A Review of Current In Silico Methods for Repositioning Drugs and Chemical Compounds

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Prioritizing antiviral drugs against SARS-CoV-2 by integrating viral complete genome sequences and drug chemical structures

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Early antiviral treatment contributes to alleviate the severity and improve the prognosis of patients with novel coronavirus disease (COVID‐19)

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Use of antiviral drugs to reduce COVID-19 transmission

(2020) Oriol Mitjà et al.   Lancet Global Health

iDrug: Integration of drug repositioning and drug-target prediction via cross-network embedding

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Transcriptome-based drug repositioning for coronavirus disease 2019 (COVID-19)

(2020) Zhilong Jia et al.   Pathogens and Disease

An Improved Anticancer Drug-Response Prediction Based on an Ensemble Method Integrating Matrix Completion and Ridge Regression

(2020) Chuanying Liu et al.   Molecular Therapy-Nucleic Acids

Identifying Effective Antiviral Drugs Against SARS-CoV-2 by Drug Repositioning Through Virus-Drug Association Prediction

(2020) Lihong Peng et al.   Frontiers in Genetics

Molecular Network-Based Drug Prediction in Thyroid Cancer

(2019) Xingyu Xu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Human geroprotector discovery by targeting the converging subnetworks of aging and age-related diseases

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Applications of Bioinformatics and Systems Biology in Precision Medicine and Immunooncology

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Drug-Target Interaction Prediction with Graph Regularized Matrix Factorization

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How much do clinical trials cost?

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Reversal of cancer gene expression correlates with drug efficacy and reveals therapeutic targets

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Common and cell-type specific responses to anti-cancer drugs revealed by high throughput transcript profiling

(2017) Mario Niepel et al.   Nature Communications

Identifying drug-pathway association pairs based on L1L2,1-integrative penalized matrix decomposition

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Computational Molecular Networks and Network Pharmacology

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A standard database for drug repositioning

(2017) Adam S. Brown et al.   Scientific Data

Predicting drug-target interactions by dual-network integrated logistic matrix factorization

(2017) Ming Hao et al.   Scientific Reports

A review of treatment modalities for Middle East Respiratory Syndrome

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Analysis and prediction of drug–drug interaction by minimum redundancy maximum relevance and incremental feature selection

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Can you teach old drugs new tricks?

(2016) Nicola Nosengo   NATURE

Axitinib blocks Wnt/β-catenin signaling and directs asymmetric cell division in cancer

(2016) Yi Qu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-based in silico drug efficacy screening

(2016) Emre Guney et al.   Nature Communications

A systematic study on drug-response associated genes using baseline gene expressions of the Cancer Cell Line Encyclopedia

(2016) Xiaoming Liu et al.   Scientific Reports

Pathway-Based Genomics Prediction using Generalized Elastic Net

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Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction

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Network-based approaches for drug response prediction and targeted therapy development in cancer

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Anticancer drug sensitivity prediction in cell lines from baseline gene expression through recursive feature selection

(2015) Zuoli Dong et al.   BMC CANCER

Matrix Factorization-Based Prediction of Novel Drug Indications by Integrating Genomic Space

(2015) Wen Dai et al.   Computational and Mathematical Methods in Medicine

Network-Based Inference Methods for Drug Repositioning

(2015) Hailin Chen et al.   Computational and Mathematical Methods in Medicine

The human Drug–Disease–Gene Network

(2015) Peng Gang Sun   INFORMATION SCIENCES

A Copula Based Approach for Design of Multivariate Random Forests for Drug Sensitivity Prediction

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Recursive Random Lasso (RRLasso) for Identifying Anti-Cancer Drug Targets

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Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity

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BalestraWeb: efficient online evaluation of drug-target interactions

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Drug repositioning by integrating target information through a heterogeneous network model

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DrugComboRanker: drug combination discovery based on target network analysis

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A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

Sequence-Based Antigenic Change Prediction by a Sparse Learning Method Incorporating Co-Evolutionary Information

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mRMRe: an R package for parallelized mRMR ensemble feature selection

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A new approach for prediction of tumor sensitivity to targeted drugs based on functional data

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Feature subset selection Filter–Wrapper based on low quality data

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Predicting Drug–Target Interactions Using Probabilistic Matrix Factorization

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Metrics other than potency reveal systematic variation in responses to cancer drugs

(2013) Mohammad Fallahi-Sichani et al.   Nature Chemical Biology

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

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Analyzing Gene Expression Profile in K562 Cells Exposed to Sodium Valproate Using Microarray Combined with the Connectivity Map Database

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Network-based characterization of drug-regulated genes, drug targets, and toxicity

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

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The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

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

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Identifying Compound-Target Associations by Combining Bioactivity Profile Similarity Search and Public Databases Mining

(2011) Tiejun Cheng et al.   Journal of Chemical Information and Modeling

Regression shrinkage and selection via the lasso: a retrospective

(2011) Robert Tibshirani   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Facing the classification of binary problems with a GSA-SVM hybrid system

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Discovery of Molecular Mechanisms of Traditional Chinese Medicinal Formula Si-Wu-Tang Using Gene Expression Microarray and Connectivity Map

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Expression profiling identifies epoxy anthraquinone derivative as a DNA topoisomerase inhibitor

(2010) Jinesh Gheeya et al.   CANCER LETTERS

Solving the apparent diversity-accuracy dilemma of recommender systems

(2010) T. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drug-Induced Regulation of Target Expression

(2010) Murat Iskar et al.   PLoS Computational Biology

Identification of a Novel Topoisomerase Inhibitor Effective in Cells Overexpressing Drug Efflux Transporters

(2009) Walid Fayad et al.   PLoS One