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

OUGENE: a disease associated over-expressed and under-expressed gene database

(2016) Xiaoyong Pan et al.   Science Bulletin

A global view of network of lncRNAs and their binding proteins

(2015) Desi Shang et al.   Molecular BioSystems

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

Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

(2015) Z. Miao et al.   NUCLEIC ACIDS RESEARCH

RPI-Pred: predicting ncRNA-protein interaction using sequence and structural information

(2015) V. Suresh et al.   NUCLEIC ACIDS RESEARCH

Transcriptomic landscape of lncRNAs in inflammatory bowel disease

(2015) Aashiq H Mirza et al.   Genome Medicine

Computationally predicting protein-RNA interactions using only positive and unlabeled examples

(2015) Zhanzhan Cheng et al.   Journal of Bioinformatics and Computational Biology

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

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

(2014) Carmen M Livi et al.   BMC BIOINFORMATICS

High-throughput characterization of protein-RNA interactions

(2014) K. B. Cook et al.   Briefings in Functional Genomics

Predicting protein–RNA interaction amino acids using random forest based on submodularity subset selection

(2014) Xiaoyong Pan et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Methods for comprehensive experimental identification of RNA-protein interactions

(2014) Colleen A McHugh et al.   GENOME BIOLOGY

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

(2013) F. Agostini et al.   BIOINFORMATICS

Computational prediction of associations between long non-coding RNAs and proteins

(2013) Qiongshi Lu et al.   BMC GENOMICS

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

NPInter v2.0: an updated database of ncRNA interactions

(2013) Jiao Yuan et al.   NUCLEIC ACIDS RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

De novo prediction of RNA–protein interactions from sequence information

(2012) Ying Wang et al.   Molecular BioSystems

ViennaRNA Package 2.0

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

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Towards better accuracy for missing value estimation of epistatic miniarray profiling data by a novel ensemble approach

(2011) Xiao-Yong Pan et al.   GENOMICS

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

In silico characterization and prediction of global protein–mRNA interactions in yeast

(2011) Vera Pancaldi et al.   NUCLEIC ACIDS RESEARCH

Diverse roles of host RNA binding proteins in RNA virus replication

(2011) Zhenghe Li et al.   RNA Biology

Long noncoding RNAs and human disease

(2011) Orly Wapinski et al.   TRENDS IN CELL BIOLOGY

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

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

(2010) Markus Hafner et al.   CELL

Signatures of RNA binding proteins globally coupled to effective microRNA target sites

(2010) A. Jacobsen et al.   GENOME RESEARCH

Large-Scale Prediction of Human Protein−Protein Interactions from Amino Acid Sequence Based on Latent Topic Features

(2010) Xiao-Yong Pan et al.   JOURNAL OF PROTEOME RESEARCH

Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

(2010) Dimitrios G Zisoulis et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

(2010) M. Khorshid et al.   NUCLEIC ACIDS RESEARCH

PRIDB: a protein-RNA interface database

(2010) B. A. Lewis et al.   NUCLEIC ACIDS RESEARCH

Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

(2009) Debashish Ray et al.   NATURE BIOTECHNOLOGY