In silico assessment of adverse drug reactions and associated mechanisms

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The Connectivity Map: Using Gene-Expression Signatures to Connect Small Molecules, Genes, and Disease

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QSAR Modeling: Where have you been? Where are you going to?

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How were new medicines discovered?

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hERG potassium channels and cardiac arrhythmia

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Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

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Walking the Interactome for Prioritization of Candidate Disease Genes

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Data-driven prediction of drug effects and interactions

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Quantitative signal detection using spontaneous ADR reporting

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A side effect resource to capture phenotypic effects of drugs

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Structure and dynamics of molecular networks: A novel paradigm of drug discovery

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Large-scale prediction and testing of drug activity on side-effect targets

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Reducing safety-related drug attrition: the use of in vitro pharmacological profiling

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Phase II and Phase III attrition rates 2011–2012

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VigiBase, the WHO Global ICSR Database System: Basic Facts

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Cellular Imaging Predictions of Clinical Drug-Induced Liver Injury

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Keynote review: In vitro safety pharmacology profiling: an essential tool for successful drug development

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Analysis of Pharmacology Data and the Prediction of Adverse Drug Reactions and Off‐Target Effects from Chemical Structure

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Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs

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When good drugs go bad

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Drug Discovery Using Chemical Systems Biology: Identification of the Protein-Ligand Binding Network To Explain the Side Effects of CETP Inhibitors

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Applications of Connectivity Map in drug discovery and development

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Predicting drug side-effect profiles: a chemical fragment-based approach

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Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms

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Relating drug–protein interaction network with drug side effects

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Overview: Generation of Gene Knockout Mice

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Ten-year trends in hospital admissions for adverse drug reactions in England 1999–2009

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Mapping Adverse Drug Reactions in Chemical Space

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The SOX2 response program in glioblastoma multiforme: an integrated ChIP-seq, expression microarray, and microRNA analysis

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Gaining Insight into Off-Target Mediated Effects of Drug Candidates with a Comprehensive Systems Chemical Biology Analysis

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Drug Side-Effect Prediction Based on the Integration of Chemical and Biological Spaces

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PubChem as a Source of Polypharmacology

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Serotonergic Drugs and Valvular Heart Disease

Rothman, R., & Baumann, M. (2009) · Expert Opinion on Drug Safety · doi:10.1517/14740330902931524 · Cited by 134 · see citing works

Predicting adverse side effects of drugs

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DIGEP-Pred: web service for in silico prediction of drug-induced gene expression profiles based on structural formula

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Predicting Adverse Drug Events Using Pharmacological Network Models

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An Algorithmic Framework for Predicting Side Effects of Drugs

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Systems Pharmacology of Arrhythmias

Berger, S., Ma’ayan, A., & Iyengar, R. (2010) · Science Signaling · doi:10.1126/scisignal.2000723 · Cited by 127 · see citing works

Systematic identification of proteins that elicit drug side effects

Kuhn, M., Banchaabouchi, M. A., Campillos, M., Jensen, L. J., Gross, C. T., Gavin, A., & Peer Bork, B. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.10 · Cited by 117 · see citing works

Modeling Liver-Related Adverse Effects of Drugs Using kNearest Neighbor Quantitative Structure−Activity Relationship Method

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Exploratory toxicology as an integrated part of drug discovery. Part I: Why and how

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Idiosyncratic toxicity: the role of toxicophores and bioactivation

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Understanding mechanisms of toxicity: Insights from drug discovery research

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A Gene Expression Signature that Predicts the Future Onset of Drug-Induced Renal Tubular Toxicity

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Exploring Off-Targets and Off-Systems for Adverse Drug Reactions via Chemical-Protein Interactome — Clozapine-Induced Agranulocytosis as a Case Study

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Profiling Bioactivity of the ToxCast Chemical Library Using BioMAP Primary Human Cell Systems

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Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome

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Toward Enhanced Pharmacovigilance Using Patient-Generated Data on the Internet

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Chemical target and pathway toxicity mechanisms defined in primary human cell systems

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In Silico Elucidation of the Molecular Mechanism Defining the Adverse Effect of Selective Estrogen Receptor Modulators

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Drug-target network in myocardial infarction reveals multiple side effects of unrelated drugs

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Predicting Adverse Drug Reactions Using Publicly Available PubChem BioAssay Data

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Identification of structure-activity relationships for adverse effects of pharmaceuticals in humans: Part B. Use of (Q)SAR systems for early detection of drug-induced hepatobiliary and urinary tract toxicities

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Prediction of drug-related cardiac adverse effects in humans-B: Use of QSAR programs for early detection of drug-induced cardiac toxicities

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Quantitative Prediction of Antitarget Interaction Profiles for Chemical Compounds

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Identifying plausible adverse drug reactions using knowledge extracted from the literature

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The value of in silico chemistry in the safety assessment of chemicals in the consumer goods and pharmaceutical industries

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Adverse Drug Reaction Prediction Using Scores Produced by Large-Scale Drug-Protein Target Docking on High-Performance Computing Machines

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Integrative relational machine-learning for understanding drug side-effect profiles

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Building the process-drug–side effect network to discover the relationship between biological Processes and side effects

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Predicting adverse drug reaction profiles by integrating protein interaction networks with drug structures

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Delays in the post-marketing withdrawal of drugs to which deaths have been attributed: a systematic investigation and analysis

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Drug Adverse Reaction Target Database (DART)

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SePreSA: a server for the prediction of populations susceptible to serious adverse drug reactions implementing the methodology of a chemical–protein interactome

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Analysis of Chemical and Biological Features Yields Mechanistic Insights into Drug Side Effects

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Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors

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Recent approaches to the prioritization of candidate disease genes

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Consideration of the cellular microenvironment: Physiologically relevant co-culture systems in drug discovery

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A Structure-Based Approach for Mapping Adverse Drug Reactions to the Perturbation of Underlying Biological Pathways

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Identification of structure–activity relationships for adverse effects of pharmaceuticals in humans. Part A: Use of FDA post-market reports to create a database of hepatobiliary and urinary tract toxicities

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In silico search of putative adverse drug reaction related proteins as a potential tool for facilitating drug adverse effect prediction

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Automatic construction of a large-scale and accurate drug-side-effect association knowledge base from biomedical literature

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Hybrid in silico models for drug‐induced liver injury using chemical descriptors and in vitro cell‐imaging information

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Identification of structure–activity relationships for adverse effects of pharmaceuticals in humans: Part C: Use of QSAR and an expert system for the estimation of the mechanism of action of drug-induced hepatobiliary and urinary tract toxicities

Matthews, E. J., Kruhlak, N. L., Benz, R. D., Sabaté, D., Marchant, C. A., & Contrera, J. F. (2009) · Regulatory Toxicology and Pharmacology · doi:10.1016/j.yrtph.2009.01.007 · Cited by 47 · see citing works

Building Predictive Models for Mechanism-of-Action Classification from Phenotypic Assay Data Sets

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Differential Mitochondrial Toxicity Screening and Multi-Parametric Data Analysis

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Predicting multiple drugs side effects with a general drug-target interaction thermodynamic Markov model

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Target Essentiality and Centrality Characterize Drug Side Effects

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Clustering gene expression data with a penalized graph-based metric

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Predictive in silico Off-Target Profiling in Drug Discovery

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Human Nephrotoxicity Prediction Models for Three Types of Kidney Injury Based on Data Sets of Pharmacological Compounds and Their Metabolites

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Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach

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In vitro transcriptomic prediction of hepatotoxicity for early drug discovery

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DITOP: drug-induced toxicity related protein database

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Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning

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Prediction of drug-related cardiac adverse effects in humans—A: Creation of a database of effects and identification of factors affecting their occurrence

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The relationship between rational drug design and drug side effects

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IntSide: a web server for the chemical and biological examination of drug side effects

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Predicting Drugs Side Effects Based on Chemical-Chemical Interactions and Protein-Chemical Interactions

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An ensemble approach for drug side effect prediction

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Inferring protein domains associated with drug side effects based on drug-target interaction network

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Development of an in vitro liver toxicity prediction model based on longer term primary rat hepatocyte culture

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Diagnosis of drug-induced renal tubular toxicity using global gene expression profiles

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Unified drug–target interaction thermodynamic Markov model using stochastic entropies to predict multiple drugs side effects

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Prediction of adverse drug reactions by a network based external link prediction method

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Computer-aided prediction of QT-prolongation

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Network Characteristic Analysis of ADR-related Proteins and Identification of ADR-ADR Associations

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