Machine Learning for Drug-Target Interaction Prediction

Prediction of potential disease-associated microRNAs using structural perturbation method

(2018) Xiangxiang Zeng et al.   BIOINFORMATICS

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

(2018) Fangping Wan et al.   BIOINFORMATICS

Computational prediction of drug–target interactions using chemogenomic approaches: an empirical survey

(2018) Ali Ezzat et al.   BRIEFINGS IN BIOINFORMATICS

Next-Generation Machine Learning for Biological Networks

(2018) Diogo M. Camacho et al.   CELL

Meta-path methods for prioritizing candidate disease miRNAs

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

Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization

(2017) Ali Ezzat 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

Drug-target interaction prediction using ensemble learning and dimensionality reduction

(2017) Ali Ezzat et al.   METHODS

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

A comprehensive overview and evaluation of circular RNA detection tools

(2017) Xiangxiang Zeng et al.   PLoS Computational Biology

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

(2016) Huimin Luo et al.   BIOINFORMATICS

Drug-target interaction prediction via class imbalance-aware ensemble learning

(2016) Ali Ezzat et al.   BMC BIOINFORMATICS

Predicting drug target interactions using meta-path-based semantic network analysis

(2016) Gang Fu et al.   BMC BIOINFORMATICS

A Classification Method for Microarrays Based on Diversity

(2016) Xubo Wang et al.   Current Bioinformatics

An Empirical Study of Features Fusion Techniques for Protein-Protein Interaction Prediction

(2016) Jiancang Zeng et al.   Current Bioinformatics

Protein Folds Prediction with Hierarchical Structured SVM

(2016) Dapeng Li et al.   Current Proteomics

Predicting potential side effects of drugs by recommender methods and ensemble learning

(2016) Wen Zhang et al.   NEUROCOMPUTING

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

PubChem BioAssay: 2017 update

(2016) Yanli Wang et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Drug–target interaction prediction: databases, web servers and computational models

(2015) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

A survey of current trends in computational drug repositioning

(2015) Jiao Li et al.   BRIEFINGS IN BIOINFORMATICS

Integrative approaches for predicting microRNA function and prioritizing disease-related microRNA using biological interaction networks

(2015) Xiangxiang Zeng et al.   BRIEFINGS IN BIOINFORMATICS

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

(2015) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

PubChem Substance and Compound databases

(2015) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

Label Propagation Prediction of Drug-Drug Interactions Based on Clinical Side Effects

(2015) Ping Zhang et al.   Scientific Reports

Toward more realistic drug-target interaction predictions

(2014) T. Pahikkala et al.   BRIEFINGS IN BIOINFORMATICS

A Discussion of MicroRNAs in Cancers

(2014) Shi Hua et al.   Current Bioinformatics

Review of Protein Subcellular Localization Prediction

(2014) Zhen Wang et al.   Current Bioinformatics

Drug–target interaction prediction via chemogenomic space: learning-based methods

(2014) Zaynab Mousavian et al.   Expert Opinion on Drug Metabolism & Toxicology

SuperPred: update on drug classification and target prediction

(2014) Janette Nickel et al.   NUCLEIC ACIDS RESEARCH

ASDCD: Antifungal Synergistic Drug Combination Database

(2014) Xing Chen et al.   PLoS One

DCDB 2.0: a major update of the drug combination database

(2014) Y. Liu et al.   Database-The Journal of Biological Databases and Curation

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Similarity-based machine learning methods for predicting drug–target interactions: a brief review

(2013) Hao Ding et al.   BRIEFINGS IN BIOINFORMATICS

Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

(2013) Murat Can Cobanoglu et al.   Journal of Chemical Information and Modeling

Therapeutic target database update 2014: a resource for targeted therapeutics

(2013) Chu Qin et al.   NUCLEIC ACIDS RESEARCH

Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile

(2013) Twan van Laarhoven et al.   PLoS One

A Semi-Supervised Method for Drug-Target Interaction Prediction with Consistency in Networks

(2013) Hailin Chen et al.   PLoS One

CancerDR: Cancer Drug Resistance Database

(2013) Rahul Kumar et al.   Scientific Reports

Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization

(2012) M. Gonen   BIOINFORMATICS

Drug–target interaction prediction by learning from local information and neighbors

(2012) Jian-Ping Mei et al.   BIOINFORMATICS

A Systematic Prediction of Multiple Drug-Target Interactions from Chemical, Genomic, and Pharmacological Data

(2012) Hua Yu et al.   PLoS One

Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Gaussian interaction profile kernels for predicting drug–target interaction

(2011) Twan van Laarhoven et al.   BIOINFORMATICS

SuperTarget goes quantitative: update on drug-target interactions

(2011) N. Hecker et al.   NUCLEIC ACIDS RESEARCH

TDR Targets: a chemogenomics resource for neglected diseases

(2011) M. P. Magarinos et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

(2010) Zheng Xia et al.   BMC Systems Biology

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

How to improve R&D productivity: the pharmaceutical industry's grand challenge

(2010) Steven M. Paul et al.   NATURE REVIEWS DRUG DISCOVERY

Supervised prediction of drug–target interactions using bipartite local models

(2009) Kevin Bleakley et al.   BIOINFORMATICS

Prediction of drug-target interaction networks from the integration of chemical and genomic spaces

(2008) Y. Yamanishi et al.   BIOINFORMATICS

Protein-ligand Docking: A Review of Recent Advances and Future Perspectives

(2008) Gerard Pujadas et al.   Current Pharmaceutical Analysis