inference with deep learning

(2016) Yifei Chen et al.   BIOINFORMATICS

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

(2016) Gianluigi Lichinchi et al.   Cell Host & Microbe

Posttranscriptional m 6 A Editing of HIV-1 mRNAs Enhances Viral Gene Expression

(2016) Edward M. Kennedy et al.   Cell Host & Microbe

MethyRNA: a web server for identification of N6-methyladenosine sites

(2016) Wei Chen et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

AthMethPre: a web server for the prediction and query of mRNA m6A sites in Arabidopsis thaliana

(2016) Shunian Xiang et al.   Molecular BioSystems

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

(2016) Shuibin Lin et al.   MOLECULAR CELL

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

(2016) Yuan Zhou et al.   NUCLEIC ACIDS RESEARCH

RNAMethPre: A Web Server for the Prediction and Query of mRNA m6A Sites

(2016) Shunian Xiang et al.   PLoS One

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

m6A-Driver: Identifying Context-Specific mRNA m6A Methylation-Driven Gene Interaction Networks

(2016) Song-Yao Zhang et al.   PLoS Computational Biology

N6-methyladenosine of HIV-1 RNA regulates viral infection and HIV-1 Gag protein expression

(2016) Nagaraja Tirumuru et al.   eLife

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

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

N6-methyladenosine Modulates Messenger RNA Translation Efficiency

(2015) Xiao Wang et al.   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

Dynamic m6A mRNA methylation directs translational control of heat shock response

(2015) Jun Zhou et al.   NATURE

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

(2015) Bastian Linder et al.   NATURE METHODS

RNA epigenetics

(2015) Nian Liu et al.   Translational Research

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

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

(2014) Guangchuang Yu et al.   BIOINFORMATICS

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

(2014) Xu Zhao et al.   CELL RESEARCH

Mammalian WTAP is a regulatory subunit of the RNA N6-methyladenosine methyltransferase

(2014) Xiao-Li Ping et al.   CELL RESEARCH

WTAP is a novel oncogenic protein in acute myeloid leukemia

(2014) H Bansal et al.   LEUKEMIA

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

(2014) Jia Meng et al.   METHODS

N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells

(2014) Yang Wang et al.   NATURE CELL BIOLOGY

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

Exome-based analysis for RNA epigenome sequencing data

(2013) Jia Meng et al.   BIOINFORMATICS

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

(2013) Jean-Michel Fustin et al.   CELL

Evaluating Genome-Wide Association Study-Identified Breast Cancer Risk Variants in African-American Women

(2013) Jirong Long et al.   PLoS One

Interpretation of Genomic Variants Using a Unified Biological Network Approach

(2013) Ekta Khurana et al.   PLoS Computational Biology

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The role of the fat mass and obesity associated gene (FTO) in breast cancer risk

(2011) Virginia Kaklamani et al.   BMC Medical Genetics

Next-generation sequencing to generate interactome datasets

(2011) Haiyuan Yu et al.   NATURE METHODS

Disease Ontology: a backbone for disease semantic integration

(2011) L. M. Schriml et al.   NUCLEIC ACIDS RESEARCH

Genome-wide inferring gene–phenotype relationship by walking on the heterogeneous network

(2010) Yongjin Li et al.   BIOINFORMATICS

iRefIndex: A consolidated protein interaction database with provenance

(2008) Sabry Razick et al.   BMC BIOINFORMATICS

Post-transcriptional Regulation of Neuro-oncological Ventral Antigen 1 by the Neuronal RNA-binding Proteins ELAV

(2008) Antonia Ratti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY