Office of Research and Development Publications

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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

Deisenroth, C., V. Soldatow, J. Ford, W. Stewart, C. Brinkman, E. LeCluyse, D. Macmillan, AND R. Thomas. Development of an In Vitro Human Thyroid Microtissue Model for Chemical Screening (ToxSci). TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 174(1):63-78, (2020). https://doi.org/10.1093/toxsci/kfz238

Borrel, A., R. Huang, S. Sakamuru, M. Xia, A. Simeonov, K. Mansouri, K. Houck, R. Judson, AND N. Kleinstreuer. High-Throughput Screening to Predict Chemical-Assay Interference. Scientific Reports. Nature Publishing Group, London, Uk, 10:3986, (2020). https://doi.org/10.1038/s41598-020-60747-3

Hallinger, D., H. Lindsay, K. Friedman, D. Suarez, AND S. Simmons. Respirometric Screening and Characterization of Mitochondrial Toxicants Within the ToxCast Phase I and II Chemical Libraries. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 176(1):175-192, (2020). https://doi.org/10.1093/toxsci/kfaa059

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

Wei, Z., S. Sakamuru, L. Zhang, J. Zhao, R. Huang, N. Kleinstreuer, Y. Chen, Y. Shu, T. Knudsen, AND M. Xia. Identification and profiling of environmental chemicals that inhibit the TGFβ/SMAD signaling pathway. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 32(12):2433-2444, (2019). https://doi.org/10.1021/acs.chemrestox.9b00228

Paul-Friedman, K., M. Martin, K. Crofton, C. Hsu, S. Sakamuru, J. Zhao, M. Xia, R. Huang, D. Stevreva, V. Soni, L. Varticovski, R. Raziuddin, G. Hager, AND K. Houck. Limited chemical structural diversity found to modulate thyroid hormone receptor in the Tox21 chemical library. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 127(9):1-16, (2019). https://doi.org/10.1289/EHP5314

Watford, S., S. Edwards, M. Angrish, R. Judson, AND K. Friedman. Progress in data interoperability to support computational toxicology and chemical safety evaluation. TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, 380(1 October 2019):114707, (2019). https://doi.org/10.1016/j.taap.2019.114707

Saili, K., J. Franzosa, N. Baker, R. Ellis-Hutchings, R. Settivari, E. Carney, R. Spencer, T. Zurlinden, N. Kleinstreuer, S. Li, M. Xia, AND T. Knudsen. Systems Modeling of Developmental Vascular Toxicity. Current Opinion in Toxicology. Elsevier BV, AMSTERDAM, Netherlands, 15(1):55-63, (2019). https://doi.org/10.1016/j.cotox.2019.04.004

Xia, M., R. Huang, Q. Shi, W. Boyd, J. Zhao, N. Sun, J. Rice, P. Dunlap, A. Hackstadt, M. Bridge, M. Smith, S. Dai, W. Zheng, P. Chu, D. Gerhold, K. Witt, M. DeVito, J. Freeman, C. Austin, K. Houck, R. Thomas, R. Paules, R. Tice, AND A. Simeonov. Comprehensive analyses and prioritization of Tox21 10K chemicals affecting mitochondrial function by in-depth mechanistic studies. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 126(7):1-16, (2018). https://doi.org/10.1289/EHP2589

Mahapatra, D., Jill A. Franzosa, K. Roell, M. Kuenemann, Keith A. Houck, D. Reif, D. Fourches, AND S. Kullman. Confirmation of High-Throughput screening data and novel mechanistic insights into VDR-xenobiotic interactions by orthogonal assays. Scientific Reports. Nature Publishing Group, London, Uk, 8(8883):1-16, (2018). https://doi.org/10.1038/s41598-018-27055-3

Kleinstreuer, N., P. Browne, X. Chang, R. Judson, W. Casey, P. Ceger, C. Deisenroth, N. Baker, K. Markey, AND R. Thomas. Evaluation of Androgen Assay Results Using a Curated Hershberger Database. REPRODUCTIVE TOXICOLOGY. Elsevier Science Ltd, New York, NY, 81:272-280, (2018). https://doi.org/10.1016/j.reprotox.2018.08.017

Strope, C., K. Mansouri, H. Clewell, J. Rabinowitz, C. Stevens, AND J. Wambaugh. High-Throughput in-silico prediction of ionization equilibria for pharmacokinetic modeling. SCIENCE OF THE TOTAL ENVIRONMENT. Elsevier BV, AMSTERDAM, Netherlands, 615:150-160, (2018). https://doi.org/10.1016/j.scitotenv.2017.09.033

Watford, S., R. Grashow, V. De La Rosa, R. Rudel, K. Paul-Friedman, AND M. Martin. Novel application of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene sets associated with disease: Use case in breast carcinogenesis. Computational Toxicology. Elsevier B.V., Amsterdam, Netherlands, 7:46-57, (2018). https://doi.org/10.1016/j.comtox.2018.06.003

Zang, Q., K. Mansouri, A. Williams, R. Judson, D. Allen, W. Casey, AND N. Kleinstreuer. In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning. Journal of Chemical Information and Modeling. American Chemical Society, Washington, DC, 57(1):36-49, (2017).

Sipes, N., J. Wambaugh, R. Pearce, S. Auerbach, B. Wetmore, J. Hsieh, A. Shapiro, D. Sboboda, M. DeVito, AND S. Ferguson. An Intuitive Approach for Predicting Human Risk with the Tox21 10k Library. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, (51):10786-10796, (2017).

Saili, K., T. Zurlinden, A. Schwab, A. Silvin, N. Baker, S. Hunter, F. Ginhoux, AND T. Knudsen. Blood-Brain Barrier Development: Systems Modeling and Predictive Toxicology. Birth Defects Research, Part C: Embryo Today: Reviews. John Wiley & Sons, Ltd., Indianapolis, IN, 109(20):1680-1710, (2017). https://doi.org/10.1002/bdr2.1180

Kleinstreuer, N., P. Ceger, Eric Watt, M. Martin, K. Houck, P. Browne, R. Thomas, W. Casey, D. Dix, D. Allen, S. Sakamuru, M. Xia, R. Huang, AND R. Judson. Development and Validation of a Computational Model for Androgen Receptor Activity. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, 30(4):946-964, (2017).

Pearce, R., Woodrow Setzer, C. Strope, N. Sipes, AND J. Wambaugh. HTTK: R Package for High-Throughput Toxicokinetics. Journal of Statistical Software. American Statistical Association, Alexandria, VA, 79(4):1-26, (2017).

Lynch, C., S. Sakamuru, R. Huang, D. Stavea, L. Varticovski, G. Hager, Richard S. Judson, Keith A. Houck, N. Kleinstreuer, W. Casey, R. Paules, A. Simeonov, AND M. Xia. Identifying Environmental Chemicals as Agonists of the Androgen Receptor by Applying a Quantitative High-throughput Screening Platform. TOXICOLOGY. Elsevier Science Ltd, New York, NY, 385:48-58, (2017).

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).

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).

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).

Baghdikian, C. AND A. Karmaus. High-Throughput Toxicity Testing: New Strategies for Assessing Chemical Safety. Food Safety Magazine. The Target Group, Inc., Glendale, CA, (Dec./Jan.):1-2, (2016).