RLFDDA: a meta-path based graph representation learning model for drug–disease association prediction

Hierarchical graph attention network for miRNA-disease association prediction

(2022) Zhengwei Li et al.   MOLECULAR THERAPY

iGRLCDA: identifying circRNA–disease association based on graph representation learning

(2022) Han-Yuan Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Attention-based Knowledge Graph Representation Learning for Predicting Drug-drug Interactions

(2022) Xiaorui Su et al.   BRIEFINGS IN BIOINFORMATICS

Identification of miRNA–disease associations via deep forest ensemble learning based on autoencoder

(2022) Wei Liu et al.   BRIEFINGS IN BIOINFORMATICS

Multi-view heterogeneous molecular network representation learning for protein–protein interaction prediction

(2022) Xiao-Rui Su et al.   BMC BIOINFORMATICS

A deep learning method for predicting metabolite–disease associations via graph neural network

(2022) Feiyue Sun et al.   BRIEFINGS IN BIOINFORMATICS

PPISB: A Novel Network-Based Algorithm of Predicting Protein-Protein Interactions With Mixed Membership Stochastic Blockmodel

(2022) Xiaojuan Wang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

A survey on computational models for predicting protein–protein interactions

(2021) Lun Hu et al.   BRIEFINGS IN BIOINFORMATICS

MGRL: Predicting Drug-Disease Associations Based on Multi-Graph Representation Learning

(2021) Bo-Wei Zhao et al.   Frontiers in Genetics

A Novel Method to Predict Drug-Target Interactions Based on Large-Scale Graph Representation Learning

(2021) Bo-Wei Zhao et al.   Cancers

Circular RNAs and complex diseases: from experimental results to computational models

(2021) Chun-Chun Wang et al.   BRIEFINGS IN BIOINFORMATICS

Inferring Gene Regulatory Networks Using the Improved Markov Blanket Discovery Algorithm

(2021) Wei Liu et al.   Interdisciplinary Sciences-Computational Life Sciences

SANE: A sequence combined attentive network embedding model for COVID-19 drug repositioning

(2021) Xiaorui Su et al.   APPLIED SOFT COMPUTING

A deep learning method for repurposing antiviral drugs against new viruses via multi-view nonnegative matrix factorization and its application to SARS-CoV-2

(2021) Xiaorui Su et al.   BRIEFINGS IN BIOINFORMATICS

HINGRL: predicting drug–disease associations with graph representation learning on heterogeneous information networks

(2021) Bo-Wei Zhao et al.   BRIEFINGS IN BIOINFORMATICS

Predicting miRNA–disease associations based on graph random propagation network and attention network

(2021) Tangbo Zhong et al.   BRIEFINGS IN BIOINFORMATICS

A Distributed Framework for Large-scale Protein-protein Interaction Data Analysis and Prediction Using MapReduce

(2021) Lun Hu et al.   IEEE-CAA Journal of Automatica Sinica

A Fast Fuzzy Clustering Algorithm for Complex Networks via a Generalized Momentum Method

(2021) Lun Hu et al.   IEEE TRANSACTIONS ON FUZZY SYSTEMS

An overview of COVID-19

(2020) Yu Shi et al.   Journal of Zhejiang University-SCIENCE B

HiSCF: leveraging higher-order structures for clustering analysis in biological networks

(2020) Lun Hu et al.   BIOINFORMATICS

Predicting drug–disease associations through layer attention graph convolutional network

(2020) Zhouxin Yu et al.   BRIEFINGS IN BIOINFORMATICS

Paclitaxel alleviates the sepsis-induced acute kidney injury via lnc-MALAT1/miR-370-3p/HMGB1 axis

(2020) Lina Xu et al.   LIFE SCIENCES

Learning Representation of Molecules in Association Network for Predicting Intermolecular Associations

(2020) Hai-Cheng Yi et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

LMTRDA: Using logistic model tree to predict MiRNA-disease associations by fusing multi-source information of sequences and similarities

(2019) Lei Wang et al.   PLoS Computational Biology

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

(2019) Xiangxiang Zeng et al.   BIOINFORMATICS

Predicting drug-disease associations by using similarity constrained matrix factorization

(2018) Wen Zhang et al.   BMC BIOINFORMATICS

DrugBank 5.0: a major update to the DrugBank database for 2018

(2017) David S Wishart et al.   NUCLEIC ACIDS RESEARCH

A network integration approach for drug-target interaction prediction and computational drug repositioning from heterogeneous information

(2017) Yunan Luo et al.   Nature Communications

Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm

(2016) Huimin Luo et al.   BIOINFORMATICS

Fuzzy Clustering in a Complex Network Based on Content Relevance and Link Structures

(2016) Lun Hu et al.   IEEE TRANSACTIONS ON FUZZY SYSTEMS

The Comparative Toxicogenomics Database: update 2017

(2016) Allan Peter Davis et al.   NUCLEIC ACIDS RESEARCH

Autoencoder for words

(2014) Cheng-Yuan Liou et al.   NEUROCOMPUTING

Construction of Drug Network Based on Side Effects and Its Application for Drug Repositioning

(2014) Hao Ye et al.   PLoS One

Drug Repositioning by Kernel-Based Integration of Molecular Structure, Molecular Activity, and Phenotype Data

(2013) Yongcui Wang et al.   PLoS One

Drug Repositioning: A Machine-Learning Approach through Data Integration

(2013) Francesco Napolitano et al.   Journal of Cheminformatics

Exploiting drug-disease relationships for computational drug repositioning

(2011) J. T. Dudley et al.   BRIEFINGS IN BIOINFORMATICS

PREDICT: a method for inferring novel drug indications with application to personalized medicine

(2011) A. Gottlieb et al.   Molecular Systems Biology