Office of Research and Development Publications

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Nyffeler, J., C. Willis, R. Lougee, A. Richard, K. Friedman, AND J. Harrill. Bioactivity screening of environmental chemicals using imaging-based high-throughput phenotypic profiling. TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, 389:114876, (2020). https://doi.org/10.1016/j.taap.2019.114876

Nelms, M., R. Lougee, D. Roberts, A. Richard, AND G. Patlewicz. Comparing and contrasting the coverage of publicly available structural alerts for protein binding. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 12:100100, (2019). https://doi.org/10.1016/j.comtox.2019.100100

Friedman, K., M. Gagne, L. Loo, P. Karamertzanis, T. Netzeva, T. Sobanski, J. Franzosa, A. Richard, R. Lougee, A. Gissi, J. Lee, M. Angrish, J. Dorne, S. Foster, K. Raffaele, T. Bahadori, M. Gwinn, J. Lambert, M. Whelan, M. Rasenberg, T. Barton-Maclaren, AND R. Thomas. Utility of In Vitro Bioactivity as a Lower Bound Estimate of In Vivo Adverse Effect Levels and in Risk-Based Prioritization. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 173(1):202-225, (2020). https://doi.org/10.1093/toxsci/kfz201

Grulke, C., A. Williams, I. Thillainadarajah, AND A. Richard. EPA’s DSSTox database: History of development of a curated chemistry resource supporting computational toxicology research. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 12:100096, (2019). https://doi.org/10.1016/j.comtox.2019.100096

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

Patlewicz, G., A. Richard, A. Williams, C. Grulke, R. Sams, J. Lambert, Pamela Noyes, M. DeVito, R. Hines, M. Strynar, A. GuiseppiElie, AND R. Thomas. A Chemical Category-Based Prioritization Approach for Selecting 75 Per- and Polyfluoroalkyl Substances (PFAS) for Tiered Toxicity and Toxicokinetic Testing. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 127(1):1-12, (2019). https://doi.org/10.1289/EHP4555

Phillips, K., A. Yau, K. Favela, K. Isaacs, A. McEachran, Chris Grulke, A. Richard, A. Williams, J. Sobus, R. Thomas, AND J. Wambaugh. Suspect Screening Analysis of Chemicals in Consumer Products. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, 52(5):3125-3135, (2018). https://doi.org/10.1021/acs.est.7b04781

Nicolas, C., K. Mansouri, K. Phillips, Chris Grulke, A. Richard, A. Williams, J. Rabinowitz, K. Isaacs, A. Yau, AND J. Wambaugh. Rapid Experimental Estimates of Physicochemical Properties to Inform Models and Testing. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, 636:901-909, (2018). https://doi.org/10.1016/j.scitotenv.2018.04.266

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).

Mansouri, K., Chris Grulke, A. Richard, R. Judson, AND A. Williams. An automated curation procedure for addressing chemical errors and inconsistencies in public datasets used in QSAR modeling. SAR AND QSAR IN ENVIRONMENTAL RESEARCH. Taylor & Francis, Inc., Philadelphia, PA, 27(11):911-937, (2016).

Rager, J., M. Strynar, S. Liang, R. McMahen, A. Richard, C. Grukle, J. Wambaugh, K. Isaacs, R. Judson, A. Williams, AND J. Sobus. Linking high resolution mass spectrometry data with exposure and toxicity forecasts to advance high-throughput environmental monitoring. ENVIRONMENT INTERNATIONAL. Elsevier Science Ltd, New York, NY, 88:269-280, (2016).

Richard, A., R. Judson, K. Houck, C. Grulke, P. Volarath, I. Thillainadarajah, C. Yang, J. Rathman, M. Martin, J. Wambaugh, T. Knudsen, K. Mansouri, J. Kancherla, G. Tier, A. Williams, S. Little, K. Crofton, AND R. Thomas. The ToxCast Chemical Landscape - Paving the Road to 21st Century Toxicology. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 29(8):1225-1251, (2016).

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).

Mansouri, K., A. Abdelaziz, A. Rybacka, A. Roncaglioni, A. Tropsha, A. Varnek, A. Zakharov, A. Worth, A. Richard, Chris Grulke, D. Trisciuzzi, D. Fourches, D. Horvath, E. Benfenati, E. Muratov, E. Wedebye, F. Grisoni, G. Mangiatordi, G. Incisivo, H. Hong, H. Ng, I. Tetko, I. Balabin, J. Kancherla, J. Shen, J. Burton, M. Nicklaus, M. Cassotti, N. Nikolov, O. Nicolotti, P. Andersson, Q. Zang, R. Politi, R. Beger, R. Todeschini, R. Huang, S. Farag, S. Rosenberg, S. Slavov, X. Hu, AND R. Judson. CERAPP: Collaborative Estrogen Receptor Activity Prediction Project. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 124(7):1023-1033, (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).

Judson, Richard S., F. Magpantay, V. Chickarmane, C. Haskell, N. Tania, J. Taylor, M. Xia, R. Huang, D. Rotroff, D. Filer, K. Houck, M. Martin, N. Sipes, A. Richard, K. Mansouri, Woodrow Setzer, T. Knudsen, K. Crofton, AND R. Thomas. Integrated Model of Chemical Perturbations of a Biological PathwayUsing 18 In Vitro High Throughput Screening Assays for the Estrogen Receptor. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, :1-42, (2015).

Yang, C., A. Tarkhov, J. Marusczyk1, B. Bienfait, J. Gasteiger, T. Kleinoeder, T. Magdziarz, O. Sacher, C. Schwab, J. Schwoebel, L. Terfloth, K. Arvidson, A. Richard, A. Worth, AND J. Rathman. A New Publicly Available Chemical Query Language, CSRML, to support Chemotype Representations for Application to Data-Mining and Modeling. Journal of Chemical Information and Modeling. American Chemical Society, Washington, DC, 55(3):510-528, (2015).

Cherkasov, A., E. Muratov, D. Fourches, A. Varnek, I. Baskin, M. Cronin, J. Dearden, P. Gramatica, Y. Martin, R. Todeschini, V. Consonni, V. E. Kuzmin, R. Cramer, R. Benigni, C. Yang, J. Rathman, L. Terfloth, J. Gasteiger, A. Richard, AND A. Tropsha. QSAR Modeling: Where Have You Been? Where Are You Going To?. JOURNAL OF MEDICINAL CHEMISTRY. American Chemical Society, Washington, DC, 57(12):4977–5010, (2013).

Attene-Ramos, M., R. Huang, S. Michael, K. Witt, A. Richard, R. Tice, A. Simeonov, C. Austin, AND M. Xia. Profiling of the Tox21 Chemical Collection for Mitochondrial Function: I. Compounds that Decrease Mitochondrial Membrane Potential. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 123(1):49-56, (2015).

Kleinstreuer, N., J. Yang, E. Berg, T. Knudsen, A. Richard, M. Martin, D. Reif, R. Judson, M. Polokoff, D. Dix, R. Kavlock, AND K. Houck. Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms. Nature Biotechnology. Elsevier Science, New York, NY, 32(6):583-591, (2014).

Shen, J., L. Xu, H. Fang, A. M. RICHARD, J. D. Bray, R. JUDSON, G. Zhou, T. J. Colatsky, J. L. Aungst, C. Teng, S. C. Harris, W. Ge, AND S. Y. Dai. EADB: An Estrogenic Activity Database for Assessing Potential Endocrine Activity. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 135(2):277-291, (2013).

Sipes, N., M. Martin, P. Kothiya, D. Reif, R. Judson, A. Richard, K. Houck, D. Dix, R. Kavlock, AND T. Knudsen. Profiling 976 ToxCast chemicals across 331 enzymatic and receptor signaling assays. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 26:878−895, (2013).

ROTROFF, D., D. J. DIX, K. A. HOUCK, R. J. KAVLOCK, T. B. KNUDSEN, M. T. MARTIN, D. REIF, A. M. RICHARD, N. SIPES, Y. A. ABASSI, C. JIN, M. STAMPFL, AND R. JUDSON. Real-Time Growth Kinetics Measuring Hormone Mimicry for ToxCast Chemicals in T‑47D Human Ductal Carcinoma Cells . CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 26(7):1097-1107, (2013).

JUDSON, R., R. J. KAVLOCK, M. T. MARTIN, D. REIF, K. A. HOUCK, T. B. KNUDSEN, A. M. RICHARD, R. R. TICE, M. WHELAN, M. XIA, R. HUANG, C. P. AUSTIN, G. P. DASTON, T. HARTUNG, J. R. FOWLE III, W. WOOGE, W. TONG, AND D. J. DIX. Perspectives on Validation of High-Throughput Assays Supporting 21st Century Toxicity Testing. Sonja von Aulock (ed.), ALTEX. Society ALTEX Edition, Kuesnacht, Switzerland, 30(1/13):51-66, (2013).

Kavlock, R., K. Chandler, K. Houck, S. Hunter, R. Judson, N. Kleinstreuer, T. Knudsen, M. Martin, S. Padilla, D. Reif, A. Richard, D. Rotroff, N. Sipes, AND D. Dix. Update on EPA’s ToxCast Program: Providing High Throughput Decision Support Tools for Chemical Risk Management. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 25(7):1287-1302, (2012).