In silico toxicology: From structure-activity relationships towards deep learning and adverse outcome pathways

Predictive Multitask Deep Neural Network Models for ADME-Tox Properties: Learning from Large Datasets

(2019) Jan Wenzel et al.   Journal of Chemical Information and Modeling

Construction of a Suite of Computable Biological Network Models Focused on Mucociliary Clearance in the Respiratory Tract

(2019) Hasmik Yepiskoposyan et al.   Frontiers in Genetics

Deep Neural Network Models for Predicting Chemically Induced Liver Toxicity Endpoints From Transcriptomic Responses

(2019) Hao Wang et al.   Frontiers in Pharmacology

Accurate Prediction of Biological Assays with High-Throughput Microscopy Images and Convolutional Networks

(2019) Markus Hofmarcher et al.   Journal of Chemical Information and Modeling

Prediction of drug response and adverse drug reactions: From twin studies to Next Generation Sequencing

(2019) Volker M. Lauschke et al.   EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES

Linking Bisphenol S to Adverse Outcome Pathways Using a Combined Text Mining and Systems Biology Approach

(2019) Jean-Charles Carvaillo et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Filling Data Gaps by Read‐across: A Mini Review on its Application, Developments and Challenges

(2019) Simona Kovarich et al.   Molecular Informatics

Curation and analysis of clinical pathology parameters and histopathologic findings from eTOXsys, a large database project (eTOX) for toxicologic studies

(2019) Mark D. Pinches et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Use of Connectivity Mapping to Support Read Across: A Deeper Dive Using Data from 186 Chemicals, 19 Cell lines and 2 Case Studies

(2019) K. Nadira De Abrew et al.   TOXICOLOGY

Computational determination of hERG-related cardiotoxicity of drug candidates

(2019) Hyang-Mi Lee et al.   BMC BIOINFORMATICS

Use of the Adverse Outcome Pathway (AOP) framework to evaluate species concordance and human relevance of Dibutyl Phthalate (DBP)-induced male reproductive toxicity

(2019) Xabier Arzuaga et al.   REPRODUCTIVE TOXICOLOGY

In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR

(2019) Gopal Pawar et al.   Frontiers in Pharmacology

Prediction of hERG K+ channel blockage using deep neural networks

(2019) Yanmin Zhang et al.   Chemical Biology & Drug Design

Using a hybrid read-across method to evaluate chemical toxicity based on chemical structure and biological data

(2019) Yajie Guo et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Designing around Structural Alerts in Drug Discovery

(2019) Amit S. Kalgutkar   JOURNAL OF MEDICINAL CHEMISTRY

Genetic toxicology in silico protocol

(2019) Catrin Hasselgren et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Towards quantitative read across: Prediction of Ames mutagenicity in a large database

(2019) Romualdo Benigni   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Support Vector Machine model for hERG inhibitory activities based on the integrated hERG database using descriptor selection by NSGA-II

(2019) Keiji Ogura et al.   Scientific Reports

Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs

(2019) Tatsuki Negami et al.   Scientific Reports

Quantitative prediction of repeat dose toxicity values using GenRA

(2019) G. Helman et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Integrated Approaches to Testing and Assessment: OECD Activities on the Development and Use of Adverse Outcome Pathways and Case Studies

(2018) Yuki Sakuratani et al.   BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY

Adverse outcome pathway networks I: Development and applications

(2018) Dries Knapen et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Multi-Descriptor Read Across (MuDRA): A Simple and Transparent Approach for Developing Accurate Quantitative Structure–Activity Relationship Models

(2018) Vinicius M. Alves et al.   Journal of Chemical Information and Modeling

Leveraging human genetic and adverse outcome pathway (AOP) data to inform susceptibility in human health risk assessment

(2018) Holly M. Mortensen et al.   MAMMALIAN GENOME

Use of toxicogenomics in drug safety evaluation: Current status and an industry perspective

(2018) John L. Vahle et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

In silico toxicology protocols

(2018) Glenn J. Myatt et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Differentiating Pathway-Specific From Nonspecific Effects in High-Throughput Toxicity Data: A Foundation for Prioritizing Adverse Outcome Pathway Development

(2018) Kellie A Fay et al.   TOXICOLOGICAL SCIENCES

Machine learning of toxicological big data enables read-across structure activity relationships (RASAR) outperforming animal test reproducibility

(2018) Thomas Luechtefeld et al.   TOXICOLOGICAL SCIENCES

Using 2D Structural Alerts to Define Chemical Categories for Molecular Initiating Events

(2018) Timothy E H Allen et al.   TOXICOLOGICAL SCIENCES

Modeling Chronic Toxicity: A Comparison of Experimental Variability With (Q)SAR/Read-Across Predictions

(2018) Christoph Helma et al.   Frontiers in Pharmacology

An Updated Review of the Molecular Mechanisms in Drug Hypersensitivity

(2018) Chun-Bing Chen et al.   Journal of Immunology Research

Quantitative Structure–Cytotoxicity Relationship of Pyrano[4,3-b]chromones

(2018) JUNKO NAGAI et al.   ANTICANCER RESEARCH

Machine Learning Based Toxicity Prediction: From Chemical Structural Description to Transcriptome Analysis

(2018) Yunyi Wu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Toxic Colors: The Use of Deep Learning for Predicting Toxicity of Compounds Merely from Their Graphic Images

(2018) Michael Fernandez et al.   Journal of Chemical Information and Modeling

OUP accepted manuscript

(2018)   MUTAGENESIS

Peeking inside the black-box: A survey on Explainable Artificial Intelligence (XAI)

(2018) Amina Adadi et al.   IEEE Access

A Comparative Study of Multitask Toxicity Modeling on a Broad Chemical Space

(2018) Sergey Sosnin et al.   Journal of Chemical Information and Modeling

Dissecting Machine-Learning Prediction of Molecular Activity: Is an Applicability Domain Needed for Quantitative Structure–Activity Relationship Models Based on Deep Neural Networks?

(2018) Ruifeng Liu et al.   Journal of Chemical Information and Modeling

Application of Bioactivity Profile-Based Fingerprints for Building Machine Learning Models

(2018) Noé Sturm et al.   Journal of Chemical Information and Modeling

Nitro-Group-Containing Drugs

(2018) Kunal Nepali et al.   JOURNAL OF MEDICINAL CHEMISTRY

Artificial Intelligence in Drug Design

(2018) Gerhard Hessler et al.   MOLECULES

Oy Vey! A Comment on “Machine Learning of Toxicological Big Data Enables Read-Across Structure Activity Relationships Outperforming Animal Test Reproducibility”

(2018) Vinicius M Alves et al.   TOXICOLOGICAL SCIENCES

Toxicogenomics: A 2020 Vision

(2018) Zhichao Liu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Formatting biological big data for modern machine learning in drug discovery

(2018) Miquel Duran-Frigola et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening

(2018) Daniel Jimenez-Carretero et al.   PLoS Computational Biology

Integrated analysis of in vitro data and the adverse outcome pathway framework for prioritization and regulatory applications: An exploratory case study using publicly available data on piperonyl butoxide and liver models

(2018) Noffisat O. Oki et al.   TOXICOLOGY IN VITRO

Principles and procedures for handling out-of-domain and indeterminate results as part of ICH M7 recommended (Q)SAR analyses

(2018) Alexander Amberg et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Molecular fingerprint-derived similarity measures for toxicological read-across: Recommendations for optimal use

(2018) C.L. Mellor et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

From the exposome to mechanistic understanding of chemical-induced adverse effects

(2017) Beate I. Escher et al.   ENVIRONMENT INTERNATIONAL

A Case Study Application of the Aggregate Exposure Pathway (AEP) and Adverse Outcome Pathway (AOP) Frameworks to Facilitate the Integration of Human Health and Ecological End Points for Cumulative Risk Assessment (CRA)

(2017) David E. Hines et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Quantitative Adverse Outcome Pathways and Their Application to Predictive Toxicology

(2017) Rory B. Conolly et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Developing Collaborative QSAR Models Without Sharing Structures

(2017) Peter Gedeck et al.   Journal of Chemical Information and Modeling

Applying Mondrian Cross-Conformal Prediction To Estimate Prediction Confidence on Large Imbalanced Bioactivity Data Sets

(2017) Jiangming Sun et al.   Journal of Chemical Information and Modeling

Deep Learning Based Regression and Multiclass Models for Acute Oral Toxicity Prediction with Automatic Chemical Feature Extraction

(2017) Youjun Xu et al.   Journal of Chemical Information and Modeling

Demystifying Multitask Deep Neural Networks for Quantitative Structure–Activity Relationships

(2017) Yuting Xu et al.   Journal of Chemical Information and Modeling

Interpretation of Quantitative Structure–Activity Relationship Models: Past, Present, and Future

(2017) Pavel Polishchuk   Journal of Chemical Information and Modeling

Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP

(2017) Sankalp Jain et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

3D-SDAR modeling of hERG potassium channel affinity: A case study in model design and toxicophore identification

(2017) Iva B. Stoyanova-Slavova et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Modification of polychlorinated phenols and evaluation of their toxicity, biodegradation and bioconcentration using three-dimensional quantitative structure–activity relationship models

(2017) Lidan Tong et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Machine learning-based prediction of adverse drug effects: An example of seizure-inducing compounds

(2017) Mengxuan Gao et al.   JOURNAL OF PHARMACOLOGICAL SCIENCES

Legacy data sharing to improve drug safety assessment: the eTOX project

(2017) Ferran Sanz et al.   NATURE REVIEWS DRUG DISCOVERY

Lessons learned from read-across case studies for repeated-dose toxicity

(2017) Terry W. Schultz et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Utility of published DNA reactivity alerts

(2017) Alun Myden et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Distinguishing between expert and statistical systems for application under ICH M7

(2017) Chris Barber et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop

(2017) Roland Buesen et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

The Role of Omics in the Application of Adverse Outcome Pathways for Chemical Risk Assessment

(2017) Erica K. Brockmeier et al.   TOXICOLOGICAL SCIENCES

A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions

(2017) Penny Nymark et al.   TOXICOLOGICAL SCIENCES

Beyond the hype: deep neural networks outperform established methods using a ChEMBL bioactivity benchmark set

(2017) Eelke B. Lenselink et al.   Journal of Cheminformatics

Modelling compound cytotoxicity using conformal prediction and PubChem HTS data

(2017) Fredrik Svensson et al.   Toxicology Research

Using Molecular Initiating Events to Develop a Structural Alert Based Screening Workflow for Nuclear Receptor Ligands Associated with Hepatic Steatosis

(2016) Claire L. Mellor et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Predicting Rat and Human Pregnane X Receptor Activators Using Bayesian Classification Models

(2016) Mohamed Diwan M. AbdulHameed et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Alarms about structural alerts

(2016) Vinicius M. Alves et al.   GREEN CHEMISTRY

Fragment Prioritization on a Large Mutagenicity Dataset

(2016) Matteo Floris et al.   Molecular Informatics

Chemoinformatic Classification Methods and their Applicability Domain

(2016) Miriam Mathea et al.   Molecular Informatics

Mutagenicity in a Molecule: Identification of Core Structural Features of Mutagenicity Using a Scaffold Analysis

(2016) Kuo-Hsiang Hsu et al.   PLoS One

Principles and procedures for implementation of ICH M7 recommended (Q)SAR analyses

(2016) Alexander Amberg et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

It's difficult, but important, to make negative predictions

(2016) Richard V. Williams et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Systematically evaluating read-across prediction and performance using a local validity approach characterized by chemical structure and bioactivity information

(2016) Imran Shah et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modelling$

(2016) K. Mansouri et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Applicability domain: towards a more formal definition$

(2016) T. Hanser et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Conformal prediction to define applicability domain – A case study on predicting ER and AR binding

(2016) U. Norinder et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

How Adverse Outcome Pathways Can Aid the Development and Use of Computational Prediction Models for Regulatory Toxicology

(2016) Clemens Wittwehr et al.   TOXICOLOGICAL SCIENCES

An integrative data mining approach to identifying adverse outcome pathway signatures

(2016) Noffisat O. Oki et al.   TOXICOLOGY

Making big sense from big data in toxicology by read-across

(2016) Thomas Hartung   ALTEX-Alternatives to Animal Experimentation

Toward Good Read-Across Practice (GRAP) guidance

(2016) Nicholas Ball   ALTEX-Alternatives to Animal Experimentation

Supporting read-across using biological data

(2016) Hao Zhu   ALTEX-Alternatives to Animal Experimentation

Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets

(2016) Isidro Cortes-Ciriano   Journal of Cheminformatics

Early drug development: assessment of proarrhythmic risk and cardiovascular safety

(2016) Robert M. Lester et al.   Expert Review of Clinical Pharmacology

Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network

(2016) Tyler B. Hughes et al.   ACS Central Science

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Large-Scale Predictive Drug Safety: From Structural Alerts to Biological Mechanisms

(2015) Ricard Garcia-Serna et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Discovering Structural Alerts for Mutagenicity Using Stable Emerging Molecular Patterns

(2015) Jean-Philippe Métivier et al.   Journal of Chemical Information and Modeling

Studies of genotoxicity and mutagenicity of nitroimidazoles: demystifying this critical relationship with the nitro group

(2015) Núbia Boechat et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

An analysis of the attrition of drug candidates from four major pharmaceutical companies

(2015) Michael J. Waring et al.   NATURE REVIEWS DRUG DISCOVERY

Deep learning in neural networks: An overview

(2015) Jürgen Schmidhuber   NEURAL NETWORKS

A strategy for structuring and reporting a read-across prediction of toxicity

(2015) T.W. Schultz et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects

(2015) Isidro Cortés-Ciriano et al.   MedChemComm

On Pixel-Wise Explanations for Non-Linear Classifier Decisions by Layer-Wise Relevance Propagation

(2015) Sebastian Bach et al.   PLoS One

Systems Toxicology: From Basic Research to Risk Assessment

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

Should the Incorporation of Structural Alerts be Restricted in Drug Design? An Analysis of Structure-Toxicity Trends with Aniline-Based Drugs

(2014) A.S. Kalgutkar   CURRENT MEDICINAL CHEMISTRY

Computational Derivation of Structural Alerts from Large Toxicology Data Sets

(2014) Ernst Ahlberg et al.   Journal of Chemical Information and Modeling

Introducing Conformal Prediction in Predictive Modeling. A Transparent and Flexible Alternative to Applicability Domain Determination

(2014) Ulf Norinder et al.   Journal of Chemical Information and Modeling

Methods for assigning confidence to toxicity data with multiple values — Identifying experimental outliers

(2014) Fabian P. Steinmetz et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Adverse Outcome Pathway (AOP) Development I: Strategies and Principles

(2014) Daniel L. Villeneuve et al.   TOXICOLOGICAL SCIENCES

Reliable estimation of prediction errors for QSAR models under model uncertainty using double cross-validation

(2014) Désirée Baumann et al.   Journal of Cheminformatics

Ligand and Structure-Based Classification Models for Prediction of P-Glycoprotein Inhibitors

(2013) Freya Klepsch et al.   Journal of Chemical Information and Modeling

Automatic knowledge extraction from chemical structures: the case of mutagenicity prediction

(2013) T. Ferrari et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

The Innovative Medicines Initiative: A European Response to the Innovation Challenge

(2012) M Goldman   CLINICAL PHARMACOLOGY & THERAPEUTICS

A Multiscale Simulation System for the Prediction of Drug-Induced Cardiotoxicity

(2011) Cristian Obiol-Pardo et al.   Journal of Chemical Information and Modeling

Size estimation of chemical space: how big is it?

(2011) Kurt L. M. Drew et al.   JOURNAL OF PHARMACY AND PHARMACOLOGY

Exhaustive Sampling of Docking Poses Reveals Binding Hypotheses for Propafenone Type Inhibitors of P-Glycoprotein

(2011) Freya Klepsch et al.   PLoS Computational Biology

The hERG Potassium Channel and Drug Trapping: Insight from Docking Studies with Propafenone Derivatives

(2010) Khac-Minh Thai et al.   ChemMedChem

Adverse outcome pathways: A conceptual framework to support ecotoxicology research and risk assessment

(2010) Gerald T. Ankley et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Trust, But Verify: On the Importance of Chemical Structure Curation in Cheminformatics and QSAR Modeling Research

(2010) Denis Fourches et al.   Journal of Chemical Information and Modeling

Best Practices for QSAR Model Development, Validation, and Exploitation

(2010) Alexander Tropsha   Molecular Informatics

Learning from Imbalanced Data

(2009) Haibo He et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Using chemical categories to fill data gaps in hazard assessment

(2009) K. van Leeuwen et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

Development and Validation of AMANDA, a New Algorithm for Selecting Highly Relevant Regions in Molecular Interaction Fields

(2008) Ángel Durán et al.   Journal of Chemical Information and Modeling

In Silico Tools for Sharing Data and Knowledge on Toxicity and Metabolism: Derek for Windows, Meteor, and Vitic

(2008) Carol A. Marchant et al.   TOXICOLOGY MECHANISMS AND METHODS