A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

(2017) Egon L. Willighagen et al.   Journal of Cheminformatics

Risk of acute and serious liver injury associated to nimesulide and other NSAIDs: data from drug-induced liver injury case-control study in Italy

(2016) Monia Donati et al.   BRITISH JOURNAL OF CLINICAL PHARMACOLOGY

Identification of selective cytotoxic and synthetic lethal drug responses in triple negative breast cancer cells

(2016) Prson Gautam et al.   Molecular Cancer

Foretelling toxicity: FDA researchers work to predict risk of liver injury from drugs

(2016) Cassandra Willyard   NATURE MEDICINE

Grouping 34 Chemicals Based on Mode of Action Using Connectivity Mapping

(2016) K. Nadira De Abrew et al.   TOXICOLOGICAL SCIENCES

Integrating Publicly Available Data to Generate Computationally Predicted Adverse Outcome Pathways for Fatty Liver

(2016) Shannon M. Bell et al.   TOXICOLOGICAL SCIENCES

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

(2016) Ruili Huang et al.   Nature Communications

Key Challenges and Opportunities Associated with the Use of In Vitro Models to Detect Human DILI: Integrated Risk Assessment and Mitigation Plans

(2016) Franck A. Atienzar et al.   Biomed Research International

Developing tools for defining and establishing pathways of toxicity

(2015) Melvin E. Andersen et al.   ARCHIVES OF TOXICOLOGY

Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline

(2015) Yasir Rahmatallah et al.   BRIEFINGS IN BIOINFORMATICS

Adverse Outcome Pathways and Drug-Induced Liver Injury Testing

(2015) Mathieu Vinken   CHEMICAL RESEARCH IN TOXICOLOGY

Lessons from Toxicology: Developing a 21st-Century Paradigm for Medical Research

(2015) Gill Langley et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Probabilistic machine learning and artificial intelligence

(2015) Zoubin Ghahramani   NATURE

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Statistical learning and selective inference

(2015) Jonathan Taylor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Setting Clinical Exposure Levels of Concern for Drug-Induced Liver Injury (DILI) Using Mechanisticin vitroAssays

(2015) Falgun Shah et al.   TOXICOLOGICAL SCIENCES

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

structSSI: Simultaneous and Selective Inference for Grouped or Hierarchically Structured Data

(2015) Kris Sankaran et al.   Journal of Statistical Software

Tidy Data

(2015) Hadley Wickham   Journal of Statistical Software

A testing strategy to predict risk for drug-induced liver injury in humans using high-content screen assays and the ‘rule-of-two’ model

(2014) Minjun Chen et al.   ARCHIVES OF TOXICOLOGY

SEURAT: Safety Evaluation Ultimately Replacing Animal Testing—Recommendations for future research in the field of predictive toxicology

(2014) George Daston et al.   ARCHIVES OF TOXICOLOGY

Cancer Biology, Toxicology and Alternative Methods Development Go Hand-in-Hand

(2014) Pekka Kohonen et al.   BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY

Probabilistic drug connectivity mapping

(2014) Juuso A Parkkinen et al.   BMC BIOINFORMATICS

Systems Toxicology: From Basic Research to Risk Assessment

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

Human drug-induced liver injury severity is highly associated with dual inhibition of liver mitochondrial function and bile salt export pump

(2014) Michael D. Aleo et al.   HEPATOLOGY

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

(2014) Nicole C Kleinstreuer et al.   NATURE BIOTECHNOLOGY

Open TG-GATEs: a large-scale toxicogenomics database

(2014) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

Genomic Models of Short-Term Exposure Accurately Predict Long-Term Chemical Carcinogenicity and Identify Putative Mechanisms of Action

(2014) Daniel Gusenleitner et al.   PLoS One

Drug-Induced Liver Injury and Drug Development: Industry Perspective

(2014) Arie Regev   SEMINARS IN LIVER DISEASE

Causal analysis approaches in Ingenuity Pathway Analysis

(2013) Andreas Krämer et al.   BIOINFORMATICS

The Liver Toxicity Knowledge Base: A Systems Approach to a Complex End Point

(2013) M Chen et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Idiosyncratic drug-induced liver injury: an update on the 2007 overview

(2013) S Hyder Hussaini et al.   Expert Opinion On Drug Safety

Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding

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

A Correlation Between the In Vitro Drug Toxicity of Drugs to Cell Lines That Express Human P450s and Their Propensity to Cause Liver Injury in Humans

(2013) Frida Gustafsson et al.   TOXICOLOGICAL SCIENCES

Incorporating New Technologies Into Toxicity Testing and Risk Assessment: Moving From 21st Century Vision to a Data-Driven Framework

(2013) Russell S. Thomas et al.   TOXICOLOGICAL SCIENCES

A high content screening assay to predict human drug-induced liver injury during drug discovery

(2013) Mikael Persson et al.   JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS

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

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs

(2012) Suleiman A Khan et al.   BMC BIOINFORMATICS

To test or not to test: Preliminary assessment of normality when comparing two independent samples

(2012) Justine Rochon et al.   BMC Medical Research Methodology

The determination and interpretation of the therapeutic index in drug development

(2012) Patrick Y. Muller et al.   NATURE REVIEWS DRUG DISCOVERY

Use of Micropatterned Cocultures to Detect Compounds That Cause Drug-Induced Liver Injury in Humans

(2012) Salman R. Khetani et al.   TOXICOLOGICAL SCIENCES

A Decade of Toxicogenomic Research and Its Contribution to Toxicological Science

(2012) Minjun Chen et al.   TOXICOLOGICAL SCIENCES

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Advancing Regulatory Science

(2011) M. A. Hamburg   SCIENCE

ROAST: rotation gene set tests for complex microarray experiments

(2010) Di Wu et al.   BIOINFORMATICS

Developing Structure−Activity Relationships for the Prediction of Hepatotoxicity

(2010) Nigel Greene et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Discovery of drug mode of action and drug repositioning from transcriptional responses

(2010) F. Iorio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Probabilistic retrieval and visualization of biologically relevant microarray experiments

(2009) J. Caldas et al.   BIOINFORMATICS

High-Throughput Cell-Based Screening of 4910 Known Drugs and Drug-like Small Molecules Identifies Disulfiram as an Inhibitor of Prostate Cancer Cell Growth

(2009) K. Iljin et al.   CLINICAL CANCER RESEARCH

Toxicology for the twenty-first century

(2009) Thomas Hartung   NATURE

Data Mining the NCI60 to Predict Generalized Cytotoxicity

(2008) Adam C. Lee et al.   Journal of Chemical Information and Modeling

The liver pharmacological and xenobiotic gene response repertoire

(2008) Georges Natsoulis et al.   Molecular Systems Biology

Network pharmacology: the next paradigm in drug discovery

(2008) Andrew L Hopkins   Nature Chemical Biology

Transforming Environmental Health Protection

(2008) Francis S. Collins et al.   SCIENCE

Cellular Imaging Predictions of Clinical Drug-Induced Liver Injury

(2008) Jinghai J. Xu et al.   TOXICOLOGICAL SCIENCES

Dose response considerations in risk assessment—An overview of recent ILSI activities

(2008) Michael P. Holsapple et al.   TOXICOLOGY LETTERS