Graph neural representational learning of RNA secondary structures for predicting RNA-protein interactions

Deep neural networks for interpreting RNA-binding protein target preferences

(2020) Mahsa Ghanbari et al.   GENOME RESEARCH

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

RNAcompete-S: Combined RNA sequence/structure preferences for RNA binding proteins derived from a single-step in vitro selection

(2017) Kate B. Cook et al.   METHODS

The MEME Suite

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

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

(2015) Sai Zhang et al.   NUCLEIC ACIDS RESEARCH

Predicting RNA 3D structure using a coarse-grain helix-centered model

(2015) Peter Kerpedjiev et al.   RNA

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

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

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

doRiNA: a database of RNA interactions in post-transcriptional regulation

(2011) Gerd Anders et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Markus Hafner et al.   CELL

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

(2010) Julian König et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2010) Hilal Kazan et al.   PLoS Computational Biology

Genome-wide Analysis of PTB-RNA Interactions Reveals a Strategy Used by the General Splicing Repressor to Modulate Exon Inclusion or Skipping

(2009) Yuanchao Xue et al.   MOLECULAR CELL

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

(2008) Donny D. Licatalosi et al.   NATURE

RNA-binding proteins in human genetic disease

(2008) Kiven E. Lukong et al.   TRENDS IN GENETICS