A Convolution Neural Network-based computational model to identify the occurrence sites of various RNA modifications by fusing varied features

Prediction of N6-methyladenosine sites using convolution neural network model based on distributed feature representations

(2020) Muhammad Tahir et al.   NEURAL NETWORKS

kDeepBind: Prediction of RNA-Proteins binding sites using convolution neural network and k-gram features

(2020) Muhammad Tahir et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach

(2019) Kunqi Chen et al.   NUCLEIC ACIDS RESEARCH

iSS-CNN: Identifying splicing sites using convolution neural network

(2019) Hilal Tayara et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

iPseU-CNN: Identifying RNA Pseudouridine Sites Using Convolutional Neural Networks

(2019) Muhammad Tahir et al.   Molecular Therapy-Nucleic Acids

iN6-Methyl (5-step): Identifying RNA N6-methyladenosine sites using deep learning mode via Chou's 5-step rules and Chou's general PseKNC

(2019) Iman Nazari et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Accurate RNA 5-methylcytosine site prediction based on heuristic physical-chemical properties reduction and classifier ensemble

(2018) Ming Zhang et al.   ANALYTICAL BIOCHEMISTRY

Convolutional neural networks for classification of alignments of non-coding RNA sequences

(2018) Genta Aoki et al.   BIOINFORMATICS

Prediction of RNA-protein sequence and structure binding preferences using deep convolutional and recurrent neural networks

(2018) Xiaoyong Pan et al.   BMC GENOMICS

Recent Trends in Deep Learning Based Natural Language Processing [Review Article]

(2018) Tom Young et al.   IEEE Computational Intelligence Magazine

Transcriptome-Wide Annotation of m5C RNA Modifications Using Machine Learning

(2018) Jie Song et al.   Frontiers in Plant Science

DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning

(2018) Yiqian Zhang et al.   BMC BIOINFORMATICS

M6AMRFS: Robust Prediction of N6-Methyladenosine Sites With Sequence-Based Features in Multiple Species

(2018) Xiaoli Qiang et al.   Frontiers in Genetics

Canonical correlation analysis networks for two-view image recognition

(2017) Xinghao Yang et al.   INFORMATION SCIENCES

Evaluating deep learning architectures for Speech Emotion Recognition

(2017) Haytham M. Fayek et al.   NEURAL NETWORKS

A novel cross-modal hashing algorithm based on multimodal deep learning

(2017) Wen Qu et al.   Science China-Information Sciences

Pse-Analysis: a python package for DNA/RNA and protein/ peptide sequence analysis based on pseudo components and kernel methods

(2017) Bin Liu et al.   Oncotarget

iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC

(2017) Pengmian Feng et al.   Molecular Therapy-Nucleic Acids

Predicting antimicrobial peptides with improved accuracy by incorporating the compositional, physico-chemical and structural features into Chou’s general PseAAC

(2017) Prabina Kumar Meher et al.   Scientific Reports

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

(2016) Zi Liu et al.   ANALYTICAL BIOCHEMISTRY

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

(2016) Bin Liu et al.   BIOINFORMATICS

Identifying 2′-O-methylationation sites by integrating nucleotide chemical properties and nucleotide compositions

(2016) Wei Chen et al.   GENOMICS

pSuc-Lys: Predict lysine succinylation sites in proteins with PseAAC and ensemble random forest approach

(2016) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

Identifying RNA 5-methylcytosine sites via pseudo nucleotide compositions

(2016) Pengmian Feng et al.   Molecular BioSystems

iNuc-STNC: a sequence-based predictor for identification of nucleosome positioning in genomes by extending the concept of SAAC and Chou's PseAAC

(2016) Muhammad Tahir et al.   Molecular BioSystems

mRNA modifications: Dynamic regulators of gene expression?

(2016) Thomas Philipp Hoernes et al.   RNA Biology

iRNA-AI: identifying the adenosine to inosine editing sites in RNA sequences

(2016) Wei Chen et al.   Oncotarget

RAMPred: identifying the N1-methyladenosine sites in eukaryotic transcriptomes

(2016) Wei Chen et al.   Scientific Reports

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

iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach

(2015) Xuan Xiao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Impacts of Bioinformatics to Medicinal Chemistry

(2015) Kuo-Chen Chou   Medicinal Chemistry

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

(2015) Wei Chen et al.   Scientific Reports

iTIS-PseTNC: A sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition

(2014) Shou-Hui Guo et al.   BIOINFORMATICS

Transcriptome-wide target profiling of RNA cytosine methyltransferases using the mechanism-based enrichment procedure Aza-IP

(2014) Vahid Khoddami et al.   Nature Protocols

The dynamic epitranscriptome: N6-methyladenosine and gene expression control

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

Sequence Based Prediction of DNA-Binding Proteins Based on Hybrid Feature Selection Using Random Forest and Gaussian Naïve Bayes

(2014) Wangchao Lou et al.   PLoS One

Internal mRNA Methylation Finally Finds Functions

(2014) T. W. Nilsen   SCIENCE

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

(2013) Schraga Schwartz et al.   CELL

iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition

(2013) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Deep Neural Networks for Acoustic Modeling in Speech Recognition: The Shared Views of Four Research Groups

(2012) Geoffrey Hinton et al.   IEEE SIGNAL PROCESSING MAGAZINE

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

(2012) Dan Dominissini et al.   NATURE

Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA

(2012) Christian Peifer et al.   NUCLEIC ACIDS RESEARCH

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA

(2012) Jeffrey E. Squires et al.   NUCLEIC ACIDS RESEARCH

MODOMICS: a database of RNA modification pathways—2013 update

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

Some remarks on protein attribute prediction and pseudo amino acid composition

(2010) Kuo-Chen Chou   JOURNAL OF THEORETICAL BIOLOGY