Combining phenome-driven drug-target interaction prediction with patients’ electronic health records-based clinical corroboration toward drug discovery

Tumor Necrosis Factor (TNF) blocking agents are associated with lower risk for Alzheimer’s disease in patients with rheumatoid arthritis and psoriasis

(2020) Mengshi Zhou et al.   PLoS One

Context-sensitive network analysis identifies food metabolites associated with Alzheimer’s disease: an exploratory study

(2019) Yang Chen et al.   BMC Medical Genomics

The diabetes drug liraglutide reverses cognitive impairment in mice and attenuates insulin receptor and synaptic pathology in a non-human primate model of Alzheimer's disease

(2018) Andre F Batista et al.   JOURNAL OF PATHOLOGY

Use of statins and the risk of dementia and mild cognitive impairment: A systematic review and meta-analysis

(2018) Che-Sheng Chu et al.   Scientific Reports

Predicting inhibitory and activatory drug targets by chemically and genetically perturbed transcriptome signatures

(2018) Ryusuke Sawada et al.   Scientific Reports

A Drug-Side Effect Context-Sensitive Network approach for drug target prediction

(2018) Mengshi Zhou et al.   BIOINFORMATICS

Large-scale mining disease comorbidity relationships from post-market drug adverse events surveillance data

(2018) Chunlei Zheng et al.   BMC BIOINFORMATICS

DrugE-Rank: improving drug–target interaction prediction of new candidate drugs or targets by ensemble learning to rank

(2016) Qingjun Yuan et al.   BIOINFORMATICS

A genomics-based systems approach towards drug repositioning for rheumatoid arthritis

(2016) Rong Xu et al.   BMC GENOMICS

Phenome-based gene discovery provides information about Parkinson’s disease drug targets

(2016) Yang Chen et al.   BMC GENOMICS

Phenome-driven disease genetics prediction toward drug discovery

(2015) Yang Chen et al.   BIOINFORMATICS

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

(2015) Xing Chen et al.   BRIEFINGS IN BIOINFORMATICS

PhenoPredict: A disease phenome-wide drug repositioning approach towards schizophrenia drug discovery

(2015) Rong Xu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Early Statin Use and the Progression of Alzheimer Disease

(2015) Feng-Cheng Lin et al.   MEDICINE

The SIDER database of drugs and side effects

(2015) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

Drug repositioning by integrating target information through a heterogeneous network model

(2014) Wenhui Wang et al.   BIOINFORMATICS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Temporal disease trajectories condensed from population-wide registry data covering 6.2 million patients

(2014) Anders Boeck Jensen et al.   Nature Communications

Predicting drug-target interactions using restricted Boltzmann machines

(2013) Yuhao Wang et al.   BIOINFORMATICS

Large-scale extraction of accurate drug-disease treatment pairs from biomedical literature for drug repurposing

(2013) Rong Xu et al.   BMC BIOINFORMATICS

Automatic signal extraction, prioritizing and filtering approaches in detecting post-marketing cardiovascular events associated with targeted cancer drugs from the FDA Adverse Event Reporting System (FAERS)

(2013) Rong Xu et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Using aggregated, de-identified electronic health record data for multivariate pharmacosurveillance: A case study of azathioprine

(2013) Vishal N. Patel et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

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

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

(2012) M. Gonen   BIOINFORMATICS

Patient characteristics associated with venous thromboembolic events: a cohort study using pooled electronic health record data

(2012) David C Kaelber et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Drug–target interaction prediction by random walk on the heterogeneous network

(2012) Xing Chen et al.   Molecular BioSystems

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

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Normalized names for clinical drugs: RxNorm at 6 years

(2011) Stuart J Nelson et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Genome-wide inferring gene–phenotype relationship by walking on the heterogeneous network

(2010) Yongjin Li et al.   BIOINFORMATICS

Predicting Drug-Target Interaction Networks Based on Functional Groups and Biological Features

(2010) Zhisong He et al.   PLoS One

Supervised prediction of drug–target interactions using bipartite local models

(2009) Kevin Bleakley et al.   BIOINFORMATICS

Systematized Nomenclature of Medicine–Clinical Terms direction and its implications on critical care

(2009) Reza Shahpori et al.   JOURNAL OF CRITICAL CARE

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

A Dynamic Network Approach for the Study of Human Phenotypes

(2009) César A. Hidalgo et al.   PLoS Computational Biology

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

(2008) Y. Yamanishi et al.   BIOINFORMATICS

Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets

(2008) Liang-Hui Chu et al.   BMC Systems Biology

Statins are associated with a reduced risk of Alzheimer disease regardless of lipophilicity. The Rotterdam Study

(2008) M D M Haag et al.   JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE