Science Inventory

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Browne, P., K. Friedman, K. Boekelheide, AND R. Thomas. Adverse effects in traditional and alternative toxicity tests. REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, 148:105579, (2024). https://doi.org/10.1016/j.yrtph.2024.105579

Friedman, K., M. Foster, L. Pham, M. Feshuk, S. Watford, J. Wambaugh, R. Judson, R. Setzer, AND R. Thomas. Reproducibility of organ-level effects in repeat dose animal studies. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 28:100287, (2023). https://doi.org/10.1016/j.comtox.2023.100287

Feshuk, M., L. Kolaczkowski, S. Watford, AND K. Paul-Friedman. ToxRefDB v2.1: update to curated in vivo study data in the Toxicity Reference Database. Frontiers in Toxicology. Frontiers, Lausanne, Switzerland, 5:1260305, (2023). https://doi.org/10.3389/ftox.2023.1260305

Pierro, J., B. Ahir, Nancy C. Baker, N. Kleinsteuer, M. Xia, AND T. Knudsen. Computational model for fetal skeletal defects potentially linked to disruption of retinoic acid signaling. Frontiers in Pharmacology. Frontiers, Lausanne, Switzerland, 13:971296, (2022). https://doi.org/10.3389/fphar.2022.971296

Tate, T., J. Wambaugh, G. Patlewicz, AND I. Shah. Repeat-dose toxicity prediction with Generalized Read-Across (GenRA) using targeted transcriptomic data: A proof-of-concept case study. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 19:100171, (2021). https://doi.org/10.1016/j.comtox.2021.100171

Corton, Jon, K. Korunes, J. Abedini, H. El-Masri, J. Brown, K. Friedman, Y. Liu, C. Martini, S. He, AND J. Rooney. Thresholds Derived from Common Measures in Rat Studies are Predictive of Liver Tumorigenic Chemicals. TOXICOLOGIC PATHOLOGY. Society of Toxicology, RESTON, VA, 48(7):857-874, (2020). https://doi.org/10.1177/0192623320960412

Pham, L., S. Watford, P. Pradeep, M. Martin, R. Thomas, R. Judson, Woodrow Setzer, AND K. Paul-Friedman. Variability in in vivo studies: Defining the upper limit of performance for predictions of systemic effect levels. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 15(August 2020):100126, (2020). https://doi.org/10.1016/j.comtox.2020.100126

Baker, N., N. Sipes, J. Franzosa, D. Belair, B. Abbott, R. Judson, AND T. Knudsen. Characterizing cleft palate toxicants using ToxCast data, chemical structure, and the biomedical literature. Birth Defects Research. John Wiley & Sons, Inc., Hoboken, NJ, , 1-21, (2019). https://doi.org/10.1002/bdr2.1581

Helman, G., I. Shah, A. Williams, J. Edwards, J. Dunne, AND G. Patlewicz. Generalised Read-Across (GenRA): A workflow implemented into the EPA CompTox Chemicals Dashboard. ALTEX. Society ALTEX Edition, Kuesnacht, Switzerland, 36(1):1-5, (2019). https://doi.org/10.14573/altex.1811292

Helman, G., G. Patlewicz, AND I. Shah. Quantitative Prediction of Repeat Dose Toxicity Values using GenRA. REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, 109:104480, (2019). https://doi.org/10.1016/j.yrtph.2019.104480

Watford, S., L. Pham, J. Wignall, R. Shin, M. Martin, AND K. Friedman. ToxRefDB version 2.0: Improved utility for predictive and retrospective toxicology analyses. REPRODUCTIVE TOXICOLOGY. Elsevier Science Ltd, New York, NY, 89:145-158, (2019). https://doi.org/10.1016/j.reprotox.2019.07.012

Helman, G., I. Shah, AND G. Patlewicz. Transitioning the Generalised Read-Across approach (GenRA) to quantitative predictions: A case study using acute oral toxicity data. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 12(November 2019):100097, (2019). https://doi.org/10.1016/j.comtox.2019.100097

Truong, L., G. Ouedraogo, L. Pham, J. Clouzeau, S. Loisel-Joubert, D. Blanchet, H. Noçairi, Woodrow Setzer, R. Judson, Chris Grulke, K. Mansouri, AND M. Martin. Predicting In Vivo Effect Levels for Repeat Dose Systemic Toxicity using Chemical, Biological, Kinetic and Study Covariates. Archives of Toxicology. Springer, New York, NY, 92(2):587-600, (2018).

Hutson, S., M. Leung, N. Baker, R. Spencer, AND T. Knudsen. Computational Model of Secondary Palate Fusion and Disruption. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 30(4):965-979, (2017).

Liu, J., G. Patlewicz, A. Williams, R. Thomas, AND I. Shah. Predicting organ toxicity using in vitro bioactivity data and chemical structure. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 30:2046−2059, (2017). https://doi.org/10.1021/acs.chemrestox.7b00084

Judson, Richard S., M. Martin, G. Patlewicz, AND Charles E. Wood. Retrospective Mining of Toxicology Data to Discover Multispecies and Chemical Class Effects: Anemia as a Case Study. REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, 86:74-92, (2017).

Theunissen, P., S. Beken, B. Beyer, W. Breslin, G. Cappon, C. Chen, G. Chmielewski, L. De Schaepdrijver, B. Enright, J. Foreman, W. Harrouk, K. Hew, A. Hoberman, J. Hui, TB Knudsen, S. Laffan, S Makris, AND M Martin. Comparing rat and rabbit embryo-fetal developmental toxicity studies for 379 pharmaceuticals: On systemic dose and developmental effects (Critical Reviews in Toxicology) . CRITICAL REVIEWS IN TOXICOLOGY. CRC Press LLC, Boca Raton, FL, , 1-13, (2016).

Theunissen, P., S. Beken, B. Beyer, W. Breslin, G. Cappon, C. Chen, G. Chmielewski, L. De Schaepdrijver, B. Enright, J. Foreman, W. Harrouk, K. Hew, A. Hoberman, J. Hui, TB Knudsen, S. Laffan, S Makris, M Martin, M. McNerney, C. Siezen, D. Stanislaus, J. Stewart, K. Thompson, B. Tornesi, G. Weinbauer, S. Wood, J. Van der Laan, AND A. Piersma. Comparison of rat and rabbit embryo-fetal developmental toxicity data for 379 pharmaceuticals: on the nature and severity of developmental effects (Critical Reviews in Toxicology) . CRITICAL REVIEWS IN TOXICOLOGY. CRC Press LLC, Boca Raton, FL, , 1-11, (2016).

Wexler, P., R. Judson, S. de Marcellus, J. De Knecht, AND E. Leinala. Health Effects of Toxicants: Online Knowledge Support. LIFE SCIENCES. Elsevier Science Ltd, New York, NY, 145:284-293, (2016).

Shah, I., J. Liu, Richard S. Judson, Russell S. Thomas, AND G. Patlewicz. Systematically evaluating read-across prediction and performance using a local validity approach characterized by chemical structure and bioactivity information. REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, 79:12-24, (2016).

Leung, M., J. Phuong, N. Baker, N. Sipes, G. Klinefelter, M. Martin, K. McLaurin, Woodrow Setzer, S. Darney, R. Judson, AND T. Knudsen. Systems Toxicology of Male Reproductive Development: Profiling 774 Chemicals for Molecular Targets and Adverse Outcomes. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 124(7):1050-1061, (2016).

JUDSON, R. S., M. T. MARTIN, P. P. EGEGHY, S. GANGWAL, D. M. REIF, P. KOTHIYA, M. A. WOLF, T. CATHEY, T. R. TRANSUE, D. SMITH, J. VAIL, A. FRAME, S. MOSHER, E. A. COHEN-HUBAL, AND A. M. RICHARD. Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System. International Journal of Molecular Sciences. MDPI, Basel, Switzerland, 13(2):1805-1831, (2012).

CROFTON, K. M., W. R. MUNDY, AND T. J. SHAFER. Developmental Neurotoxicity Testing: A Path Forward . Yuji Nakajima (ed.), Congenital Anomalies. Wiley-Blackwell, Hoboken, NJ, 52(3):140-146, (2012).

MARTIN, M. T., T. B. KNUDSEN, R. JUDSON, R. J. KAVLOCK, AND D. J. DIX. Economic benefits of using adaptive predictive models of reproductive toxicity in the context of a tiered testing program . Stephen A. Krawetz (Editor-in-Chief) (ed.), Systems Biology in Reproductive Medicine. Informa Healthcare USA, New York, NY, 58(1):3-9, (2012).

KLEINSTREUER, N., D. J. DIX, K. A. HOUCK, R. J. KAVLOCK, T. B. KNUDSEN, M. T. MARTIN, K. B. PAUL, D. REIF, K. M. CROFTON, K. HAMILTON, R. HUNTER, I. A. SHAH, AND R. JUDSON. In vitro Perturbations of Targets in Cancer Hallmark Processes Predict Rodent Chemical Carcinogenesis. TOXICOLOGICAL SCIENCES. Oxford University Press, Cary, NC, Epub(Advance Access):1-44, (2012).