LPI-HyADBS: a hybrid framework for lncRNA-protein interaction prediction integrating feature selection and classification

Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm

(2021) Pedro M. Martins et al.   BMC BIOINFORMATICS

Two-stage convolutional encoder-decoder network to improve the performance and reliability of deep learning models for topology optimization

(2021) Gorkem Can Ates et al.   STRUCTURAL AND MULTIDISCIPLINARY OPTIMIZATION

Ensemble Deep Learning Based on Multi-level Information Enhancement and Greedy Fuzzy Decision for Plant miRNA–lncRNA Interaction Prediction

(2021) Qiang Kang et al.   Interdisciplinary Sciences-Computational Life Sciences

Using Network Distance Analysis to Predict lncRNA–miRNA Interactions

(2021) Li Zhang et al.   Interdisciplinary Sciences-Computational Life Sciences

Classification of Breast Cancer and Breast Neoplasm Scenarios Based on Machine Learning and Sequence Features from lncRNAs–miRNAs-Diseases Associations

(2021) Juan Gutiérrez-Cárdenas et al.   Interdisciplinary Sciences-Computational Life Sciences

Multilabel Feature Selection With Constrained Latent Structure Shared Term

(2021) Wanfu Gao et al.   IEEE Transactions on Neural Networks and Learning Systems

An efficient XGBoost–DNN-based classification model for network intrusion detection system

(2020) Preethi Devan et al.   NEURAL COMPUTING & APPLICATIONS

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

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

Probing lncRNA–Protein Interactions: Data Repositories, Models, and Algorithms

(2020) Lihong Peng et al.   Frontiers in Genetics

LPI-CNNCP: Prediction of lncRNA-protein interactions by using convolutional neural network with the copy-padding trick

(2020) Shao-Wu Zhang et al.   ANALYTICAL BIOCHEMISTRY

AC-Caps: Attention Based Capsule Network for Predicting RBP Binding Sites of LncRNA

(2020) Jinmiao Song et al.   Interdisciplinary Sciences-Computational Life Sciences

Multi-feature fusion for deep learning to predict plant lncRNA-protein interaction

(2020) Jael Sanyanda Wekesa et al.   GENOMICS

lncRNA ZNF667‐AS1 (NR_036521.1) inhibits the progression of colorectal cancer via regulating ANK2/JAK2 expression

(2020) Lin Zhuang et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Comprehensive Analysis of Long Non-coding RNA-Associated Competing Endogenous RNA Network in Duchenne Muscular Dystrophy

(2020) Xiaoxue Xu et al.   Interdisciplinary Sciences-Computational Life Sciences

Deciphering LncRNA–protein interactions using docking complexes

(2020) Renuka Suravajhala et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Long Non-coding RNAs RN7SK and GAS5 Regulate Macrophage Polarization and Innate Immune Responses

(2020) Imran Ahmad et al.   Frontiers in Immunology

ICLRBBN: a tool for accurate prediction of potential lncRNA disease associations

(2020) Yuqi Wang et al.   Molecular Therapy-Nucleic Acids

Rn7SK small nuclear RNA is involved in cellular senescence

(2019) Maryam Musavi et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Multivariate Information Fusion With Fast Kernel Learning to Kernel Ridge Regression in Predicting LncRNA-Protein Interactions

(2019) Cong Shen et al.   Frontiers in Genetics

Methods to study RNA–protein interactions

(2019) Muthukumar Ramanathan et al.   NATURE METHODS

PlncRNADB: a repository of plant lncRNAs and lncRNA-RBP protein interactions

(2019) Youhuang Bai et al.   Current Bioinformatics

PyFeat: A Python-based Effective Feature Generation Tool for DNA, RNA, and Protein Sequences

(2019) Rafsanjani Muhammod et al.   BIOINFORMATICS

Ensemble of decision tree reveals potential miRNA-disease associations

(2019) Xing Chen et al.   PLoS Computational Biology

Long non‐coding RNA ZNF667‐AS1 reduces tumor invasion and metastasis in cervical cancer by counteracting microRNA‐93‐3p‐dependent PEG3 downregulation

(2019) Yong‐Jie Li et al.   Molecular Oncology

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

(2019) Xiao-Nan Fan et al.   NEUROCOMPUTING

Predicting lncRNA–miRNA interactions based on logistic matrix factorization with neighborhood regularized

(2019) Hongsheng Liu et al.   KNOWLEDGE-BASED SYSTEMS

Plant miRNA–lncRNA Interaction Prediction with the Ensemble of CNN and IndRNN

(2019) Peng Zhang et al.   Interdisciplinary Sciences-Computational Life Sciences

Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data

(2018) Anna Marco-Ramell et al.   BMC BIOINFORMATICS

Comparative genome and phenotypic analysis of three Clostridioides difficile strains isolated from a single patient provide insight into multiple infection of C. difficile

(2018) Uwe Groß et al.   BMC GENOMICS

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

(2018) Wen Zhang et al.   NEUROCOMPUTING

Class-specific mutual information variation for feature selection

(2018) Wanfu Gao et al.   PATTERN RECOGNITION

EGBMMDA: Extreme Gradient Boosting Machine for MiRNA-Disease Association prediction

(2018) Xing Chen et al.   Cell Death & Disease

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

(2018) Qi Zhao et al.   Frontiers in Genetics

Computational models for lncRNA function prediction and functional similarity calculation

(2018) Xing Chen et al.   Briefings in Functional Genomics

MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction

(2018) Xing Chen et al.   PLoS Computational Biology

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver

(2018) Arun Prasad Pandurangan 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

Rn7SK small nuclear RNA is involved in neuronal differentiation

(2017) Zahra Bazi et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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

(2017) Huan Hu et al.   Molecular BioSystems

A survey of deep neural network architectures and their applications

(2017) Weibo Liu et al.   NEUROCOMPUTING

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

(2017) Hongsheng Liu et al.   Oncotarget

Text-Attentional Convolutional Neural Network for Scene Text Detection

(2016) Tong He et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

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

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

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

(2016) Valentina Cappello et al.   Scientific Reports

Revealing protein–lncRNA interaction

(2015) Fabrizio Ferrè et al.   BRIEFINGS IN BIOINFORMATICS

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

Learning Nonlinear Functions Using Regularized Greedy Forest

(2013) Rie Johnson et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

NPInter v2.0: an updated database of ncRNA interactions

(2013) Jiao Yuan et al.   NUCLEIC ACIDS RESEARCH

NONCODEv4: exploring the world of long non-coding RNA genes

(2013) Chaoyong Xie et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of RNA–protein interactions from sequence information

(2012) Ying Wang et al.   Molecular BioSystems

Flaws in evaluation schemes for pair-input computational predictions

(2012) Yungki Park et al.   NATURE METHODS

Predicting RNA-Protein Interactions Using Only Sequence Information

(2011) Usha K Muppirala et al.   BMC BIOINFORMATICS