All Stories

  1. The database makes the poison: How the selection of datasets in QSAR models impacts toxicant prediction of higher tier endpoints

    Article • Regulatory Toxicology and Pharmacology, August 2024, Elsevier

    Dr Lyle Burgoon

  2. Comment on “Application of an in Vitro Assay to Identify Chemicals That Increase Estradiol and Progesterone Synthesis and Are Potential Breast Cancer Risk Factors”

    Article • Environmental Health Perspectives, May 2022, Environmental Health Perspectives

    Dr Lyle Burgoon

  3. A novel approach to calculating the kinetically derived maximum dose

    Article • Archives of Toxicology, February 2022, Springer Science + Business Media

    Dr Lyle Burgoon

  4. Principles of dose-setting in toxicology studies: the importance of kinetics for ensuring human safety

    Article • Archives of Toxicology, October 2021, Springer Science + Business Media

    Dr Lyle Burgoon

  5. Progress towards an OECD reporting framework for transcriptomics and metabolomics in regulatory toxicology

    Article • Regulatory Toxicology and Pharmacology, October 2021, Elsevier

    Dr Antony John Williams, Dr Lyle Burgoon

  6. Community Approaches for Integrating Environmental Exposures into Human Models of Disease

    Article • Environmental Health Perspectives, December 2020, Environmental Health Perspectives

    Dr Lyle Burgoon

  7. Evaluation of the Inherent Toxicity Concept in Environmental Toxicology and Risk Assessment

    Article • Environmental Toxicology and Chemistry, November 2020, Wiley

    Dr Lyle Burgoon

  8. Assessment of Transcriptomic and Apical Responses of Daphnia magna Exposed to a Polyethylene Microplastic in a 21‐d Chronic Study

    Article • Environmental Toxicology and Chemistry, June 2020, Wiley

    Dr Lyle Burgoon

  9. Organizing mechanism-related information on chemical interactions using a framework based on the aggregate exposure and adverse outcome pathways

    Article • Environment International, May 2020, Elsevier

    Dr Lyle Burgoon

  10. Big Data Integration and Inference

    Article • December 2019, Royal Society of Chemistry

    Dr Lyle Burgoon

  11. Predicting the Probability that a Chemical Causes Steatosis Using Adverse Outcome Pathway Bayesian Networks (AOPBNs)

    Article • Risk Analysis, November 2019, Wiley

    Dr Lyle Burgoon

  12. Different as night and day: Behavioural and life history responses to varied photoperiods in Daphnia magna

    Article • Molecular Ecology, September 2019, Wiley

    Dr Lyle Burgoon

  13. Building and Applying Quantitative Adverse Outcome Pathway Models for Chemical Hazard and Risk Assessment

    Article • Environmental Toxicology and Chemistry, August 2019, Wiley

    Dr Lyle Burgoon

  14. Development of Adverse Outcome Pathway for PPARγ Antagonism Leading to Pulmonary Fibrosis and Chemical Selection for Its Validation: ToxCast Database and a Deep Learning Artificial Neural Network Model-Based Approach

    Article • Chemical Research in Toxicology, May 2019, American Chemical Society (ACS)

    Dr Lyle Burgoon

  15. Chemical hazard prediction and hypothesis testing using quantitative adverse outcome pathways

    Article • ALTEX, January 2019, ALTEX Edition

    Dr Lyle Burgoon

  16. Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials

    Article • Frontiers in Genetics, December 2018, Frontiers

    Professor Chris Evelo, Dr Lyle Burgoon

  17. The AOPOntology: A Semantic Artificial Intelligence Tool for Predictive Toxicology

    Article • March 2018, Cold Spring Harbor Laboratory Press

    Dr Lyle Burgoon

  18. Building a developmental toxicity ontology

    Article • Birth Defects Research, January 2018, Wiley

    Dr Lyle Burgoon

  19. The AOPOntology: A Semantic Artificial Intelligence Tool for Predictive Toxicology

    Article • Applied In Vitro Toxicology, September 2017, Mary Ann Liebert Inc

    Dr Lyle Burgoon

  20. Linking Environmental Exposure to Toxicity

    Article • March 2017, Royal Society of Chemistry

    Dr Lyle Burgoon

  21. Autoencoder Predicting Estrogenic Chemical Substances (APECS): An Improved Approach for Screening Potentially Estrogenic Chemicals Using In Vitro Assays and Deep Learning

    Article • Computational Toxicology, March 2017, Elsevier

    Dr Lyle Burgoon

  22. A decision analysis framework for estimating the potential hazards for drinking water resources of chemicals used in hydraulic fracturing fluids

    Article • The Science of The Total Environment, January 2017, Elsevier

    Dr Lyle Burgoon

  23. Response to Cohen et al. (2016) regarding response to Druwe and Burgoon

    Article • Archives of Toxicology, October 2016, Springer Science + Business Media

    Dr Lyle Burgoon

  24. Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure–Activity Relationship Modeling

    Article • Environmental Science & Technology, July 2016, American Chemical Society (ACS)

    Dr Lyle Burgoon

  25. Revisiting Cohen et al. 2015, Cohen et al. 2014 and Waalkes et al. 2014: a bayesian re-analysis of tumor incidences

    Article • Archives of Toxicology, June 2016, Springer Science + Business Media

    Dr Lyle Burgoon

  26. Overview of Chronic Oral Toxicity Values for Chemicals Present in Hydraulic Fracturing Fluids, Flowback, and Produced Waters

    Article • Environmental Science & Technology, May 2016, American Chemical Society (ACS)

    Dr Lyle Burgoon

  27. The Next Generation of Risk Assessment Multi-Year Study—Highlights of Findings, Applications to Risk Assessment, and Future Directions

    Article • Environmental Health Perspectives, April 2016, Environmental Health Perspectives

    Dr Lyle Burgoon

  28. A Market-Basket Approach to Predict the Acute Aquatic Toxicity of Munitions and Energetic Materials

    Article • Bulletin of Environmental Contamination and Toxicology, April 2016, Springer Science + Business Media

    Dr Lyle Burgoon

  29. Using In Vitro High-Throughput Screening Data for Predicting Benzo[k]Fluoranthene Human Health Hazards

    Article • Risk Analysis, April 2016, Wiley

    Dr Lyle Burgoon

  30. Systems Biology and Biomarkers of Early Effects for Occupational Exposure Limit Setting

    Article • Journal of Occupational and Environmental Hygiene, November 2015, Taylor & Francis

    Dr Lyle Burgoon

  31. Adverse Outcome Pathways for Regulatory Applications: Examination of Four Case Studies With Different Degrees of Completeness and Scientific Confidence

    Article • Toxicological Sciences, October 2015, Oxford University Press (OUP)

    Dr Lyle Burgoon

  32. AOP: An R Package For Sufficient Causal Analysis in Pathway-based Screening of Drugs and Chemicals for Adversity

    Article • October 2015, Cold Spring Harbor Laboratory Press

    Dr Lyle Burgoon

  33. Loss of Hif-2α Rescues the Hif-1α Deletion Phenotype of Neonatal Respiratory Distress In Mice

    Article • PLoS ONE, September 2015, PLOS

    Dr Lyle Burgoon

  34. Applying comprehensive environmental assessment to research planning for multiwalled carbon nanotubes: Refinements to inform future stakeholder engagement

    Article • Integrated Environmental Assessment and Management, July 2015, Wiley

    Dr Lyle Burgoon

  35. Can Data Science Inform Environmental Justice and Community Risk Screening for Type 2 Diabetes?

    Article • PLoS ONE, April 2015, PLOS

    Dr Lyle Burgoon

  36. Systematic Omics Analysis Review (SOAR) Tool to Support Risk Assessment

    Article • PLoS ONE, December 2014, PLOS

    Dr Lyle Burgoon

  37. A Framework for the Next Generation of Risk Science

    Article • Environmental Health Perspectives, April 2014, Environmental Health Perspectives

    Dr Lyle Burgoon

  38. Burst and principal components analyses of MEA data for 16 chemicals describe at least three effects classes

    Article • NeuroToxicology, January 2014, Elsevier

    Dr Lyle Burgoon

  39. What do the data show? Knowledge map development for comprehensive environmental assessment

    Article • Integrated Environmental Assessment and Management, December 2013, Wiley

    Dr Lyle Burgoon

  40. Molecular target sequence similarity as a basis for species extrapolation to assess the ecological risk of chemicals with known modes of action

    Article • Aquatic Toxicology, November 2013, Elsevier

    Dr Lyle Burgoon

  41. PPARα-mediated responses in human adult liver stem cells: In vivo/in vitro and cross-species comparisons

    Article • The Journal of Steroid Biochemistry and Molecular Biology, November 2013, Elsevier

    Dr Lyle Burgoon

  42. A graphical systems model and tissue-specific functional gene sets to aid transcriptomic analysis of chemical impacts on the female teleost reproductive axis

    Article • Mutation Research/Genetic Toxicology and Environmental Mutagenesis, August 2012, Elsevier

    Dr Lyle Burgoon

  43. Time Course And Dose Response Of Ozone-Induced Differential Gene Expression Profiles In Primary Human Bronchial Epithelial Cells

    Article • May 2012, American Thoracic Society

    Dr Lyle Burgoon

  44. Plastids Are Major Regulators of Light Signaling in Arabidopsis

    Article • PLANT PHYSIOLOGY, March 2012, American Society of Plant Biologists (ASPB)

    Dr Lyle Burgoon

  45. MIPHENO: data normalization for high throughput metabolite analysis

    Article • BMC Bioinformatics, January 2012, Springer Science + Business Media

    Dr Lyle Burgoon

  46. 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

    Article • Toxicology and Applied Pharmacology, October 2011, Elsevier

    Dr Lyle Burgoon

  47. Comparative Metabolomic and Genomic Analyses of TCDD-Elicited Metabolic Disruption in Mouse and Rat Liver

    Article • Toxicological Sciences, September 2011, Oxford University Press (OUP)

    Dr Lyle Burgoon

  48. Pulmonary Inflammatory and Fibrotic Responses in Fischer 344 Rats After Intratracheal Instillation Exposure to Libby Amphibole

    Article • Journal of Toxicology and Environmental Health Part A, September 2011, Taylor & Francis

    Dr Lyle Burgoon

  49. Genome-Wide Computational Analysis of Dioxin Response Element Location and Distribution in the Human, Mouse, and Rat Genomes

    Article • Chemical Research in Toxicology, April 2011, American Chemical Society (ACS)

    Dr Lyle Burgoon

  50. Differences in TCDD-elicited gene expression profiles in human HepG2, mouse Hepa1c1c7 and rat H4IIE hepatoma cells

    Article • BMC Genomics, April 2011, Springer Science + Business Media

    Dr Lyle Burgoon

  51. Hypoxia-inducible factor-1α regulates the expression of genes in hypoxic hepatic stellate cells important for collagen deposition and angiogenesis

    Article • Liver International, September 2010, Wiley

    Dr Lyle Burgoon

  52. Automated Dose-Response Analysis and Comparative Toxicogenomic Evaluation of the Hepatic Effects Elicited by TCDD, TCDF, and PCB126 in C57BL/6 Mice

    Article • Toxicological Sciences, August 2010, Oxford University Press (OUP)

    Dr Lyle Burgoon

  53. Effects of tamoxifen and ethynylestradiol cotreatment on uterine gene expression in immature, ovariectomized mice

    Article • Journal of Molecular Endocrinology, July 2010, Bioscientifica

    Dr Lyle Burgoon

  54. Effects of TCDD on the expression of nuclear encoded mitochondrial genes

    Article • Toxicology and Applied Pharmacology, July 2010, Elsevier

    Dr Lyle Burgoon

  55. Oxidative stress is important in the pathogenesis of liver injury induced by sulindac and lipopolysaccharide cotreatment

    Article • Toxicology, June 2010, Elsevier

    Dr Lyle Burgoon

  56. Estrogen receptor-dependent regulation of CYP2B6 in human breast cancer cells

    Article • Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, May 2010, Elsevier

    Dr Lyle Burgoon

  57. PCB153-elicited hepatic responses in the immature, ovariectomized C57BL/6 mice: Comparative toxicogenomic effects of dioxin and non-dioxin-like ligands

    Article • Toxicology and Applied Pharmacology, March 2010, Elsevier

    Dr Lyle Burgoon

  58. Analysis of Toxicogenomic Databases

    Article • December 2009, Wiley

    Dr Lyle Burgoon

  59. Toxicoinformatics for Systems Toxicology

    Article • October 2009, Wiley

    Dr Lyle Burgoon

  60. Comparative Analysis of AhR-Mediated TCDD-Elicited Gene Expression in Human Liver Adult Stem Cells

    Article • Toxicological Sciences, August 2009, Oxford University Press (OUP)

    Dr Lyle Burgoon

  61. Automated Dose-Response Analysis of the Relative Hepatic Gene Expression Potency of TCDF in C57BL/6 Mice

    Article • Toxicological Sciences, August 2009, Oxford University Press (OUP)

    Dr Lyle Burgoon

  62. The Constitutive Active/Androstane Receptor Facilitates Unique Phenobarbital-Induced Expression Changes of Genes Involved in Key Pathways in Precancerous Liver and Liver Tumors

    Article • Toxicological Sciences, May 2009, Oxford University Press (OUP)

    Dr Lyle Burgoon

  63. Tamoxifen-elicited uterotrophy: cross-species and cross-ligand analysis of the gene expression program

    Article • BMC Medical Genomics, April 2009, Springer Science + Business Media

    Dr Lyle Burgoon

  64. Phenobarbital Elicits Unique, Early Changes in the Expression of Hepatic Genes that Affect Critical Pathways in Tumor-Prone B6C3F1 Mice

    Article • Toxicological Sciences, March 2009, Oxford University Press (OUP)

    Dr Lyle Burgoon

  65. Development of analytical methods for NMR spectra and application to a 13C toxicology study

    Article • Metabolomics, December 2008, Springer Science + Business Media

    Dr Lyle Burgoon

  66. Species-specific regulation of PXR/CAR/ER-target genes in the mouse and rat liver elicited by o, p'-DDT

    Article • BMC Genomics, October 2008, Springer Science + Business Media

    Dr Lyle Burgoon

  67. 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

    Article • Toxicology and Applied Pharmacology, October 2008, Elsevier

    Dr Lyle Burgoon

  68. ERRATUM

    Article • Toxicological Sciences, June 2008, Oxford University Press (OUP)

    Dr Lyle Burgoon

  69. Automated Quantitative Dose-Response Modeling and Point of Departure Determination for Large Toxicogenomic and High-Throughput Screening Data Sets

    Article • Toxicological Sciences, April 2008, Oxford University Press (OUP)

    Dr Lyle Burgoon

  70. Comparative Temporal Toxicogenomic Analysis of TCDD- and TCDF-Mediated Hepatic Effects in Immature Female C57BL/6 Mice

    Article • Toxicological Sciences, March 2008, Oxford University Press (OUP)

    Dr Lyle Burgoon

  71. o,p'-DDT Elicits PXR/CAR-, Not ER-, Mediated Responses in the Immature Ovariectomized Rat Liver

    Article • Toxicological Sciences, February 2008, Oxford University Press (OUP)

    Dr Lyle Burgoon

  72. Bioinformatics: Databasing and Gene Annotation

    Article • January 2008, Springer Science + Business Media

    Dr Lyle Burgoon

  73. Comparative Toxicogenomics in Mechanistic and Predictive Toxicology

    Article • December 2007, Taylor & Francis

    Dr Lyle Burgoon

  74. Inhibition of Estrogen-Mediated Uterine Gene Expression Responses by Dioxin

    Article • Molecular Pharmacology, October 2007, American Society for Pharmacology & Experimental Therapeutics (ASPET)

    Dr Lyle Burgoon

  75. Comparative Toxicogenomic Examination of the Hepatic Effects of PCB126 and TCDD in Immature, Ovariectomized C57BL/6 Mice

    Article • Toxicological Sciences, October 2007, Oxford University Press (OUP)

    Dr Lyle Burgoon

  76. Transcription factor crosstalk controls the transcriptional response to AhR over activation by TCDD in thymic epithelial cells

    Article • Toxicology Letters, October 2007, Elsevier

    Dr Lyle Burgoon

  77. The minimum information required for reporting a molecular interaction experiment (MIMIx)

    Article • Nature Biotechnology, August 2007, Springer Science + Business Media

    Professor Gary D Bader, Dr Lyle Burgoon, Dr. Peter Uetz

  78. Toward a Checklist for Exchange and Interpretation of Data from a Toxicology Study

    Article • Toxicological Sciences, June 2007, Oxford University Press (OUP)

    Dr Lyle Burgoon

  79. Clearing the Standards Landscape: the Semantics of Terminology and their Impact on Toxicogenomics

    Article • Toxicological Sciences, May 2007, Oxford University Press (OUP)

    Dr Lyle Burgoon

  80. dbZach Toxicogenomic Information Management System

    Article • Pharmacogenomics, February 2007, Taylor & Francis

    Dr Lyle Burgoon

  81. Comparative temporal and dose-dependent morphological and transcriptional uterine effects elicited by tamoxifen and ethynylestradiol in immature, ovariectomized mice

    Article • BMC Genomics, January 2007, Springer Science + Business Media

    Dr Lyle Burgoon

  82. 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

    Article • Chemical Research in Toxicology, December 2006, American Chemical Society (ACS)

    Dr Lyle Burgoon

  83. The need for standards, not guidelines, in biological data reporting and sharing

    Article • Nature Biotechnology, November 2006, Springer Science + Business Media

    Dr Lyle Burgoon

  84. Identification and Characterization of Genes Susceptible to Transcriptional Cross-Talk between the Hypoxia and Dioxin Signaling Cascades

    Article • Chemical Research in Toxicology, September 2006, American Chemical Society (ACS)

    Dr Lyle Burgoon

  85. Effects of culture conditions on estrogen-mediated hepatic in vitro gene expression and correlation to in vivo responses

    Article • Toxicology and Applied Pharmacology, August 2006, Elsevier

    Dr Lyle Burgoon

  86. Comparative Toxicogenomic Analysis of the Hepatotoxic Effects of TCDD in Sprague Dawley Rats and C57BL/6 Mice

    Article • Toxicological Sciences, July 2006, Oxford University Press (OUP)

    Dr Lyle Burgoon

  87. In vivo – in vitro toxicogenomic comparison of TCDD-elicited gene expression in Hepa1c1c7 mouse hepatoma cells and C57BL/6 hepatic tissue

    Article • BMC Genomics, April 2006, Springer Science + Business Media

    Dr Lyle Burgoon

  88. Dioxin Induces an Estrogen-Like, Estrogen Receptor-Dependent Gene Expression Response in the Murine Uterus

    Article • Molecular Pharmacology, February 2006, American Society for Pharmacology & Experimental Therapeutics (ASPET)

    Dr Lyle Burgoon

  89. dbZach: A MIAME-Compliant Toxicogenomic Supportive Relational Database

    Article • Toxicological Sciences, December 2005, Oxford University Press (OUP)

    Dr Lyle Burgoon

  90. Protocols for the assurance of microarray data quality and process control

    Article • Nucleic Acids Research, October 2005, Oxford University Press (OUP)

    Dr Lyle Burgoon

  91. A cross-species analysis of the rodent uterotrophic program: elucidation of conserved responses and targets of estrogen signaling

    Article • Physiological Genomics, September 2005, American Physiological Society

    Dr Lyle Burgoon

  92. Pharmacogenomics

    Article • September 2005, Taylor & Francis

    Dr Lyle Burgoon

  93. Comparative Microarray Analysis of Basal Gene Expression in Mouse Hepa-1c1c7 Wild-Type and Mutant Cell Lines

    Article • Toxicological Sciences, May 2005, Oxford University Press (OUP)

    Dr Lyle Burgoon

  94. Temporal and Dose-Dependent Hepatic Gene Expression Patterns in Mice Provide New Insights into TCDD-Mediated Hepatotoxicity

    Article • Toxicological Sciences, February 2005, Oxford University Press (OUP)

    Dr Lyle Burgoon

  95. Empirical Bayes Gene Screening Tool for Time-Course or Dose–Response Microarray Data

    Article • Journal of Biopharmaceutical Statistics, December 2004, Taylor & Francis

    Dr Lyle Burgoon

  96. Normalization of two-channel microarray experiments: a semiparametric approach

    Article • Bioinformatics, October 2004, Oxford University Press (OUP)

    Dr Lyle Burgoon

  97. Comparative analysis of dioxin response elements in human, mouse and rat genomic sequences

    Article • Nucleic Acids Research, August 2004, Oxford University Press (OUP)

    Dr Lyle Burgoon

  98. Gene Expression Analysis Points to Hemostasis in Livers of Rats Cotreated with Lipopolysaccharide and Ranitidine

    Article • Toxicological Sciences, March 2004, Oxford University Press (OUP)

    Dr Lyle Burgoon

  99. Temporal- and dose-dependent hepatic gene expression changes in immature ovariectomized mice following exposure to ethynyl estradiol

    Article • Carcinogenesis, January 2004, Oxford University Press (OUP)

    Dr Lyle Burgoon

  100. Time course analysis of the Tamoxifen (Tam)-regulated transcriptome in mouse uterus

    Article • Nuclear Receptor Signaling Atlas

    Dr Lyle Burgoon

  101. Time course comparative analysis of the 17α-ethinylestradiol (17αEE2)-regulated transcriptome in mouse uterus

    Article • Nuclear Receptor Signaling Atlas

    Dr Lyle Burgoon

  102. Time course transcriptomic analysis of the 17α-ethinylestradiol (17αEE2)-regulated transcriptome in mouse liver

    Article • Nuclear Receptor Signaling Atlas

    Dr Lyle Burgoon