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

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

(2018) Xiaoyong Pan et al.   BIOINFORMATICS

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

A Compendium of RNA-Binding Proteins that Regulate MicroRNA Biogenesis

(2017) Thomas Treiber et al.   MOLECULAR CELL

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

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

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

IPMiner: hidden ncRNA-protein interaction sequential pattern mining with stacked autoencoder for accurate computational prediction

(2016) Xiaoyong Pan et al.   BMC GENOMICS

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications

(2016) Marco Pietrosanto et al.   NUCLEIC ACIDS RESEARCH

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

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

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

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

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures

(2014) Carmen M Livi et al.   BMC BIOINFORMATICS

Identifying mRNA sequence elements for target recognition by human Argonaute proteins

(2014) J. Li et al.   GENOME RESEARCH

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

(2014) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

(2014) Tsukasa Fukunaga et al.   GENOME BIOLOGY

catRAPID omics: a web server for large-scale prediction of protein-RNA interactions

(2013) F. Agostini et al.   BIOINFORMATICS

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

TDP-43 and FUS RNA-binding Proteins Bind Distinct Sets of Cytoplasmic Messenger RNAs and Differently Regulate Their Post-transcriptional Fate in Motoneuron-like Cells

(2012) Claudia Colombrita et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RNA targets of wild-type and mutant FET family proteins

(2011) Jessica I Hoell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data

(2010) Robert C McLeay et al.   BMC BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure

(2010) X. Li et al.   RNA

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

(2010) Hilal Kazan et al.   PLoS Computational Biology

MicroRNAs: Target Recognition and Regulatory Functions

(2009) David P. Bartel   CELL

MEME SUITE: tools for motif discovery and searching

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