A Hybrid Prediction Method for Plant lncRNA-Protein Interaction

New Insights into the Interplay between Non-Coding RNAs and RNA-Binding Protein HnRNPK in Regulating Cellular Functions

(2019) Yongjie Xu et al.   Cells

A High Efficient Biological Language Model for Predicting Protein–Protein Interactions

(2019) Yanbin Wang et al.   Cells

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

(2018) Cheng Yang et al.   BIOINFORMATICS

The lncLocator: a subcellular localization predictor for long non-coding RNAs based on a stacked ensemble classifier

(2018) Zhen Cao 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

OUP accepted manuscript

(2018)   BRIEFINGS IN BIOINFORMATICS

A deep learning-based multi-model ensemble method for cancer prediction

(2018) Yawen Xiao et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

HLPI-Ensemble: Prediction of human lncRNA-protein interactions based on ensemble strategy

(2018) Huan Hu et al.   RNA Biology

A Deep Learning Framework for Robust and Accurate Prediction of ncRNA-Protein Interactions Using Evolutionary Information

(2018) Hai-Cheng Yi et al.   Molecular Therapy-Nucleic Acids

IRWNRLPI: Integrating Random Walk and Neighborhood Regularized Logistic Matrix Factorization for lncRNA-Protein Interaction Prediction

(2018) Qi Zhao et al.   Frontiers in Genetics

A Stacked Autoencoder-Based Deep Neural Network for Achieving Gearbox Fault Diagnosis

(2018) Guifang Liu et al.   MATHEMATICAL PROBLEMS IN ENGINEERING

Enhanced Prediction of Hot Spots at Protein-Protein Interfaces Using Extreme Gradient Boosting

(2018) Hao Wang et al.   Scientific Reports

High-Performance Deep Neural Network-Based Tomato Plant Diseases and Pests Diagnosis System With Refinement Filter Bank

(2018) Alvaro F. Fuentes et al.   Frontiers in Plant Science

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

(2018) Wen Zhang et al.   PLoS Computational Biology

Deep Learning-Based Multi-Omics Data Integration Reveals Two Prognostic Subtypes in High-Risk Neuroblastoma

(2018) Li Zhang et al.   Frontiers in Genetics

Accurate Prediction of ncRNA-Protein Interactions From the Integration of Sequence and Evolutionary Information

(2018) Zhao-Hui Zhan et al.   Frontiers in Genetics

Group sparse autoencoder

(2017) Anush Sankaran et al.   IMAGE AND VISION COMPUTING

LPI-ETSLP: lncRNA–protein interaction prediction using eigenvalue transformation-based semi-supervised link prediction

(2017) Huan Hu et al.   Molecular BioSystems

Detection of nucleic acid–protein interactions in plant leaves using fluorescence lifetime imaging microscopy

(2017) Laurent Camborde et al.   Nature Protocols

PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea

(2017) Urminder Singh et al.   NUCLEIC ACIDS RESEARCH

LPI-NRLMF: lncRNA-protein interaction prediction by neighborhood regularized logistic matrix factorization

(2017) Hongsheng Liu et al.   Oncotarget

Modular function of long noncoding RNA, COLDAIR, in the vernalization response

(2017) Dong-Hwan Kim et al.   PLoS Genetics

Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome

(2016) Kaori Kashi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

RBPPred: predicting RNA-binding proteins from sequence using SVM

(2016) Xiaoli Zhang 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

Prediction of protein-RNA interactions using sequence and structure descriptors

(2016) Zhi-Ping Liu et al.   NEUROCOMPUTING

Deep Learning of Part-Based Representation of Data Using Sparse Autoencoders With Nonnegativity Constraints

(2016) Ehsan Hosseini-Asl et al.   IEEE Transactions on Neural Networks and Learning Systems

Using Deep Learning for Image-Based Plant Disease Detection

(2016) Sharada P. Mohanty et al.   Frontiers in Plant Science

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

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

Genome-Wide Analysis of Long Noncoding RNAs and Their Responses to Drought Stress in Cotton (Gossypium hirsutum L.)

(2016) Xuke Lu et al.   PLoS One

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

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

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

Predicting Long Noncoding RNA and Protein Interactions Using Heterogeneous Network Model

(2015) Ao Li et al.   Biomed Research International

Long Non-coding RNAs and Their Biological Roles in Plants

(2015) Xue Liu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Coming of age: orphan genes in plants

(2014) Zebulun W. Arendsee et al.   TRENDS IN PLANT SCIENCE

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

(2013) Qiongshi Lu et al.   BMC GENOMICS

De novo prediction of RNA–protein interactions from sequence information

(2012) Ying Wang et al.   Molecular BioSystems

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS