RBPsuite: RNA-protein binding sites prediction suite based on deep learning

Recent methodology progress of deep learning for RNA–protein interaction prediction

(2019) Xiaoyong Pan et al.   Wiley Interdisciplinary Reviews-RNA

CRIP: predicting circRNA-RBP interaction sites using a codon-based encoding and hybrid deep neural networks

(2019) Kaiming Zhang et al.   RNA

pysster: classification of biological sequences by learning sequence and structure motifs with convolutional neural networks

(2018) Stefan Budach et al.   BIOINFORMATICS

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

(2018) Xiaoyong Pan 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

beRBP: binding estimation for human RNA-binding proteins

(2018) Hui Yu et al.   NUCLEIC ACIDS RESEARCH

Identifying RNA-binding proteins using multi-label deep learning

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

A combined sequence and structure based method for discovering enriched motifs in RNA from in vivo binding data

(2017) Maya Polishchuk et al.   METHODS

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

(2016) Martin Stražar et al.   BIOINFORMATICS

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A census of human RNA-binding proteins

(2014) Stefanie Gerstberger et al.   NATURE REVIEWS GENETICS

GraphProt: modeling binding preferences of RNA-binding proteins

(2014) Daniel Maticzka et al.   GENOME BIOLOGY

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

RNA-binding proteins in neurodegenerative disease: TDP-43 and beyond

(2011) Keith A. Hanson et al.   Wiley Interdisciplinary Reviews-RNA

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS