All Stories

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

    Article • March 2018, Cold Spring Harbor Laboratory Press

    Dr Lyle Burgoon

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

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

    Article • Risk Analysis, April 2016, Wiley

    Dr Lyle Burgoon

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

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

    Article • PLoS ONE, April 2015, PLOS

    Dr Lyle Burgoon

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

    Article • PLoS ONE, December 2014, PLOS

    Dr Lyle Burgoon

  18. A Framework for the Next Generation of Risk Science

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

    Dr Lyle Burgoon

  19. 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

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

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

    Dr Lyle Burgoon

  21. 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

  22. 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

  23. 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

  24. 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

  25. Plastids Are Major Regulators of Light Signaling in Arabidopsis

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

    Dr Lyle Burgoon

  26. MIPHENO: data normalization for high throughput metabolite analysis

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

    Dr Lyle Burgoon

  27. 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

  28. 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

  29. Toxicoinformatics for Systems Toxicology

    Article • September 2011, Wiley

    Dr Lyle Burgoon

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

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

    Article • Toxicology and Applied Pharmacology, July 2010, Elsevier

    Dr Lyle Burgoon

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

    Article • Toxicology, June 2010, Elsevier

    Dr Lyle Burgoon

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. ERRATUM

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

    Dr Lyle Burgoon

  48. 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

  49. 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

  50. 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

  51. Bioinformatics: Databasing and Gene Annotation

    Article • January 2008, Springer Science + Business Media

    Dr Lyle Burgoon

  52. Species-Specific Regulation of PXR/CAR/ER-Target Genes in the Mouse and Rat Liver Elicited by o,p'-DDT

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

    Dr Lyle Burgoon

  53. Comparative Toxicogenomics in Mechanistic and Predictive Toxicology

    Article • December 2007, Taylor & Francis

    Dr Lyle Burgoon

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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

  60. dbZach toxicogenomic information management system

    Article • Pharmacogenomics, March 2007, Future Medicine

    Dr Lyle Burgoon

  61. 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

  62. 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

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

    Article • Nature Biotechnology, November 2006, Nature

    Dr Lyle Burgoon

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

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

    Dr Lyle Burgoon

  65. 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

  66. 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

  67. 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

  68. Article • BMC Genomics, January 2006, Springer Science + Business Media

    Dr Lyle Burgoon

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

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

    Dr Lyle Burgoon

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

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

    Dr Lyle Burgoon

  71. 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

  72. Pharmacogenomics

    Article • September 2005, Taylor & Francis

    Dr Lyle Burgoon

  73. 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

  74. 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

  75. 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

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

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

    Dr Lyle Burgoon

  77. 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

  78. 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

  79. 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

  80. Analysis of Toxicogenomic Databases

    Article • Wiley

    Dr Lyle Burgoon

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

    Article • Nuclear Receptor Signaling Atlas

    Dr Lyle Burgoon

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

    Article • Nuclear Receptor Signaling Atlas

    Dr Lyle Burgoon

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

    Article • Nuclear Receptor Signaling Atlas

    Dr Lyle Burgoon