Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA

O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique

(2018) Cangzhi Jia et al.   BIOINFORMATICS

Prediction of enhancer-promoter interactions via natural language processing

(2018) Wanwen Zeng et al.   BMC GENOMICS

70ProPred: a predictor for discovering sigma70 promoters based on combining multiple features

(2018) Wenying He et al.   BMC Systems Biology

R-2HG Exhibits Anti-tumor Activity by Targeting FTO/m 6 A/MYC/CEBPA Signaling

(2018) Rui Su et al.   CELL

ProtDet-CCH: Protein remote homology detection by combining Long Short-Term Memory and ranking methods

(2018) Bin Liu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Prediction of human protein subcellular localization using deep learning

(2018) Leyi Wei et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Integration of deep feature representations and handcrafted features to improve the prediction of N 6 -methyladenosine sites

(2018) Leyi Wei et al.   NEUROCOMPUTING

RFAthM6A: a new tool for predicting m6A sites in Arabidopsis thaliana

(2018) Xiaofeng Wang et al.   PLANT MOLECULAR BIOLOGY

METTL3-mediated m6A modification is required for cerebellar development

(2018) Chen-Xin Wang et al.   PLOS BIOLOGY

N6-methyladenosine modification and the YTHDF2 reader protein play cell type specific roles in lytic viral gene expression during Kaposi's sarcoma-associated herpesvirus infection

(2018) Charles R. Hesser et al.   PLoS Pathogens

iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites

(2018) Wei Chen et al.   Molecular Therapy-Nucleic Acids

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species

(2018) Leyi Wei et al.   BIOINFORMATICS

Deep learning in omics: a survey and guideline

(2018) Zhiqiang Zhang et al.   Briefings in Functional Genomics

Survey of Machine Learning Techniques in Drug Discovery

(2018) Natalie Stephenson et al.   CURRENT DRUG METABOLISM

IDP–CRF: Intrinsically Disordered Protein/Region Identification Based on Conditional Random Fields

(2018) Yumeng Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

PhosPred-RF: A Novel Sequence-Based Predictor for Phosphorylation Sites Using Sequential Information Only

(2017) Leyi Wei et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Fast prediction of protein methylation sites using a sequence-based feature selection technique

(2017) Leyi Wei et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

ProLanGO: Protein Function Prediction Using Neural Machine Translation Based on a Recurrent Neural Network

(2017) Renzhi Cao et al.   MOLECULES

Deep learning of the splicing (epi)genetic code reveals a novel candidate mechanism linking histone modifications to ESC fate decision

(2017) Yungang Xu 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

m 6 A RNA Methylation Regulates the Self-Renewal and Tumorigenesis of Glioblastoma Stem Cells

(2017) Qi Cui et al.   Cell Reports

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

iRSpot-EL: identify recombination spots with an ensemble learning approach

(2016) Bin Liu et al.   BIOINFORMATICS

Dynamics of Human and Viral RNA Methylation during Zika Virus Infection

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

N6 -Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection

(2016) Nandan S. Gokhale 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

Identifying N 6-methyladenosine sites in the Arabidopsis thaliana transcriptome

(2016) Wei Chen et al.   MOLECULAR GENETICS AND GENOMICS

Deep learning for computational biology

(2016) Christof Angermueller et al.   Molecular Systems Biology

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

Word2Vec

(2016) KENNETH WARD CHURCH   Natural Language Engineering

Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells

(2016) Gianluigi Lichinchi et al.   Nature Microbiology

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

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

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

RNAN6-methyladenosine methylation in post-transcriptional gene expression regulation

(2015) Yanan Yue et al.   GENES & DEVELOPMENT

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

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

(2015) Bastian Linder et al.   NATURE METHODS

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

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

nDNA-prot: identification of DNA-binding proteins based on unbalanced classification

(2014) Li Song et al.   BMC BIOINFORMATICS

Transcriptome-wide N6-methyladenosine profiling of rice callus and leaf reveals the presence of tissue-specific competitors involved in selective mRNA modification

(2014) Yuli Li et al.   RNA Biology

Unique features of the m6A methylome in Arabidopsis thaliana

(2014) Guan-Zheng Luo et al.   Nature Communications

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

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

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