selected publications
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academic article
- A decision analysis framework for estimating the potential hazards for drinking water resources of chemicals used in hydraulic fracturing fluids. The Science of the total environment. 574:1544-1558. 2017
- Autoencoder Predicting Estrogenic Chemical Substances (APECS): An Improved Approach for Screening Potentially Estrogenic Chemicals Using In Vitro Assays and Deep Learning. Computational Toxicology. 2017
- A Market-Basket Approach to Predict the Acute Aquatic Toxicity of Munitions and Energetic Materials. Bulletin of environmental contamination and toxicology. 96:779-783. 2016
- Applying comprehensive environmental assessment to research planning for multiwalled carbon nanotubes: Refinements to inform future stakeholder engagement. Integrated environmental assessment and management. 12:96-108. 2016
- Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure–Activity Relationship Modeling. Environmental science & technology. acs.est.5b05327. 2016
- Overview of Chronic Oral Toxicity Values for Chemicals Present in Hydraulic Fracturing Fluids, Flowback, and Produced Waters. Environmental science & technology. 50:4788-4797. 2016
- Response to Cohen et al. (2016) regarding response to Druwe and Burgoon. Archives of toxicology. 90:3131-3132. 2016
- Revisiting Cohen et al. 2015, Cohen et al. 2014 and Waalkes et al. 2014: a bayesian re-analysis of tumor incidences. Archives of toxicology. 90:2047-2048. 2016
- The Next Generation of Risk Assessment Multiyear Study— Highlights of Findings, Applications to Risk Assessment and Future Directions. Environmental health perspectives. 2016
- UsingIn VitroHigh-Throughput Screening Data for Predicting Benzo[k]Fluoranthene Human Health Hazards. Risk analysis : an official publication of the Society for Risk Analysis. 2016
- Can Data Science Inform Environmental Justice and Community Risk Screening for Type 2 Diabetes?. PLoS ONE. 10:e0121855. 2015
- Loss of Hif-2α Rescues the Hif-1α Deletion Phenotype of Neonatal Respiratory Distress In Mice. PLoS ONE. 10:e0139270. 2015
- Systems Biology and Biomarkers of Early Effects for Occupational Exposure Limit Setting. Journal of occupational and environmental hygiene. 12:S41-S54. 2015
- A Framework for the Next Generation of Risk Science. Environmental health perspectives. 2014
- Burst and principal components analyses of MEA data for 16 chemicals describe at least three effects classes. Neurotoxicology. 40:75-85. 2014
- Systematic Omics Analysis Review (SOAR) Tool to Support Risk Assessment. PLoS ONE. 9:e110379. 2014
- What do the data show? Knowledge map development for comprehensive environmental assessment. Integrated environmental assessment and management. 10:37-47. 2014
- Molecular target sequence similarity as a basis for species extrapolation to assess the ecological risk of chemicals with known modes of action. Aquatic toxicology (Amsterdam, Netherlands). 144-145:141-154. 2013
- PPARα-mediated responses in human adult liver stem cells: In vivo/in vitro and cross-species comparisons. The Journal of steroid biochemistry and molecular biology. 138:236-247. 2013
- A graphical systems model and tissue-specific functional gene sets to aid transcriptomic analysis of chemical impacts on the female teleost reproductive axis. Mutation research. Genetic toxicology and environmental mutagenesis. 746:151-162. 2012
- Comparative Metabolomic and Genomic Analyses of TCDD-Elicited Metabolic Disruption in Mouse and Rat Liver. Toxicological sciences : an official journal of the Society of Toxicology. 125:41-55. 2012
- MIPHENO: data normalization for high throughput metabolite analysis. BMC Bioinformatics. 13:10. 2012
- Plastids Are Major Regulators of Light Signaling in Arabidopsis. Plant physiology. 159:366-390. 2012
- Differences in TCDD-elicited gene expression profiles in human HepG2, mouse Hepa1c1c7 and rat H4IIE hepatoma cells. BMC Genomics. 12:193. 2011
- Genome-Wide Computational Analysis of Dioxin Response Element Location and Distribution in the Human, Mouse, and Rat Genomes. Chemical research in toxicology. 24:494-504. 2011
- Hypoxia-inducible factor-1α regulates the expression of genes in hypoxic hepatic stellate cells important for collagen deposition and angiogenesis. Liver international : official journal of the International Association for the Study of the Liver. 31:230-244. 2011
- Non-additive hepatic gene expression elicited by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and 2,2′,4,4′,5,5′-hexachlorobiphenyl (PCB153) co-treatment in C57BL/6 mice. Toxicology and applied pharmacology. 256:154-167. 2011
- Pulmonary Inflammatory and Fibrotic Responses in Fischer 344 Rats After Intratracheal Instillation Exposure to Libby Amphibole. Journal of toxicology and environmental health. Part A. 74:1111-1132. 2011
- Automated Dose-Response Analysis and Comparative Toxicogenomic Evaluation of the Hepatic Effects Elicited by TCDD, TCDF, and PCB126 in C57BL/6 Mice. Toxicological sciences : an official journal of the Society of Toxicology. 118:286-297. 2010
- Effects of TCDD on the expression of nuclear encoded mitochondrial genes. Toxicology and applied pharmacology. 246:58-65. 2010
- Effects of tamoxifen and ethynylestradiol cotreatment on uterine gene expression in immature, ovariectomized mice. Journal of molecular endocrinology. 45:161-173. 2010
- Estrogen receptor-dependent regulation of CYP2B6 in human breast cancer cells. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1799:469-479. 2010
- Oxidative stress is important in the pathogenesis of liver injury induced by sulindac and lipopolysaccharide cotreatment. Toxicology. 272:32-38. 2010
- PCB153-elicited hepatic responses in the immature, ovariectomized C57BL/6 mice: Comparative toxicogenomic effects of dioxin and non-dioxin-like ligands. Toxicology and applied pharmacology. 243:359-371. 2010
- Automated Dose-Response Analysis of the Relative Hepatic Gene Expression Potency of TCDF in C57BL/6 Mice. Toxicological sciences : an official journal of the Society of Toxicology. 112:221-228. 2009
- Comparative Analysis of AhR-Mediated TCDD-Elicited Gene Expression in Human Liver Adult Stem Cells. Toxicological sciences : an official journal of the Society of Toxicology. 112:229-244. 2009
- Development of analytical methods for NMR spectra and application to a 13C toxicology study. Metabolomics : Official journal of the Metabolomic Society. 5:253-262. 2009
- Phenobarbital Elicits Unique, Early Changes in the Expression of Hepatic Genes that Affect Critical Pathways in Tumor-Prone B6C3F1 Mice. Toxicological sciences : an official journal of the Society of Toxicology. 109:193-205. 2009
- Tamoxifen-elicited uterotrophy: cross-species and cross-ligand analysis of the gene expression program. BMC Medical Genomics. 2:19. 2009
- The Constitutive Active/Androstane Receptor Facilitates Unique Phenobarbital-Induced Expression Changes of Genes Involved in Key Pathways in Precancerous Liver and Liver Tumors. Toxicological sciences : an official journal of the Society of Toxicology. 110:319-333. 2009
- Comparative Temporal Toxicogenomic Analysis of TCDD- and TCDF-Mediated Hepatic Effects in Immature Female C57BL/6 Mice. Toxicological sciences : an official journal of the Society of Toxicology. 103:285-297. 2008
- ERRATUM. Toxicological sciences : an official journal of the Society of Toxicology. 105:231-231. 2008
- ERRATUM. Toxicological sciences : an official journal of the Society of Toxicology. 105:231-231. 2008
- Promoter analysis of TCDD-inducible genes in a thymic epithelial cell line indicates the potential for cell-specific transcription factor crosstalk in the AhR response. Toxicology and applied pharmacology. 232:268-279. 2008
- Species-Specific Regulation of PXR/CAR/ER-Target Genes in the Mouse and Rat Liver Elicited by o,p'-DDT. BMC Genomics. 9:487. 2008
- o,p'-DDT Elicits PXR/CAR-, Not ER-, Mediated Responses in the Immature Ovariectomized Rat Liver. Toxicological sciences : an official journal of the Society of Toxicology. 101:350-363. 2008
- Automated Quantitative Dose-Response Modeling and Point of Departure Determination for Large Toxicogenomic and High-Throughput Screening Data Sets. Toxicological sciences : an official journal of the Society of Toxicology. 104:412-418. 2007
- Clearing the Standards Landscape: the Semantics of Terminology and their Impact on Toxicogenomics. Toxicological sciences : an official journal of the Society of Toxicology. 99:403-412. 2007
- Comparative Toxicogenomic Examination of the Hepatic Effects of PCB126 and TCDD in Immature, Ovariectomized C57BL/6 Mice. Toxicological sciences : an official journal of the Society of Toxicology. 102:61-75. 2007
- Comparative temporal and dose-dependent morphological and transcriptional uterine effects elicited by tamoxifen and ethynylestradiol in immature, ovariectomized mice. BMC Genomics. 8:151. 2007
- Inhibition of Estrogen-Mediated Uterine Gene Expression Responses by Dioxin. Molecular pharmacology. 73:82-93. 2007
- The minimum information required for reporting a molecular interaction experiment (MIMIx). Nature biotechnology. 25:894-898. 2007
- Toward a Checklist for Exchange and Interpretation of Data from a Toxicology Study. Toxicological sciences : an official journal of the Society of Toxicology. 99:26-34. 2007
- Transcription factor crosstalk controls the transcriptional response to AhR over activation by TCDD in thymic epithelial cells. Toxicology letters. 172:S144-S145. 2007
- dbZach toxicogenomic information management system. Pharmacogenomics. 8:287-291. 2007
- Comparative Toxicogenomic Analysis of the Hepatotoxic Effects of TCDD in Sprague Dawley Rats and C57BL/6 Mice. Toxicological sciences : an official journal of the Society of Toxicology. 94:398-416. 2006
- Dioxin Induces an Estrogen-Like, Estrogen Receptor-Dependent Gene Expression Response in the Murine Uterus. Molecular pharmacology. 69:1599-1606. 2006
- Effects of culture conditions on estrogen-mediated hepatic in vitro gene expression and correlation to in vivo responses. Toxicology and applied pharmacology. 215:37-50. 2006
- Identification and Characterization of Genes Susceptible to Transcriptional Cross-Talk between the Hypoxia and Dioxin Signaling Cascades. Chemical research in toxicology. 19:1284-1293. 2006
- Identification and Characterization of Genes Susceptible to Transcriptional Cross-Talk between the Hypoxia and Dioxin Signaling Cascades Volume 19, Number 10, October, 2006, pp 1284−1293. Chemical research in toxicology. 19:1702-1702. 2006
- In vivo – in vitro toxicogenomic comparison of TCDD-elicited gene expression in Hepa1c1c7 mouse hepatoma cells and C57BL/6 hepatic tissue. BMC Genomics. 7:80. 2006
- The need for standards, not guidelines, in biological data reporting and sharing. Nature biotechnology. 24:1369-1373. 2006
- A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling. Physiological genomics. 23:327-342. 2005
- Comparative Microarray Analysis of Basal Gene Expression in Mouse Hepa-1c1c7 Wild-Type and Mutant Cell Lines. Toxicological sciences : an official journal of the Society of Toxicology. 86:342-353. 2005
- Normalization of two-channel microarray experiments: a semiparametric approach. Bioinformatics (Oxford, England). 21:1078-1083. 2005
- Protocols for the assurance of microarray data quality and process control. Nucleic acids research. 33:e172-e172. 2005
- Temporal and Dose-Dependent Hepatic Gene Expression Patterns in Mice Provide New Insights into TCDD-Mediated Hepatotoxicity. Toxicological sciences : an official journal of the Society of Toxicology. 85:1048-1063. 2005
- dbZach: A MIAME-Compliant Toxicogenomic Supportive Relational Database. Toxicological sciences : an official journal of the Society of Toxicology. 90:558-568. 2005
- Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences. Nucleic Acids Research. 32:4512-4523. 2004
- Empirical Bayes Gene Screening Tool for Time-Course or Dose–Response Microarray Data. Journal of biopharmaceutical statistics. 14:647-670. 2004
- Gene Expression Analysis Points to Hemostasis in Livers of Rats Cotreated with Lipopolysaccharide and Ranitidine. Toxicological Sciences. 80:203-213. 2004
- Temporal- and dose-dependent hepatic gene expression changes in immature ovariectomized mice following exposure to ethynyl estradiol. Carcinogenesis. 25:1277-1291. 2004
- Adverse Outcome Pathways for Regulatory Applications: Examination of Four Case Studies With Different Degrees of Completeness and Scientific Confidence. Toxicological sciences : an official journal of the Society of Toxicology. 148:14-25.
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article
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chapter
- Bioinformatics: Databasing and Gene Annotation. Essential Concepts in Toxicogenomics. 145-157. 2008
- Comparative Toxicogenomics in Mechanistic and Predictive Toxicology. Comparative Genomics. 299-320. 2007
- Pharmacogenomics. Drugs and the Pharmaceutical Sciences. 515-556. 2005
- Analysis of Toxicogenomic Databases. Pharmaceutical Data Mining. 301-315.
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conference paper
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dataset
- Time course analysis of the Tamoxifen (Tam)-regulated transcriptome in mouse uterus
- Time course comparative analysis of the 17α-ethinylestradiol (17αEE2)-regulated transcriptome in mouse uterus
- Time course transcriptomic analysis of the 17α-ethinylestradiol (17αEE2)-regulated transcriptome in mouse liver
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report