List of works - Russell S. Thomas

A bistable switch underlying B-cell differentiation and its disruption by the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin

scientific article

A cellular genetics approach identifies gene-drug interactions and pinpoints drug toxicity pathway nodes

scientific article

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

scientific article (publication date: August 2010)

A comparison of transcriptomic and metabonomic technologies for identifying biomarkers predictive of two-year rodent cancer bioassays.

scientific article published on 17 November 2006

A comprehensive statistical analysis of predicting in vivo hazard using high-throughput in vitro screening

scientific article published on 26 April 2012

A functional map of NFkappaB signaling identifies novel modulators and multiple system controls

scientific article

A genomics-based analysis of relative potencies of dioxin-like compounds in primary rat hepatocytes.

scientific article published on 17 September 2013

A method to integrate benchmark dose estimates with genomic data to assess the functional effects of chemical exposure

scientific article

A multi-stakeholder perspective on the use of alternative test strategies for nanomaterial safety assessment

journal article published in 2013

A physiologically based pharmacodynamic analysis of hepatic foci within a medium-term liver bioassay using pentachlorobenzene as a promoter and diethylnitrosamine as an initiator.

scientific article published in July 2000

Accelerating the Pace of Chemical Risk Assessment.

scientific article published on 30 March 2018

Activation of the aryl-hydrocarbon receptor inhibits invasive and metastatic features of human breast cancer cells and promotes breast cancer cell differentiation

scientific article

All-or-none suppression of B cell terminal differentiation by environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin

scientific article published on 26 January 2013

An integrated genomic analysis of aryl hydrocarbon receptor-mediated inhibition of B-cell differentiation

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

Application of genomic biomarkers to predict increased lung tumor incidence in 2-year rodent cancer bioassays.

scientific article published on 20 February 2007

Application of transcriptional benchmark dose values in quantitative cancer and noncancer risk assessment

scientific article published on 22 November 2010

Aryl hydrocarbon receptor deficiency causes dysregulated cellular matrix metabolism and age-related macular degeneration-like pathology

scientific article published on 08 October 2013

Aryl hydrocarbon receptor knock-out exacerbates choroidal neovascularization via multiple pathogenic pathways

scientific article

Aryl hydrocarbon receptor knockout rats are insensitive to the pathological effects of repeated oral exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin.

scientific article published on 17 August 2015

Aryl hydrocarbon receptor regulates cell cycle progression in human breast cancer cells via a functional interaction with cyclin-dependent kinase 4.

scientific article

BMDExpress: a software tool for the benchmark dose analyses of genomic data

scientific article

Basal gene expression in male and female Sprague-Dawley rat nasal respiratory and olfactory epithelium

scientific article published on September 2007

Biological networks for predicting chemical hepatocarcinogenicity using gene expression data from treated mice and relevance across human and rat species

scientific article

Biological responses in rats exposed to cigarette smoke and Middle East sand (dust).

scientific article published in January 2012

Chemical mixture toxicology: from descriptive to mechanistic, and going on to in silico toxicology

journal article published in 2004

Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments

scientific article

Concentration- and time-dependent genomic changes in the mouse urinary bladder following exposure to arsenate in drinking water for up to 12 weeks.

scientific article published on 27 July 2011

Cross-species comparisons of transcriptomic alterations in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin

scientific article

Cross-species transcriptomic analysis of mouse and rat lung exposed to chloroprene

scientific article

Determination of velocity correction factors for real-time air velocity monitoring in underground mines

journal article published in 2017

Developing toxicologically predictive gene sets using cDNA microarrays and Bayesian classification.

scientific article published in January 2002

Development of 3D dynamic flow model of human liver and its application to prediction of metabolic clearance of 7-ethoxycoumarin

scientific article published on 4 March 2014

Dose-dependent transitions in Nrf2-mediated adaptive response and related stress responses to hypochlorous acid in mouse macrophages

scientific article published on 17 April 2009

Dose-response modeling in reproductive toxicology in the systems biology era.

scientific article

EDGE: a centralized resource for the comparison, analysis, and distribution of toxicogenomic information

scientific article

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

Enhanced regional expression of glutathione S-transferase P1-1 with colocalized AP-1 and CYP 1A2 induction in chlorobenzene-induced porphyria

scientific article published on May 1998

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

scientific article published on 8 March 2011

Evaluation of gene expression changes in human primary uroepithelial cells following 24-hr exposures to inorganic arsenic and its methylated metabolites

scientific article

Evidence for hepatocarcinogenic activity of pentachlorobenzene with intralobular variation in foci incidence.

scientific article published in October 1998

Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome

scientific article

Formaldehyde: integrating dosimetry, cytotoxicity, and genomics to understand dose-dependent transitions for an endogenous compound

scientific article published on 30 September 2010

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes

scientific article

Gene expression changes following acute hydrogen sulfide (H2S)-induced nasal respiratory epithelial injury

scientific article

Genome-scale functional profiling of the mammalian AP-1 signaling pathway

scientific article

Genome-wide analysis of DNA methylation and gene expression changes in the mouse lung following subchronic arsenate exposure.

scientific article published on 28 July 2010

Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival

scientific article published on 23 June 2006

Genomic analysis of human lung fibroblasts exposed to vanadium pentoxide to identify candidate genes for occupational bronchitis

scientific article (publication date: 25 April 2007)

Genomic signatures and dose-dependent transitions in nasal epithelial responses to inhaled formaldehyde in the rat.

scientific article published on 21 May 2008

IVT-seq reveals extreme bias in RNA sequencing

scientific article

Identification of gene expression predictors of occupational benzene exposure

journal article published in 2018

Identification of modulators of the nuclear receptor peroxisome proliferator-activated receptor α (PPARα) in a mouse liver gene expression compendium

scientific article

Identifying genes that mediate anthracyline toxicity in immune cells

scientific article

Immune cell-based screening assay for response to anticancer agents: applications in pharmacogenomics

scientific article

In utero exposure to chloroquine alters sexual development in the male fetal rat.

scientific article published on 22 April 2009

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

scientific article published on 22 April 2014

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

scientific article

Incorporating Monte Carlo simulation into physiologically based pharmacokinetic models using advanced continuous simulation language (ACSL): a computational method

scientific article published in May 1996

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

scientific article published on 16 July 2010

Incorporating new technologies into toxicity testing and risk assessment: moving from 21st century vision to a data-driven framework.

scientific article

Incorporating population variability and susceptible subpopulations into dosimetry for high-throughput toxicity testing

scientific article published on 21 August 2014

Integrating pathway-based transcriptomic data into quantitative chemical risk assessment: a five chemical case study

scientific article

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

scientific article

Knockout of the aryl hydrocarbon receptor results in distinct hepatic and renal phenotypes in rats and mice.

scientific article published on 13 July 2013

Lineage-dependent effects of aryl hydrocarbon receptor agonists contribute to liver tumorigenesis.

scientific article

MYC is an early response regulator of human adipogenesis in adipose stem cells

scientific article

New directions in incidence-dose modeling

scientific article

Physiologically based pharmacokinetic/pharmacodynamic modeling of chemical mixtures and possible applications in risk assessment.

scientific article published in December 1995

Physiologically based pharmacokinetic/pharmacodynamic modeling of the toxicologic interaction between carbon tetrachloride and Kepone.

scientific article published in January 1996

Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure

scientific article published on 9 March 2015

Quantitative analyses and transcriptomic profiling of circulating messenger RNAs as biomarkers of rat liver injury

scientific article published in June 2010

Regulation of Bach2 by the aryl hydrocarbon receptor as a mechanism for suppression of B-cell differentiation by 2,3,7,8-tetrachlorodibenzo-p-dioxin

scientific article

Regulation of aryl hydrocarbon receptor function by selective estrogen receptor modulators

scientific article

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

scientific article

Research toward the development of a biologically based dose response assessment for inorganic arsenic carcinogenicity: a progress report

scientific article published on 30 March 2007

Screening Chemicals for Estrogen Receptor Bioactivity Using a Computational Model

scientific article

Sequence variation and phylogenetic history of the mouse Ahr gene

scientific article published in March 2002

Stochastic modeling of B lymphocyte terminal differentiation and its suppression by dioxin

scientific article

Stochastic simulation of hepatic preneoplastic foci development for four chlorobenzene congeners in a medium-term bioassay

scientific article published on 15 April 2003

Subchronic Hepatotoxicity Evaluation of 1,2,4-Tribromobenzene in Sprague-Dawley Rats

scientific article published on 03 April 2012

Subchronic Hepatotoxicity Evaluation of Hydrazobenzene in Fischer 344 Rats

scientific article published on 06 November 2012

Subchronic hepatotoxicity evaluation of 2,3,4,6-tetrachlorophenol in sprague dawley rats

scientific article

Subchronic hepatotoxicity evaluation of bromobenzene in Fischer 344 rats.

scientific article published on 9 March 2012

Subchronic thyroid toxicity evaluation of 4,4'-methylenebis(N,N'-dimethyl)aniline in Fischer 344 rats

scientific article published in January 2012

Subchronic toxicity evaluation of anthraquinone in Fischer 344 rats

scientific article

Subchronic toxicity evaluation of potassium bromate in Fischer 344 rats.

scientific article published on 19 October 2013

Subchronic urinary bladder toxicity evaluation of N-Nitrosodiphenylamine in Fischer 344 rats

scientific article published on 14 August 2012

Systems pharmacology assessment of the 5-fluorouracil pathway

scientific article

Technical guide for applications of gene expression profiling in human health risk assessment of environmental chemicals.

scientific article published on 2 May 2015

Temporal concordance between apical and transcriptional points of departure for chemical risk assessment.

scientific article published on 17 April 2013

The Aryl-Hydrocarbon Receptor Protein Interaction Network (AHR-PIN) as Identified by Tandem Affinity Purification (TAP) and Mass Spectrometry

scientific article published on 5 December 2013

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 SEURAT-1 approach towards animal free human safety assessment

scientific article published on 5 November 2014

The Tox21 10K Compound Library: Collaborative Chemistry Advancing Toxicology

scientific article published on 03 November 2020

The application of physiologically based pharmacokinetic/pharmacodynamic (PBPK/PD) modeling for exploring risk assessment approaches of chemical mixtures

scientific article

The aryl hydrocarbon receptor interacts with ATP5α1, a subunit of the ATP synthase complex, and modulates mitochondrial function

scientific article published on 12 May 2011

The human toxome project

scientific article

The identification of protein kinase C iota as a regulator of the Mammalian heat shock response using functional genomic screens

scientific article

The use of physiologically-based pharmacokinetic/pharmacodynamic dosimetry models for chemical mixtures

scientific article published on December 1995

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

scientific article (publication date: 15 August 2016)

Toxicokinetic Triage for Environmental Chemicals

scientific article

Transcriptional responses in the rat nasal epithelium following subchronic inhalation of naphthalene vapor

scientific article published on 27 June 2014

Use of a medium-term liver focus bioassay to assess the hepatocarcinogenicity of 1,2,4,5-tetrachlorobenzene and 1,4-dichlorobenzene

scientific article published on July 1998

Use of short-term transcriptional profiles to assess the long-term cancer-related safety of environmental and industrial chemicals

scientific article published on 23 September 2009

List of works by Russell S. Thomas

A bistable switch underlying B-cell differentiation and its disruption by the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin

A cellular genetics approach identifies gene-drug interactions and pinpoints drug toxicity pathway nodes

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

A comparison of transcriptomic and metabonomic technologies for identifying biomarkers predictive of two-year rodent cancer bioassays.

A comprehensive statistical analysis of predicting in vivo hazard using high-throughput in vitro screening

A functional map of NFkappaB signaling identifies novel modulators and multiple system controls

A genomics-based analysis of relative potencies of dioxin-like compounds in primary rat hepatocytes.

A method to integrate benchmark dose estimates with genomic data to assess the functional effects of chemical exposure

A multi-stakeholder perspective on the use of alternative test strategies for nanomaterial safety assessment

A physiologically based pharmacodynamic analysis of hepatic foci within a medium-term liver bioassay using pentachlorobenzene as a promoter and diethylnitrosamine as an initiator.

Accelerating the Pace of Chemical Risk Assessment.

Activation of the aryl-hydrocarbon receptor inhibits invasive and metastatic features of human breast cancer cells and promotes breast cancer cell differentiation

All-or-none suppression of B cell terminal differentiation by environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin

An integrated genomic analysis of aryl hydrocarbon receptor-mediated inhibition of B-cell differentiation

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

Application of genomic biomarkers to predict increased lung tumor incidence in 2-year rodent cancer bioassays.

Application of transcriptional benchmark dose values in quantitative cancer and noncancer risk assessment

Aryl hydrocarbon receptor deficiency causes dysregulated cellular matrix metabolism and age-related macular degeneration-like pathology

Aryl hydrocarbon receptor knock-out exacerbates choroidal neovascularization via multiple pathogenic pathways

Aryl hydrocarbon receptor knockout rats are insensitive to the pathological effects of repeated oral exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin.

Aryl hydrocarbon receptor regulates cell cycle progression in human breast cancer cells via a functional interaction with cyclin-dependent kinase 4.

BMDExpress: a software tool for the benchmark dose analyses of genomic data

Basal gene expression in male and female Sprague-Dawley rat nasal respiratory and olfactory epithelium

Biological networks for predicting chemical hepatocarcinogenicity using gene expression data from treated mice and relevance across human and rat species

Biological responses in rats exposed to cigarette smoke and Middle East sand (dust).

Chemical mixture toxicology: from descriptive to mechanistic, and going on to in silico toxicology

Comparison of microarrays and RNA-seq for gene expression analyses of dose-response experiments

Concentration- and time-dependent genomic changes in the mouse urinary bladder following exposure to arsenate in drinking water for up to 12 weeks.

Cross-species comparisons of transcriptomic alterations in human and rat primary hepatocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin

Cross-species transcriptomic analysis of mouse and rat lung exposed to chloroprene

Determination of velocity correction factors for real-time air velocity monitoring in underground mines

Developing toxicologically predictive gene sets using cDNA microarrays and Bayesian classification.

Development of 3D dynamic flow model of human liver and its application to prediction of metabolic clearance of 7-ethoxycoumarin

Dose-dependent transitions in Nrf2-mediated adaptive response and related stress responses to hypochlorous acid in mouse macrophages

Dose-response modeling in reproductive toxicology in the systems biology era.

EDGE: a centralized resource for the comparison, analysis, and distribution of toxicogenomic information

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

Enhanced regional expression of glutathione S-transferase P1-1 with colocalized AP-1 and CYP 1A2 induction in chlorobenzene-induced porphyria

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

Evaluation of gene expression changes in human primary uroepithelial cells following 24-hr exposures to inorganic arsenic and its methylated metabolites

Evidence for hepatocarcinogenic activity of pentachlorobenzene with intralobular variation in foci incidence.

Expression profiling in canine osteosarcoma: identification of biomarkers and pathways associated with outcome

Formaldehyde: integrating dosimetry, cytotoxicity, and genomics to understand dose-dependent transitions for an endogenous compound

Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes

Gene expression changes following acute hydrogen sulfide (H2S)-induced nasal respiratory epithelial injury

Genome-scale functional profiling of the mammalian AP-1 signaling pathway

Genome-wide analysis of DNA methylation and gene expression changes in the mouse lung following subchronic arsenate exposure.

Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival

Genomic analysis of human lung fibroblasts exposed to vanadium pentoxide to identify candidate genes for occupational bronchitis

Genomic signatures and dose-dependent transitions in nasal epithelial responses to inhaled formaldehyde in the rat.

IVT-seq reveals extreme bias in RNA sequencing

Identification of gene expression predictors of occupational benzene exposure

Identification of modulators of the nuclear receptor peroxisome proliferator-activated receptor α (PPARα) in a mouse liver gene expression compendium

Identifying genes that mediate anthracyline toxicity in immune cells

Immune cell-based screening assay for response to anticancer agents: applications in pharmacogenomics

In utero exposure to chloroquine alters sexual development in the male fetal rat.

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

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

Incorporating Monte Carlo simulation into physiologically based pharmacokinetic models using advanced continuous simulation language (ACSL): a computational method

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

Incorporating new technologies into toxicity testing and risk assessment: moving from 21st century vision to a data-driven framework.

Incorporating population variability and susceptible subpopulations into dosimetry for high-throughput toxicity testing

Integrating pathway-based transcriptomic data into quantitative chemical risk assessment: a five chemical case study

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

Knockout of the aryl hydrocarbon receptor results in distinct hepatic and renal phenotypes in rats and mice.

Lineage-dependent effects of aryl hydrocarbon receptor agonists contribute to liver tumorigenesis.

MYC is an early response regulator of human adipogenesis in adipose stem cells

New directions in incidence-dose modeling

Physiologically based pharmacokinetic/pharmacodynamic modeling of chemical mixtures and possible applications in risk assessment.

Physiologically based pharmacokinetic/pharmacodynamic modeling of the toxicologic interaction between carbon tetrachloride and Kepone.

Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure

Quantitative analyses and transcriptomic profiling of circulating messenger RNAs as biomarkers of rat liver injury

Regulation of Bach2 by the aryl hydrocarbon receptor as a mechanism for suppression of B-cell differentiation by 2,3,7,8-tetrachlorodibenzo-p-dioxin

Regulation of aryl hydrocarbon receptor function by selective estrogen receptor modulators

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

Research toward the development of a biologically based dose response assessment for inorganic arsenic carcinogenicity: a progress report

Screening Chemicals for Estrogen Receptor Bioactivity Using a Computational Model

Sequence variation and phylogenetic history of the mouse Ahr gene

Stochastic modeling of B lymphocyte terminal differentiation and its suppression by dioxin