Biomarker-based drug safety assessment in the age of systems pharmacology: from foundational to regulatory science

Systems Pharmacological Analysis of Drugs Inducing Stevens–Johnson Syndrome and Toxic Epidermal Necrolysis

(2015) Junguk Hur et al.   CHEMICAL RESEARCH IN TOXICOLOGY

In silico prediction of chemical toxicity on avian species using chemical category approaches

(2015) Chen Zhang et al.   CHEMOSPHERE

Association of Aspirin and NSAID Use With Risk of Colorectal Cancer According to Genetic Variants

(2015) Hongmei Nan et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Federalist principles for healthcare data networks

(2015) Kenneth D Mandl et al.   NATURE BIOTECHNOLOGY

FDA as a catalyst for translation

(2015) Robert M. Califf et al.   Science Translational Medicine

FXR antagonism of NSAIDs contributes to drug-induced liver injury identified by systems pharmacology approach

(2015) Weiqiang Lu et al.   Scientific Reports

Classification of Cytochrome P450 Inhibitors and Noninhibitors Using Combined Classifiers

(2015) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Workshop report: Identifying opportunities for global integration of toxicogenomics databases, 26–27 June 2013, Research Triangle Park, NC, USA

(2014) Diana M. Hendrickx et al.   ARCHIVES OF TOXICOLOGY

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

(2014) Teresa Juan-Blanco et al.   BIOINFORMATICS

miRNAs and their application in drug-induced liver injury

(2014) Yuping Wang et al.   Biomarkers in Medicine

Emerging efforts for discovering new biomarkers of liver disease and hepatotoxicity

(2014) Huixiao Hong et al.   Biomarkers in Medicine

Competitive molecular docking approach for predicting estrogen receptor subtype α agonists and antagonists

(2014) Hui Wen Ng et al.   BMC BIOINFORMATICS

Systems Toxicology: From Basic Research to Risk Assessment

(2014) Shana J. Sturla et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Next-Generation Medicines: Past Regulatory Experience and Considerations for the Future

(2014) M A Pacanowski et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Computational models to predict endocrine-disrupting chemical binding with androgen or oestrogen receptors

(2014) Yingjie Chen et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

In Silico Prediction of Chemical Acute Oral Toxicity Using Multi-Classification Methods

(2014) Xiao Li et al.   Journal of Chemical Information and Modeling

A three-stage genome-wide association study identifies a susceptibility locus for late radiotherapy toxicity at 2q24.1

(2014) Laura Fachal et al.   NATURE GENETICS

T3DB: the toxic exposome database

(2014) David Wishart et al.   NUCLEIC ACIDS RESEARCH

Lean Big Data integration in systems biology and systems pharmacology

(2014) Avi Ma’ayan et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

A chemo-centric view of human health and disease

(2014) Miquel Duran-Frigola et al.   Nature Communications

Computational prediction of microRNA networks incorporating environmental toxicity and disease etiology

(2014) Jie Li et al.   Scientific Reports

Structural Systems Pharmacology: The Role of 3D Structures in Next-Generation Drug Development

(2013) Miquel Duran-Frigola et al.   CHEMISTRY & BIOLOGY

The Future of Population-Based Postmarket Drug Risk Assessment: A Regulator’s Perspective

(2013) T A Hammad et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Connecting the Dots: Applications of Network Medicine in Pharmacology and Disease

(2013) A Jacunski et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Clinical Pharmacology and the Catalysis of Regulatory Science: Opportunities for the Advancement of Drug Development and Evaluation

(2013) I Zineh et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

In Silico ADMET Prediction: Recent Advances, Current Challenges and Future Trends

(2013) Feixiong Cheng et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Case study: the role of mechanistic network models in systems toxicology

(2013) Julia Hoeng et al.   DRUG DISCOVERY TODAY

Prediction of Polypharmacological Profiles of Drugs by the Integration of Chemical, Side Effect, and Therapeutic Space

(2013) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Adverse Drug Events: Database Construction and in Silico Prediction

(2013) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Prediction of human genes and diseases targeted by xenobiotics using predictive toxicogenomic-derived models (PTDMs)

(2013) Feixiong Cheng et al.   Molecular BioSystems

Systematic identification of proteins that elicit drug side effects

(2013) M. Kuhn et al.   Molecular Systems Biology

Target identification and mechanism of action in chemical biology and drug discovery

(2013) Monica Schenone et al.   Nature Chemical Biology

Pharmacogenetics in the evaluation of new drugs: a multiregional regulatory perspective

(2013) Marc Maliepaard et al.   NATURE REVIEWS DRUG DISCOVERY

The Reactome pathway knowledgebase

(2013) David Croft et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

RETRACTED ARTICLE: SNPs in genes implicated in radiation response are associated with radiotoxicity and evoke roles as predictive and prognostic biomarkers

(2013) Ghazi Alsbeih et al.   Radiation Oncology

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

(2013) Xiujie Chen et al.   Scientific Reports

Target Essentiality and Centrality Characterize Drug Side Effects

(2013) Xiujuan Wang et al.   PLoS Computational Biology

Systems Pharmacology to Predict Drug Toxicity: Integration Across Levels of Biological Organization

(2012) Jane P.F. Bai et al.   Annual Review of Pharmacology and Toxicology

Rat α-Fetoprotein Binding Affinities of a Large Set of Structurally Diverse Chemicals Elucidated the Relationships between Structures and Binding Affinities

(2012) Huixiao Hong et al.   CHEMICAL RESEARCH IN TOXICOLOGY

In silico Prediction of Chemical Ames Mutagenicity

(2012) Congying Xu et al.   Journal of Chemical Information and Modeling

admetSAR: A Comprehensive Source and Free Tool for Assessment of Chemical ADMET Properties

(2012) Feixiong Cheng et al.   Journal of Chemical Information and Modeling

Prediction of chemical–protein interactions: multitarget-QSAR versus computational chemogenomic methods

(2012) Feixiong Cheng et al.   Molecular BioSystems

Automated design of ligands to polypharmacological profiles

(2012) Jérémy Besnard et al.   NATURE

GlaxoSmithKline opens the door on clinical data sharing

(2012) Charlotte Harrison   NATURE REVIEWS DRUG DISCOVERY

ChemProt-2.0: visual navigation in a disease chemical biology database

(2012) Sonny Kim Kjærulff et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2013 update

(2012) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

Prediction of Chemical-Protein Interactions Network with Weighted Network-Based Inference Method

(2012) Feixiong Cheng et al.   PLoS One

Data-Driven Prediction of Drug Effects and Interactions

(2012) N. P. Tatonetti et al.   Science Translational Medicine

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

(2012) Feixiong Cheng et al.   PLoS Computational Biology

Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action

(2011) Shan Zhao et al.   Annual Review of Pharmacology and Toxicology

Xenobiotic Metabolomics: Major Impact on the Metabolome

(2011) Caroline H. Johnson et al.   Annual Review of Pharmacology and Toxicology

Using Genome-Wide Association Studies to Identify Genes Important in Serious Adverse Drug Reactions

(2011) Ann K. Daly   Annual Review of Pharmacology and Toxicology

Omics and Drug Response

(2011) Urs A. Meyer et al.   Annual Review of Pharmacology and Toxicology

Application of Computational Systems Biology to Explore Environmental Toxicity Hazards

(2011) Karine Audouze et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Insights into Molecular Basis of Cytochrome P450 Inhibitory Promiscuity of Compounds

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

Mechanisms of drug-induced liver injury: from bedside to bench

(2011) Shannan Tujios et al.   Nature Reviews Gastroenterology & Hepatology

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

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

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

(2011) Lun Yang et al.   PLoS Computational Biology

Molecular biomarkers: a US FDA effort

(2010) Huixiao Hong et al.   Biomarkers in Medicine

Protein Adducts As Prospective Biomarkers of Nevirapine Toxicity

(2010) Alexandra M. M. Antunes et al.   CHEMICAL RESEARCH IN TOXICOLOGY

In silico prediction of Tetrahymena pyriformis toxicity for diverse industrial chemicals with substructure pattern recognition and machine learning methods

(2010) Feixiong Cheng et al.   CHEMOSPHERE

Regulatory Science: What It Is and Why We Need It

(2010) G A FitzGerald   CLINICAL PHARMACOLOGY & THERAPEUTICS

Estimation of ADME Properties with Substructure Pattern Recognition

(2010) Jie Shen et al.   Journal of Chemical Information and Modeling

Pharmacophore modeling of human adenosine receptor A2A antagonists

(2010) Zhejun Xu et al.   JOURNAL OF MOLECULAR MODELING

A side effect resource to capture phenotypic effects of drugs

(2010) Michael Kuhn et al.   Molecular Systems Biology

Pathway Commons, a web resource for biological pathway data

(2010) E. G. Cerami et al.   NUCLEIC ACIDS RESEARCH

DrugBank 3.0: a comprehensive resource for 'Omics' research on drugs

(2010) C. Knox et al.   NUCLEIC ACIDS RESEARCH

Role of systems pharmacology in understanding drug adverse events

(2010) Seth I. Berger et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Launching HITECH

(2009) David Blumenthal   NEW ENGLAND JOURNAL OF MEDICINE

PubChem: a public information system for analyzing bioactivities of small molecules

(2009) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Lun Yang et al.   PLoS Computational Biology

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

(2009) Li Xie et al.   PLoS Computational Biology

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks

(2008) A. P. Davis et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Transforming Environmental Health Protection

(2008) Francis S. Collins et al.   SCIENCE

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE