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

Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks

(2018) Xiaoyong Pan et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   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

A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties

(2018) Gaofeng Pan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network

(2018) Xiaoyong Pan et al.   NEUROCOMPUTING

Vehicle Detection and Counting in High-Resolution Aerial Images Using Convolutional Regression Neural Network

(2018) Hilal Tayara et al.   IEEE Access

Identifying RNA-binding proteins using multi-label deep learning

(2018) Xiaoyong Pan et al.   Science China-Information Sciences

Object Detection in Very High-Resolution Aerial Images Using One-Stage Densely Connected Feature Pyramid Network

(2018) Hilal Tayara et al.   SENSORS

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

(2016) Martin Stražar et al.   BIOINFORMATICS

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

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

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Revealing protein–lncRNA interaction

(2015) Fabrizio Ferrè et al.   BRIEFINGS IN BIOINFORMATICS

In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces

(2015) Zhonghua Wu et al.   FEBS LETTERS

Deep learning

(2015) Yann LeCun et al.   NATURE

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

A deep learning framework for modeling structural features of RNA-binding protein targets

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

DoRiNA 2.0—upgrading the doRiNA database of RNA interactions in post-transcriptional regulation

(2014) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

Transcriptome-wide identification of RNA binding sites by CLIP-seq

(2013) Valentine Murigneux et al.   METHODS

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

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

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins

(2010) Hilal Kazan et al.   PLoS Computational Biology

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH