NPI-GNN: Predicting ncRNA–protein interactions with deep graph neural networks

Predicting lncRNA–Protein Interactions With miRNAs as Mediators in a Heterogeneous Network Model

(2020) Yuan-Ke Zhou et al.   Frontiers in Genetics

A deep learning model for plant lncRNA-protein interaction prediction with graph attention

(2020) Jael Sanyanda Wekesa et al.   MOLECULAR GENETICS AND GENOMICS

LPI-SKF: Predicting lncRNA-Protein Interactions Using Similarity Kernel Fusions

(2020) Yuan-Ke Zhou et al.   Frontiers in Genetics

deepDR: A network-based deep learning approach to in silico drug repositioning

(2019) Xiangxiang Zeng et al.   BIOINFORMATICS

LPI-BLS: Predicting lncRNA–protein interactions with a broad learning system-based stacked ensemble classifier

(2019) Xiao-Nan Fan et al.   NEUROCOMPUTING

LncADeep: an ab initio lncRNA identification and functional annotation tool based on deep learning

(2018) Cheng Yang et al.   BIOINFORMATICS

The linear neighborhood propagation method for predicting long non-coding RNA–protein interactions

(2018) Wen Zhang et al.   NEUROCOMPUTING

The Bipartite Network Projection Recommended Algorithm for predicting long non-coding RNA–protein interactions

(2018) Qi Zhao et al.   Molecular Therapy-Nucleic Acids

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions

(2018) Wen Zhang et al.   PLoS Computational Biology

Meta-path methods for prioritizing candidate disease miRNAs

(2017) Xuan Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Prediction and Validation of Disease Genes Using HeteSim Scores

(2017) Xiangxiang Zeng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2016) Xiaoyong Pan et al.   BMC GENOMICS

Recommendations for Management of Clinically Significant Drug-Drug Interactions With Statins and Select Agents Used in Patients With Cardiovascular Disease: A Scientific Statement From the American Heart Association

(2016) Barbara S. Wiggins et al.   CIRCULATION

A Bipartite Network-based Method for Prediction of Long Non-coding RNA–protein Interactions

(2016) Mengqu Ge et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2013) Qiongshi Lu et al.   BMC GENOMICS

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Emerging epigenetic mechanisms of long non-coding RNAs

(2013) K. Schaukowitch et al.   NEUROSCIENCE

NPInter v2.0: an updated database of ncRNA interactions

(2013) Jiao Yuan et al.   NUCLEIC ACIDS RESEARCH

Reconstructing dynamic microRNA-regulated interaction networks

(2013) M. H. Schulz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reprint of: The anatomy of a large-scale hypertextual web search engine

(2012) Sergey Brin et al.   Computer Networks

Divergent roles of ALS-linked proteins FUS/TLS and TDP-43 intersect in processing long pre-mRNAs

(2012) Clotilde Lagier-Tourenne et al.   NATURE NEUROSCIENCE

Update on activities at the Universal Protein Resource (UniProt) in 2013

(2012)   NUCLEIC ACIDS RESEARCH

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression

(2011) S. Kishore et al.   Briefings in Functional Genomics

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

NONCODE v3.0: integrative annotation of long noncoding RNAs

(2011) D. Bu et al.   NUCLEIC ACIDS RESEARCH

Long noncoding RNAs and human disease

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

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

(2010) Markus Hafner et al.   CELL

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

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

Long intronic noncoding RNA transcription: Expression noise or expression choice?

(2008) Rodrigo Louro et al.   GENOMICS

The Graph Neural Network Model

(2008) F. Scarselli et al.   IEEE TRANSACTIONS ON NEURAL NETWORKS

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

(2008) Donny D. Licatalosi et al.   NATURE

Endogenous small interfering RNAs in animals

(2008) Katsutomo Okamura et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA-binding proteins in human genetic disease

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

A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli

(2008) Jason Ernst et al.   PLoS Computational Biology