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List of works by Richard S. Judson

A comparison of machine learning algorithms for chemical toxicity classification using a simulated multi-scale data model

scientific article

A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics.

scientific article published on 20 February 2018

A large-scale experiment to assess protein structure prediction methods.

scientific article

A mechanistic framework for integrating chemical structure and high-throughput screening results to improve toxicity predictions

article

A novel framework for predicting in vivo toxicities from in vitro data using optimal methods for dense and sparse matrix reordering and logistic regression

scientific article

A systematic evaluation of analogs and automated read-across prediction of estrogenicity: A case study using hindered phenols

ACToR — Aggregated Computational Toxicology Resource

Activity profiles of 309 ToxCast™ chemicals evaluated across 292 biochemical targets

scientific article published on 18 January 2011

Advancements in Life Cycle Human Exposure and Toxicity Characterization

article

Aggregating data for computational toxicology applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System

scientific article

Allelic dropout in long QT syndrome genetic testing: a possible mechanism underlying false-negative results

scientific article

An "EAR" on Environmental Surveillance and Monitoring: A Case Study on the Use of Exposure-Activity Ratios (EARs) to Prioritize Sites, Chemicals, and Bioactivities of Concern in Great Lakes Waters.

scientific article

Analysis of eight oil spill dispersants using rapid, in vitro tests for endocrine and other biological activity

scientific article

Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space.

scientific article

Assessing bioactivity-exposure profiles of fruit and vegetable extracts in the BioMAP profiling system

scientific article published on 12 September 2018

Bayesian meta-analysis of genetic association studies with different sets of markers

scientific article published on April 2008

Binary classification of a large collection of environmental chemicals from estrogen receptor assays by quantitative structure-activity relationship and machine learning methods.

scientific article published on 11 December 2013

CERAPP: Collaborative Estrogen Receptor Activity Prediction Project

scientific article published in July 2016

Characterizing cleft palate toxicants using ToxCast data, chemical structure, and the biomedical literature

scientific article published on 30 August 2019

Chemical Safety Assessment Using Read-Across: Assessing the Use of Novel Testing Methods to Strengthen the Evidence Base for Decision Making

scientific article

Chemical genomics profiling of environmental chemical modulation of human nuclear receptors

scientific article

CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity

scientific article published on 07 February 2020

Comment on "On the Utility of ToxCast™ and ToxPi as Methods for Identifying New Obesogens".

scientific article published on January 2017

Comparison of Approaches for Determining Bioactivity Hits from High-Dimensional Profiling Data

scientific article published on 29 August 2020

Computational Exposure Science: An Emerging Discipline to Support 21st-Century Risk Assessment

scientific article

Computational toxicology--a state of the science mini review

scientific article published on 07 December 2007

Considerations for Strategic Use of High-Throughput Transcriptomics Chemical Screening Data in Regulatory Decisions

scientific article published on 01 January 2019

Correction to Screening Chemicals for Estrogen Receptor Bioactivity Using a Computational Model

scientific article

Corrigendum to: "Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity"

scientific article published on 11 June 2020

Development and Validation of a Computational Model for Androgen Receptor Activity

scientific article

Development of a consumer product ingredient database for chemical exposure screening and prioritization

scientific article published on 27 December 2013

Development of a curated Hershberger database

article

Development of a prioritization method for chemical-mediated effects on steroidogenesis using an integrated statistical analysis of high-throughput H295R data

scientific article published on 29 October 2019

Development of a quantitative morphological assessment of toxicant-treated zebrafish larvae using brightfield imaging and high-content analysis

scientific article published on 29 February 2016

Development, validation and integration of in silico models to identify androgen active chemicals

article

Docking-based classification models for exploratory toxicology studies on high-quality estrogenic experimental data

scientific article

Dosimetric anchoring of in vivo and in vitro studies for perfluorooctanoate and perfluorooctanesulfonate

scientific article published on 17 September 2013

EADB: an estrogenic activity database for assessing potential endocrine activity.

scientific article published on 28 July 2013

Economic benefits of using adaptive predictive models of reproductive toxicity in the context of a tiered testing program

scientific article published in February 2012

Editor's Highlight: Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space.

scientific article

Editor's Highlight: Genetic Targets of Acute Toluene Inhalation in Drosophila melanogaster

scientific article published on 24 December 2016

Editor's Highlight: Negative Predictors of Carcinogenicity for Environmental Chemicals

scientific article

Empirical Models for Anatomical and Physiological Changes in a Human Mother and Fetus During Pregnancy and Gestation

Empirical models for anatomical and physiological changes in a human mother and fetus during pregnancy and gestation

scientific article published on 02 May 2019

Endocrine profiling and prioritization of environmental chemicals using ToxCast data

scientific article

Environmental impact on vascular development predicted by high-throughput screening

scientific article

Erratum to "High-Throughput H295R Steroidogenesis Assay: Utility as an Alternative and a Statistical Approach to Characterize Effects on Steroidogenesis"

scientific article published on 01 August 2018

Estimating toxicity-related biological pathway altering doses for high-throughput chemical risk assessment

scientific article published on 8 March 2011

Evaluation of 309 environmental chemicals using a mouse embryonic stem cell adherent cell differentiation and cytotoxicity assay

scientific article

Evaluation of androgen assay results using a curated Hershberger database

scientific article published on 08 September 2018

Evaluation of high-throughput genotoxicity assays used in profiling the US EPA ToxCast chemicals

scientific article

Evidence-based toxicology for the 21st century: opportunities and challenges

scientific article published in January 2013

Exploring consumer exposure pathways and patterns of use for chemicals in the environment

scientific article published on 2 January 2015

Genome-wide evaluation of the public SNP databases

scientific article published in November 2003

Haplotypes of the cholesteryl ester transfer protein gene predict lipid-modifying response to statin therapy

scientific article published in January 2003

High throughput heuristics for prioritizing human exposure to environmental chemicals

scientific article published on 24 October 2014

High-Throughput Screening to Predict Chemical-Assay Interference

scientific article published on 04 March 2020

High-throughput H295R steroidogenesis assay: utility as an alternative and a statistical approach to characterize effects on steroidogenesis

scientific article published in December 2017

High-throughput models for exposure-based chemical prioritization in the ExpoCast project

scientific article published on 11 July 2013

How many SNPs does a genome-wide haplotype map require?

scientific article

Identification of potential endocrine disrupting chemicals using gene expression biomarkers

scientific article published on 17 July 2019

Identifying environmental chemicals as agonists of the androgen receptor by using a quantitative high-throughput screening platform

scientific article

Impact of environmental chemicals on key transcription regulators and correlation to toxicity end points within EPA's ToxCast program.

scientific article

In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning

scientific article published on 22 December 2016

In Silico Study of In Vitro GPCR Assays by QSAR Modeling

scientific article

In vitro and modelling approaches to risk assessment from the U.S. Environmental Protection Agency ToxCast programme

scientific article published on 22 April 2014

In vitro perturbations of targets in cancer hallmark processes predict rodent chemical carcinogenesis

scientific article

In vitro screening of environmental chemicals for targeted testing prioritization: the ToxCast project

scientific article

Incorporating Biological, Chemical, and Toxicological Knowledge Into Predictive Models of Toxicity

article

Incorporating High-Throughput Exposure Predictions With Dosimetry-Adjusted In Vitro Bioactivity to Inform Chemical Toxicity Testing

scientific article

Incorporating exposure information into the toxicological prioritization index decision support framework

scientific article published on 2 August 2012

Incorporating human dosimetry and exposure into high-throughput in vitro toxicity screening.

scientific article published on 16 July 2010

Inelastic probabilities above the three-body breakup threshold via a projection operator formalism

Integrated Model of Chemical Perturbations of a Biological Pathway Using 18 In Vitro High-Throughput Screening Assays for the Estrogen Receptor.

scientific article published on 13 August 2015

Integrating data gap filling techniques: A case study predicting TEFs for neurotoxicity TEQs to facilitate the hazard assessment of polychlorinated biphenyls

Integration of dosimetry, exposure, and high-throughput screening data in chemical toxicity assessment

scientific article

Linking high resolution mass spectrometry data with exposure and toxicity forecasts to advance high-throughput environmental monitoring

scientific article

Modeling In Vitro Cell-Based Assays Experiments

Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium

scientific article published on 10 February 2016

New and confirmatory evidence of an association between APOE genotype and baseline C-reactive protein in dyslipidemic individuals

scientific article

Notes from the SNP vs. haplotype front

OPERA models for predicting physicochemical properties and environmental fate endpoints.

scientific article

On selecting a minimal set of in vitro assays to reliably determine estrogen agonist activity

scientific article published on 6 October 2017

Perspectives on validation of high-throughput assays supporting 21st century toxicity testing

scientific article (publication date: 2013)

Pharmacogenomics in Drug Development

article

Pharmacogenomics in Drug Development and Clinical Research

article

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

scientific article

Predicting estrogen receptor activation by a group of substituted phenols: An integrated approach to testing and assessment case study

scientific article published on 20 May 2019

Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure

scientific article published on 9 March 2015

Predicting in vivo effect levels for repeat-dose systemic toxicity using chemical, biological, kinetic and study covariates

scientific article published on 27 October 2017

Prediction of Estrogenic Bioactivity of Environmental Chemical Metabolites

scientific article published on 10 August 2016

Predictive Structure-Based Toxicology Approaches To Assess the Androgenic Potential of Chemicals.

scientific article

Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses

scientific article published on 10 July 2014

Predictive model of rat reproductive toxicity from ToxCast high throughput screening

scientific article

Predictive models and computational toxicology

scientific article

Predictive models of prenatal developmental toxicity from ToxCast high-throughput screening data

scientific article

Prioritizing Environmental Chemicals for Obesity and Diabetes Outcomes Research: A Screening Approach Using ToxCast™ High-Throughput Data

scientific article

Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays

scientific article published on 16 May 2013

Profiling bioactivity of the ToxCast chemical library using BioMAP primary human cell systems

scientific article

Profiling chemicals based on chronic toxicity results from the U.S. EPA ToxRef Database

scientific article published on 20 October 2008

Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway

scientific article

Profiling the ToxCast Library With a Pluripotent Human (H9) Stem Cell Line-Based Biomarker Assay for Developmental Toxicity

scientific article published on 01 April 2020

Profiling the activity of environmental chemicals in prenatal developmental toxicity studies using the U.S. EPA's ToxRefDB.

scientific article published on 10 April 2009

Profiling the reproductive toxicity of chemicals from multigeneration studies in the toxicity reference database

scientific article

Progress in data interoperability to support computational toxicology and chemical safety evaluation

scientific article published on 09 August 2019

Public databases supporting computational toxicology

scientific article published on February 2010

Real-time growth kinetics measuring hormone mimicry for ToxCast chemicals in T-47D human ductal carcinoma cells

scientific article published on 10 June 2013

Relative impact of incorporating pharmacokinetics on predicting in vivo hazard and mode of action from high-throughput in vitro toxicity assays

scientific article

Restoring value to stalled Phase II compounds: the case for developing a novel compound for depression using pharmacogenetics

Retrospective mining of toxicology data to discover multispecies and chemical class effects: Anemia as a case study.

scientific article

Screening Chemicals for Estrogen Receptor Bioactivity Using a Computational Model

scientific article

Selecting a minimal set of androgen receptor assays for screening chemicals

scientific article published on 13 August 2020

Spectrum and prevalence of cardiac sodium channel variants among black, white, Asian, and Hispanic individuals: implications for arrhythmogenic susceptibility and Brugada/long QT syndrome genetic testing

scientific article

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

scientific article

Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes

scientific article

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

scientific article

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

scientific article

The Next Generation Blueprint of Computational Toxicology at the U.S. Environmental Protection Agency

scientific article published on 01 June 2019

The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology

scientific article published on 03 November 2020

The exposure data landscape for manufactured chemicals

scientific article

The next generation of risk assessment multi-year study - highlights of findings, applications to risk assessment, and future directions

journal article published in 2016

The toxicity data landscape for environmental chemicals

scientific article

Tiered High-Throughput Screening Approach to Identify Thyroperoxidase Inhibitors Within the ToxCast Phase I and II Chemical Libraries

scientific article published on 15 February 2016

Time-dependent wave-packet method for the complete determination ofS-matrix elements for reactive molecular collisions in three dimensions

scientific article published on 01 July 1990

ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology

scientific article (publication date: 15 August 2016)

ToxCast: Predicting Toxicity Potential Through High-Throughput Bioactivity Profiling

article

ToxPi GUI: an interactive visualization tool for transparent integration of data from diverse sources of evidence

scientific article

Toxicity data informatics: supporting a new paradigm for toxicity prediction

scientific article

Toxicokinetic Triage for Environmental Chemicals

scientific article

Uncertainty quantification in ToxCast high throughput screening

scientific article published in PLoS ONE

Update on EPA's ToxCast program: providing high throughput decision support tools for chemical risk management.

scientific article published on 15 May 2012

Using ToxCast™ Data to Reconstruct Dynamic Cell State Trajectories and Estimate Toxicological Points of Departure

scientific article

Using in vitro high throughput screening assays to identify potential endocrine-disrupting chemicals.

scientific article published on 28 September 2012

Using multiple drug exposure levels to optimize power in pharmacogenetic trials

scientific article

Using nuclear receptor activity to stratify hepatocarcinogens

scientific article

Using pathway modules as targets for assay development in xenobiotic screening

scientific article

Variability in <i>in vivo</i> studies: Defining the upper limit of performance for predictions of systemic effect levels

scientific article published on 01 August 2020

Vision of a near future: Bridging the human health-environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment

scientific article published on 25 October 2019

Workflow for defining reference chemicals for assessing performance of in vitro assays

scientific article published on 17 December 2018

Xenobiotic-metabolizing enzyme and transporter gene expression in primary cultures of human hepatocytes modulated by ToxCast chemicals

scientific article published on February 2010

tcpl: the ToxCast pipeline for high-throughput screening data

scientific article

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