Office of Research and Development Publications

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Rivetti, C., T. Allen, J. Brown, E. Butler, P. Carmichael, J. Colbourne, M. Dent, F. Falciani, L. Gunnarsson, S. Gutsell, J. Harrill, G. Hodges, P. Jennings, R. Judson, A. Kienzler, L. Margiotta-Casaluci, I. Muller, S. Owen, C. Rendal, P. Russell, S. Scott, F. Sewell, I. Shah, I. Sorrel, M. Viant, C. Westmoreland, A. White, AND B. Campos. Vision of a near future: bridging the Human Health – Environment divide. Toward an integrated strategy to understand mechanisms across species for chemical safety assessment. TOXICOLOGY IN VITRO. Elsevier Science Ltd, New York, NY, 62:104692, (2020). https://doi.org/10.1016/j.tiv.2019.104692

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

Saili, K., T. Antonijevic, T. Zurlinden, I. Shah, C. Deisenroth, AND T. Knudsen. Molecular characterization of a toxicological tipping point during human stem cell differentiation. REPRODUCTIVE TOXICOLOGY. Elsevier Science Ltd, New York, NY, 91(January 2020):1-13, (2020). https://doi.org/10.1016/j.reprotox.2019.10.001

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

Mansouri, K., N. Kleinstreuer, R. Judson, A. Williams, I. Shah, AND A. Richard. CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 128(2):27002, (2020). https://doi.org/10.1289/EHP5580

Harrill, J., I. Shah, R. Setzer, D. Haggard, S. Auerbach, R. Judson, AND R. Thomas. Considerations for Strategic Use of High-Throughput Transcriptomics Chemical Screening Data in Regulatory Decisions. Current Opinion in Toxicology. Elsevier BV, AMSTERDAM, Netherlands, 15:64-75, (2019). https://doi.org/10.1016/j.cotox.2019.05.004

Helman, G., I. Shah, AND G. Patlewicz. Extending the Generalised Read-Across approach (GenRA): A systematic analysis of the impact of physicochemical property information on read-across performance. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 8:34-50, (2018). https://doi.org/10.1016/j.comtox.2018.07.001

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

Hartung, T., R. FitzGerald, P. Jennings, G. Mirams, M. Peitsch, A. ostami-Hodjegan, I. Shah, M. Wilks, AND S. Sturla. Systems Toxicology: Real World Applications and Opportunities. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 30(4):870-882, (2017). https://doi.org/10.1021/acs.chemrestox.7b00003

Sauer, S., M. Tarpley, I. Shah, A. Save, H. Lyerly, S. Patierno, K. Williams, AND G. Devi. Bisphenol A activates EGFR and ERK promoting proliferation, tumor spheroid formation and resistance to EGFR pathway inhibition in estrogen receptor negative inflammatory breast cancer cells. CARCINOGENESIS. Oxford University Press, Cary, NC, 38(3):252–260, (2017).

Patlewicz, G., G. Helman, P. Pradeep, AND I. Shah. Navigating through the minefield of read-across tools: A review of in silico tools for grouping. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 3:1-18, (2017).

Williams, A., Chris Grulke, J. Edwards, A. McEachran, K. Mansouri, N. Baker, G. Patlewicz, I. Shah, J. Wambaugh, R. Judson, AND A. Richard. The CompTox Chemistry Dashboard - A Community Data Resource for Environmental Chemistry. Journal of Cheminformatics. Springer, New York, NY, 9(61):1-27, (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, R., K. Houck, M. Martin, A. Richard, T. Knudsen, I. Shah, S. Little, J. Wambaugh, Woodrow Setzer, P. Kothiya, J. Phuong, D. Filer, D. Smith, D. Reif, D. Rotroff, N. Kleinstreuer, N. Sipes, M. Xia, R. Huang, K. Crofton, AND R. Thomas. Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 152(2):323-339, (2016).

Shah, I., Woodrow Setzer, J. Jack, K. Houck, R. Judson, T. Knudsen, J. Liu, M. Martin, D. Reif, Ann M. Richard, Russell S. Thomas, K. Crofton, David J. Dix, AND Robert J. Kavlock. Using ToxCast data to reconstruct dynamic cell state trajectories and estimate toxicological points of departure. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 124(7):910-919, (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).

Wambaugh, J., B. Wetmore, R. Pearce, C. Strope, R. Goldsmith, J. Sluka, A. Sedykh, A. Tropsha, S. Bosgra, I. Shah, R. Judson, R. Thomas, AND Woodrow Setzer. Toxicokinetic Triage for Environmental Chemicals. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 147(1):55-67, (2015).

Liu, J., K. Mansouri, Richard S. Judson, Matthew T. Martin, H. Hong, M. Chen, X. Xu, Russell S. Thomas, AND I. Shah. Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 28(4):738-751, (2015).

Judson, R., K. Houck, M. Martin, T. Knudsen, R. Thomas, N. Sipes, I. Shah, J. Wambaugh, AND K. Crofton. In Vitro and Modeling Approaches to Risk Assessment from the U.S. Environmental Protection Agency ToxCast Program. BASIC AND CLINICAL PHARMACOLOGY AND TOXICOLOGY. Blackwell Publishing, Malden, MA, 115(1):69-76, (2014).

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).

DIX, D. J., K. A. HOUCK, R. JUDSON, N. KLEINSTREUER, T. B. KNUDSEN, M. T. MARTIN, D. REIF, A. M. RICHARD, I. A. SHAH, N. SIPES, AND R. J. KAVLOCK. Incorporating Biological, Chemical and Toxicological Knowledge into Predictive Models of Toxicity: Letter to the Editor. TOXICOLOGICAL SCIENCES. Oxford University Press, Cary, NC, 130(2):440-441, (2012).

JUDSON, R., H. M. MORTENSEN, I. A. SHAH, T. B. KNUDSEN, AND F. ELLOUMI. Using pathway modules as targets for assay development in xenobiotic screening . Molecular BioSystems. RSC Publishing, Cambridge, Uk, 8(2):531-542, (2012).

COHEN-HUBAL, E. A., A. M. RICHARD, I. A. SHAH, J. GALLAGHER, R. J. KAVLOCK, J. N. BLANCATO, AND S. W. EDWARDS. Exposure Science and the US EPA National Center for Computational Toxicology. Journal of Exposure Science and Environmental Epidemiology . Nature Publishing Group, London, Uk, 20(3):231-236, (2010).

JACK, J., J. F. WAMBAUGH, AND I. A. SHAH. Simulating Quantitative Cellular Responses Using Asynchronous Threshold Boolean Network Ensembles. Online, BMC Systems Biology. BioMed Central Ltd, London, Uk, 5(109):1-13, (2011).

SHAH, I. A., K. A. HOUCK, R. JUDSON, R. J. KAVLOCK, M. T. MARTIN, D. REIF, J. F. WAMBAUGH, AND D. J. DIX. Using Nuclear Receptor Activity to Stratify Hepatocarcinogens. Stefan Wolfl (ed.), PLOS ONE . Public Library of Science, San Francisco, CA, 6(2; (e14584)):1-11, (2011).