Publications

2019


The US Federal Tox21 Program: A Strategic and Operational Plan for Continued Leadership

Thomas, R.S., R.S. Paules, A. Simeonov, S.C. Fitzpatrick, K.M. Crofton, W.M. Casey, and D.L. Mendrick. The US Federal Tox21 Program: A Strategic and Operational Plan for Continued Leadership. ALTEX. Society ALTEX Edition, Kuesnacht, SWITZERLAND, 35(2): 163-168, (2018). https://doi.org/10.14573/altex.1803011

The next generation blueprint of computational toxicology at the U.S. Environmental Protection Agency

Thomas, R., T. Bahadori, T. Buckley, J. Cowden, C. Deisenroth, K. Dionisio, J. Frithsen, C. Grulke, M. Gwinn, J. Harrill, M. Higuchi, K. Houck, M. Hughes, S. Hunter, K. Isaacs, R. Judson, T. Knudsen, J. Lambert, M. Linnenbrink, T. Martin, S. Newton, S. Padilla, G. Patlewicz, K. Paul-Friedman, K. Phillips, A. Richard, R. Sams, T. Shafer, W. Setzer, I. Shah, J. Simmons, S. Simmons, A. Singh, J. Sobus, M. Strynar, A. Swank, R. Tornero-Velez, E. Ulrich, D. Villeneuve, J. Wambaugh, B. Wetmore, and A. Williams. The next generation blueprint of computational toxicology at the U.S. Environmental Protection Agency. TOXICOLOGICAL SCIENCES. Society of Toxicology, RESTON, VA, 1-33, (2019). https://doi.org/10.1093/toxsci/kfz058

The NCATS BioPlanet – An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics.

Huang R, Grishagin I, Wang Y, Zhao T, Greene J, Obenauer JC, Ngan D, Nguyen DT, Guha R, Jadhav A, Southall N, Simeonov A, Austin CP. The NCATS BioPlanet – An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics. Front Pharmacol.;10:445. doi: 10.3389/fphar.2019.00445. eCollection 2019.

Consensus Statement on the need for innovation, transition and implementation of developmental neurotoxicity (DNT) testing for regulatory purposes

Fritsche, E., P. Grandjean, K. Crofton, S.H. Bennekou, M. Leist, M. Sachana, R. Solecki, A. Terron, M. Wilks, and A. Bal-Price. Consensus Statement on the need for innovation, transition and implementation of developmental neurotoxicity (DNT) testing for regulatory purposes. TOXICOLOGY AND APPLIED PHARMACOLOGY. Academic Press Incorporated, Orlando, FL, USA, 354: 3-6, (2018). https://doi.org/10.1016/j.taap.2018.02.004

Using Tox21 High-Throughput Screening Assays for the Evaluation of Botanical and Dietary Supplements

Hubbard TD, Hsieh JH, Rider CV, Sipes NS, Sedykh A, Collins BJ, Auerbach SS, Xia M, Huang R, Walker NJ, DeVito MJ (2019) Using Tox21 High-Throughput Screening Assays for the Evaluation of Botanical and Dietary Supplements. Appl In Vitro Toxicol. 5(1):10-25.

Toxicogenomics: A 2020 Vision

Liu Z, Huang R, Roberts R, Tong W (2019) Toxicogenomics: A 2020 Vision. Trends Pharmacol Sci.

Drug-Induced Rhabdomyolysis Atlas (DIRA) for idiosyncratic adverse drug reaction management

Wen Z, Liang Y, Hao Y, Delavan B, Huang R, Mikailov M, Tong W, Li M, Liu Z (2019) Drug-Induced Rhabdomyolysis Atlas (DIRA) for idiosyncratic adverse drug reaction management. Drug Discov Today. 24(1):9-15.

Systems modeling of developmental vascular toxicity

Saili KS, Franzosa JA, Baker NC, Ellis-Hutchings RG, Settivari RS, Carney EW, Spencer R, Zurlinden TJ, Kleinstreuer NC, Li S, Xia M, Knudsen TB (2019) Systems modeling of developmental vascular toxicity. Current Opinion in Toxicology, in press

Identifying Compounds with Genotoxicity Potential Using Tox21 High Throughput Screening Assays

Hsieh J, Smith-Roe S, Huang R, Sedykh A, Shockley K, Auerbach S, Merrick B, Xia M, Tice R, Witt K (2019) Identifying Compounds with Genotoxicity Potential Using Tox21 High Throughput Screening Assays. Chemical Research in Toxicology, Epub ahead of print

Identification of Compounds That Inhibit Estrogen-Related Receptor Alpha Signaling Using High-Throughput Screening Assays

Lynch C, Zhao J, Sakamuru S, Zhang L, Huang R, Witt KL, Merrick BA, Teng CT, Xia M (2019) Identification of Compounds That Inhibit Estrogen-Related Receptor Alpha Signaling Using High-Throughput Screening Assays. Molecules. 24(5).

Use of high-throughput enzyme-based assay with xenobiotic metabolic capability to evaluate the inhibition of acetylcholinesterase activity by organophosphorous pesticides

Li S, Zhao J, Huang R, Santillo MF, Houck KA, Xia M (2019) Use of high-throughput enzyme-based assay with xenobiotic metabolic capability to evaluate the inhibition of acetylcholinesterase activity by organophosphorous pesticides. Toxicol In Vitro. 56:93-100.

Identification of Modulators That Activate the Constitutive Androstane Receptor From the Tox21 10K Compound Library

Lynch C, Mackowiak B, Huang R, Li L, Heyward S, Sakamuru S, Wang H, Xia M (2019) Identification of Modulators That Activate the Constitutive Androstane Receptor From the Tox21 10K Compound Library. Toxicol Sci. 167(1):282-292.

Triazole-Based Inhibitors of the Wnt/β-Catenin Signaling Pathway Improve Glucose and Lipid Metabolisms in Diet-Induced Obese Mice

Obianom ON, Ai Y, Li Y, Yang W, Guo D, Yang H, Sakamuru S, Xia M, Xue F, Shu Y (2019) Triazole-Based Inhibitors of the Wnt/β-Catenin Signaling Pathway Improve Glucose and Lipid Metabolisms in Diet-Induced Obese Mice. J Med Chem. 62(2):727-741.

2018


Confirmation of High-Throughput screening data and novel mechanistic insights into VDR-xenobiotic interactions by orthogonal assays

Mahapatra, D., J.A. Franzosa, K. Roell, M.A. Kuenemann, K.A. Houck, D.M. Reif, D. Fourches, and S.W. 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

Comment on “On the Utility of ToxCast and ToxPi as Methods for Identifying New Obesogens”

Houck, K., R. Judson, T. Knudsen, M. Martin, A. Richard, K. Crofton, A. Simeonov, R. Paules, J. Bucher, and R. Thomas. Comment on “On the Utility of ToxCast and ToxPi as Methods for Identifying New Obesogens”. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, USA, 125(1): A8-A11, (2017). https://doi.org/10.1289/EHP881

A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics

Mav, D., R.R. Shah, B.E. Howard, S.S. Auerbach, P.R. Bushel, J.B. Collins, D.L. Gerhold, R. Judson, A.L. Karmaus, E.A. Maull, D.L. Mendrick, B.A. Merrick, N.S. Sipes, D. Svoboda, and R.S. Paules. A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PLoS ONE. Public Library of Science, San Francisco, CA, USA, 13(2): 1-17, (2018). https://doi.org/10.1371/journal.pone.0191105

Comprehensive analyses and prioritization of Tox21 10K chemicals affecting mitochondrial function by in-depth mechanistic studies

Xia, M., R. Huang, Q. Shi, W. Boyd, J. Zhao, N. Sun, J.R. Rice, P.E. Dunlap, A.J. Hackstadt, M.F. Bridge, M.V. Smith, S. Dai, W. Zheng, P. Chu, D. Gerhold, K.L. Witt, M. DeVito, J.H. Freeman, C.P. Austin, K. Houck, R. Thomas, R.S. Paules, R.B. 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, USA, 126(7): 1-16, (2018). https://doi.org/10.1289/EHP2589

Novel application of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene sets associated with disease: Use case in breast carcinogenesis

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). 

(ENVIRONMENTAL SCIENCE and TECHNOLOGY) An Intuitive Approach for Predicting Human Risk with the Tox21 10k Library

Sipes, N., J. Wambaugh, R. Pearce, S. Auerbach, B. Wetmore, J. Hsieh, A. Shapiro, D. Sboboda, M. DeVito, and S. Ferguson. (ENVIRONMENTAL SCIENCE and TECHNOLOGY) An Intuitive Approach for Predicting Human Risk with the Tox21 10k Library. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, USA, issue}: 10786-10796, (2017). https://doi.org/10.1021/acs.est.7b00650

High-Throughput in-silico prediction of ionization equilibria for pharmacokinetic modeling

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)

Identification of Estrogen-Related Receptor α Agonists in the Tox21 Compound Library

Lynch C, Zhao J, Huang R, Kanaya N, Bernal L, Hsieh JH, Auerbach SS, Witt KL, Merrick BA, Chen S, Teng CT, Xia M. (2018) Identification of Estrogen-Related Receptor α Agonists in the Tox21 Compound Library. Endocrinology, 159(2):744-753.

Expanding biological space coverage enhances the prediction of drug adverse effects in human using in vitro activity profiles

Huang R, Xia M, Sakamuru S, Zhao J, Lynch C, Zhao T, Zhu H, Austin CP, Simeonov A. (2018) Expanding biological space coverage enhances the prediction of drug adverse effects in human using in vitro activity profiles. Scientific Reports, 8(1):3783.

The Toxmatrix: Chemo-genomic profiling identifies interactions that reveal mechanisms of toxicity

Tong ZB, Huang R, Wang Y, Klumpp-Thomas CA, Braisted JC, Itkin Z, Shinn P, Xia M, Simeonov A, and Gerhold DL. (2018) The Toxmatrix: Chemo-genomic profiling identifies interactions that reveal mechanisms of toxicity. Chemical Research in Technology, 31(2):127-136.

2017


Integrating tools for non-targeted analysis research and chemical safety evaluations at the US EPA

Sobus, J., J. Wambaugh, K. Isaacs, A. Williams, A. McEachran, A. Richard, Chris Grulke, E. Ulrich, J. Rager, M. Strynar, AND S. Newton. Integrating tools for non-targeted analysis research and chemical safety evaluations at the US EPA. Journal of Exposure Science and Environmental Epidemiology . Nature Publishing Group, London, Uk, 28:411-426, (2018). 

Blood-Brain Barrier Development: Systems Modeling and Predictive Toxicology

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).

(Toxicology) Identifying Environmental Chemicals as Agonists of the Androgen Receptor by Applying a Quantitative High-throughput Screening Platform

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

(Chemical Research in Toxicology) Development and Validation of a Computational Model for Androgen Receptor Activity

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

HTTK: R Package for High-Throughput Toxicokinetics

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).

In Silico Prediction of Physicochemical Properties of Environmental Chemicals Using Molecular Fingerprints and Machine Learning

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).

A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics

Mav D, Shah RR, Howard BE, Auerbach SS, Bushel PR, Collins JB, Gerhold DL, et al. (2017) A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PLoS One, 13(2):e0191105.

Why are most PLD inducers also hERG blockers? Archives of Toxicology, 91(12):3885-3895.

Slavov S, Stoyanova-Slavova I, Li S, Zhao J, Huang R, Xia M, Beger R. (2017) Why are most PLD inducers also hERG blockers? Archives of Toxicology, 91(12):3885-3895.

Development and Validation of a Computational Model for Androgen Receptor Activity

Kleinstreuer NC, Ceger P, Watt ED, Martin M, Houck K, Browne P, Thomas RS, Casey WM, Dix DJ, Allen D, Sakamuru S, Xia M, Huang R, Judson R. (2017) Development and Validation of a Computational Model for Androgen Receptor Activity. Chemical Research in Technology, 30(4):946-964.

QSAR Development and Profiling of 72,524 REACH Substances for PXR Activation and CYP3A4 Induction

Rosenberg SA, Nikolov NG, Wedebye E, Xia M, Huang R, Dybdahl M. (2017) QSAR Development and Profiling of 72,524 REACH Substances for PXR Activation and CYP3A4 Induction. Computational Toxicology, 1:39-48.

Comprehensive analyses and prioritization of Tox21 10K chemicals affecting mitochondrial function by in-depth mechanistic studies

Xia M, Huang R, Shi Q, Boyd W, Zhao J, Sun N, Rice JR, Dunlap PE, Hackstadt AJ, Bridge MF, Smith MV, Dai S, Zheng W, Chu P, Gerhold D, Witt KL, DeVito M, Freedman JH, Austin CP, Houck KA, Thomas RS, Paules RS, Tice RR, Simeonov A. (2017) Comprehensive analyses and prioritization of Tox21 10K chemicals affecting mitochondrial function by in-depth mechanistic studies, 126(7):077010.

Assessment of the DNA damaging potential of environmental chemicals using a quantitative high-throughput screening approach to measure p53 activation

Witt K, Hsieh J, Smith-Roe S, Xia M, Huang R, Zhao J, Auerbach S, Hur J, Tice R. (2017) Assessment of the DNA damaging potential of environmental chemicals using a quantitative high-throughput screening approach to measure p53 activation. Environmental and Molecular Mutagenesis, 58(7):494-507.

Development of novel cell lines for high throughput screening to detect estrogen- related receptor alpha modulators

Teng C, Hsieh J, Zhao J, Huang R, Xia M, Martin N, Gao X, Dixon D, Auerbach S, Witt KL, Merrick A. (2017) Development of novel cell lines for high throughput screening to detect estrogen- related receptor alpha modulators. SLAS Discovery, 22:720-731.

Real-time cell toxicity profiling of Tox21 10K compounds reveals cytotoxicity dependent toxicity pathway linkage

Hsieh JH, Huang R, Lin JA, Sedykh A, Zhao J, Tice RR, Paules RS, Xia M, Auerbach SS. (2017) Real-time cell toxicity profiling of Tox21 10K compounds reveals cytotoxicity dependent toxicity pathway linkage. PLoS One, 12(5):e0177902.

Identifying Environmental Chemicals as Agonists of the Androgen Receptor by Using a Quantitative High-throughput Screening Platform

Lynch C, Sakamuru S, Huang R, Stavreva DA, Varticovski L, Hager GL, Judson RS, Houck KA, Kleinsteuer NC, Casey W, Paules RS, Simeonov A, Xia M. (2017) Identifying Environmental Chemicals as Agonists of the Androgen Receptor by Using a Quantitative High-throughput Screening Platform. Toxicology, 385:48-58.

Alternative approaches for identifying acute systemic toxicity: Moving from research to regulatory testing

Hamm J, Sullivan K, Clippinger AJ, Strickland J, Bell S, Bhhatarai B, Blaauboer B, Casey W, Dorman D, Forsby A, Garcia-Reyero N, Gehen S, Graepel R, Hotchkiss J, Lowit A, Matheson J, Reaves E, Scarano L, Tunkel J, Wilson D, Xia M, Hao Zhu, Allen D. (2017) Alternative approaches for identifying acute systemic toxicity: Moving from research to regulatory testing. Toxicology In Vitro, 41:245-259.

Identification of acetylcholinesterase inhibitors using homogenous cell-based assays in quantitative high-throughput screening platforms

Li S, Huang R, Solomon S, Liu Y, Zhao B, Santillo MF, Xia M. (2017) Identification of acetylcholinesterase inhibitors using homogenous cell-based assays in quantitative high-throughput screening platforms. Biotechnology Journal, 12(5).

Integrating Drug’s Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury

Wu L, Liu Z, Auerbach S, Huang R, Chen M, McEuen K, Xu J, Fang H, Tong W. (2017) Integrating Drug’s Mode of Action into Quantitative Structure-Activity Relationships for Improved Prediction of Drug-Induced Liver Injury. Journal of Chemical Information and Modeling, 57(4):1000-1006.

Prediction of hERG Liability Using SVM Classification, Bootstrapping and Jackknifing

Sun H, Huang R, Xia M, Shahane S, Southall N, Wang Y. (2017) Prediction of hERG Liability Using SVM Classification, Bootstrapping and Jackknifing. Molecular Informatics, 36(4).

Development and application of human renal proximal tubule epithelial cells for assessment of compound toxicity

Li S, Zhao J, Huang R, Steiner T, Bourner M, Mitchell M, Thompson DC, Zhao B, Xia M. (2017) Development and application of human renal proximal tubule epithelial cells for assessment of compound toxicity. Current Chemical Genomics and Translational Medicine, 11:19-30.

Editorial: Tox21 challenge to build predictive models of nuclear receptor and stress response pathways as mediated by exposure to environmental toxicants and drugs

Huang R, Xia M. (2017) Editorial: Tox21 challenge to build predictive models of nuclear receptor and stress response pathways as mediated by exposure to environmental toxicants and drugs. Frontiers in Environmental Science, 5:3.

Advances in high-throughput screening technology for toxicology

Hsu C, Huang R, Attene-Ramos MS, Austin CP, Simeonov A, Xia M. (2017) Advances in high-throughput screening technology for toxicology. International Journal of Risk Assessment and Management, 20:109-135.

2016


(Chemical Research in Toxicology) The ToxCast Chemical Landscape – Paving the Road to 21st Century Toxicology

Richard, A., R. Judson, K. Houck, C.M. 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. (Chemical Research in Toxicology) The ToxCast Chemical Landscape – Paving the Road to 21st Century Toxicology. CHEMICAL RESEARCH IN TOXICOLOGY. American Chemical Society, Washington, DC, USA, 1-78, (2016).

(Toxicological Sciences) Analysis of the Effects of Cell Stress and Cytotoxicity on In Vitro Assay Activity Across a Diverse Chemical and Assay Space

Judson , R., K. Houck , M. Martin , A. Richard , T. Knudsen , I. Shah , S. Little , J. Wambaugh , W. 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. (Toxicological Sciences) 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, 1-47, (2016).

Linking high resolution mass spectrometry data with exposure and toxicity forecasts to advance high-throughput environmental monitoring

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).

Differential modulation of FXR activity by chlorophacinone and ivermectin analogs

Hsu CW, Hsieh JH, Huang R, Pijnenburg D, Khuc T, Hamm J, Zhao J, Lynch C, van Beuningen R, Chang X, Houtman R, Xia M. (2016) Differential modulation of FXR activity by chlorophacinone and ivermectin analogs. Toxicology and Applied Pharmacology, 313:138-148.

Good Cell Culture Practice for stem cells and stem-cell-derived models

Pamies D, Bal-Price A, Simeonov A, Tagle D, Allen D, Gerhold D, Yin D, Pistollato F, Inutsuka T, Sullivan K, Stacey G, Salem H, Leist M, Daneshian M, Vemuri MC, McFarland R, Coecke S, Fitzpatrick SC, Lakshmipathy U, Mack A, Wang WB, Daiju Y, Sekino Y, Kanda Y, Smirnova L, Hartung T. (2016) Good Cell Culture Practice for stem cells and stem-cell-derived models. ALTEX, 34(1):95-132.

Using β-lactamase and nanoLuc luciferase reporter gene assays to identify inhibitors of the HIF-1 signaling pathway

Khuc T, Chia-Wen Hsu, Sakamuru S, Xia M. (2016) Using β-lactamase and nanoLuc luciferase reporter gene assays to identify inhibitors of the HIF-1 signaling pathway. In: Zhu H, Xia M (Ed.), High-throughput screening assay in toxicology, Methods in Molecular Biology, 1473:23-31.

Cell-based assay for identifying the modulators of antioxidant response element signaling pathway

Zhao J, Shukla SJ, Xia M. (2016) Cell-based assay for identifying the modulators of antioxidant response element signaling pathway. In: Zhu H, Xia M. (Ed.), High-throughput screening assay in toxicology, Methods in Molecular Biology, 1473:55-62.

A Quantitative High-Throughput Screening Data Analysis Pipeline for Activity Profiling

Huang R. (2016) A Quantitative High-Throughput Screening Data Analysis Pipeline for Activity Profiling. Methods in Molecular Biology, 1473:111-22.

Mechanism Profiling of Hepatotoxicity Caused by Oxidative Stress Using the Antioxidant Response Element Reporter Gene Assay Models and Big Data

Kim MT, Huang R, Sedykh A, Wang W, Xia M, Zhu H. (2016) Mechanism Profiling of Hepatotoxicity Caused by Oxidative Stress Using the Antioxidant Response Element Reporter Gene Assay Models and Big Data. Environmental Health Perspectives, 124(5):634-41.

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

Huang R, Xia M, Sakamuru S, Zhao J, Shahane SA, Attene-Ramos M, Zhao T, Austin CP, Simeonov A. (2016) Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization. Nature Communications, 7:10425.

The Next Generation of Risk Assessment Multiyear Study- Highlights of Findings, Applications to Risk Assessment and Future Directions

Cote I, Andersen ME, Ankley GT, Barone S, Birnbaum LS, Boekelheide K, Bois FY, Burgoon LD, Chiu WA, Crawford-Brown D…Simeonov A…Xia M…et al. (2016) The Next Generation of Risk Assessment Multiyear Study- Highlights of Findings, Applications to Risk Assessment and Future Directions. Environ Health Perspectives, 124(11): 1671–1682.

Analysis of the effects of cell stress and cytotoxicity on in vitro assay activity across a diverse chemical and assay space

Judson R, Houck K, Martin M, Richard AM, Knudsen TB, Shah I, Little S, Wambaugh J, Setzer W, Kothy P, Phuong J, Filer D, Smith D, Reif D, Rotroff D, Kleinstreuer N, Sipes N, Xia M, Huang R, Crofton K, Thomas RS. (2016) Analysis of the effects of cell stress and cytotoxicity on in vitro assay activity across a diverse chemical and assay space. Toxicological Sciences, 153(2):409.

A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives

Grimm FA, Iwata Y, Sirenko O, Chappell GA, Wright FA, Reif DM, Braisted J, Gerhold DL, Yeakley JM, Shepard P, Seligmann B, Roy T, Boogaard PJ, Ketelslegers HB, Rohde AM, Rusyn I. (2016) A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives. Green Chemistry, (18) 4407-4419.

Mitochondrial membrane potential

Sakamuru S, Attene-Ramos MS, Xia M. (2016) Mitochondrial membrane potential. In: Zhu H, Xia M (Ed.), High-throughput screening assay in toxicology, Methods in Molecular Biology, 1473:17-22.

Quantitative high-throughput luciferase screening in identifying CAR modulators

Lynch C, Zhao J, Wang H, Xia M. (2016) Quantitative high-throughput luciferase screening in identifying CAR modulators. In: Zhu H, Xia M. (Ed.), High-throughput screening assay in toxicology, Methods in Molecular Biology, 1473:33-42.

Transactivation and coactivator recruitment assays for measuring farnesoid X receptor activity

Hsu CW, Zhao J, Xia M. (2016) Transactivation and coactivator recruitment assays for measuring farnesoid X receptor activity. In: Zhu H, Xia M. (Ed.), High-throughput screening assay in toxicology, Methods in Molecular Biology, 1473:43-53.

Determination of histone H2AX phosphorylation in DT40 cells

Nishihara K, Shahane SA, Xia M. (2016) Determination of histone H2AX phosphorylation in DT40 cells. In: Zhu H, Xia M. (Ed.), High-throughput screening assay in toxicology, Methods in Molecular Biology, 1473:71-76.

High-throughput and high-content micronucleus assay in CHO-K1 cells

Shahane SA, Nishihara K, Xia M. (2016) High-throughput and high-content micronucleus assay in CHO-K1 cells. In: Zhu H, Xia M. (Ed.), High-throughput screening assay in toxicology. Methods in Molecular Biology, 1473:77-85.

CERAPP: Collaborative Estrogen Receptor Activity Prediction Project, Environ Health Perspect, 124(7):1023-33.

Mansouri K, Abdelaziz A, Rybacka A, Roncaglioni A, Tropsha A, Varnek A, Zakharov A, Worth A, Richard AM, Grulke CM…Huang R…et al. (2016) CERAPP: Collaborative Estrogen Receptor Activity Prediction Project, Environ Health Perspect, 124(7):1023-33.

Characterization of three human cell line models for high-throughput neuronal cytotoxicity screening

Tong ZB, Hogberg H, Kuo D, Sakamuru S, Xia M, Smirnova L, Hartung T, Gerhold D. (2016) Characterization of three human cell line models for high-throughput neuronal cytotoxicity screening. Journal of Applied Toxicology, 37(2):167-180.

Identification of compounds that modulate retinol signaling using a cell-based qHTS assay

Chen Y, Sakamuru S, Huang R, Reese DH, Xia M. (2016) Identification of compounds that modulate retinol signaling using a cell-based qHTS assay. Toxicology In Vitro, 32(4):287-296.

Discovery of Transcriptional Targets Regulated by Nuclear Receptors Using a Probabilistic Graphical Model

Lee M, Huang R, Tong W. (2016) Discovery of Transcriptional Targets Regulated by Nuclear Receptors Using a Probabilistic Graphical Model. Toxicological Sciences, 150(1):64-73.

Identification of approved and investigational drugs that inhibit hypoxia-inducible factor-1 signaling

Hsu CW, Huang R, Khuc T, Shou D, Bullock J, Grooby S, Griffin S, Zou C, Little A, Astley H, Xia M. (2016) Identification of approved and investigational drugs that inhibit hypoxia-inducible factor-1 signaling. Oncotarget, 7:8172-8183.

Identification of HDAC inhibitors using a cell-based HDAC I/II assay

Hsu CW, Shou D, Huang R, Khuc T, Sheng D, Klumpp-Thomas C, Zheng W, Xia M. (2016) Identification of HDAC inhibitors using a cell-based HDAC I/II assay. Journal of Biomolecular Screening, 21(6):643-652.

Tox21Challenge to Build Predictive Models of Nuclear Receptor and Stress Response Pathways as Mediated by Exposure to Environmental Chemicals and Drugs

Huang R, Xia M, Nguyen D, Zhao T, Sakamuru S, Zhao J, Shahane SA, Rossoshek A, Simeonov A. (2016) Tox21Challenge to Build Predictive Models of Nuclear Receptor and Stress Response Pathways as Mediated by Exposure to Environmental Chemicals and Drugs. Frontiers in Environmental Science, (3)85:1-9.

Identification of genotoxic compounds using isogenic DNA repair deficient DT40 cell lines on a quantitative high throughput screening platform

Nishihara K, Huang R, Zhao J, Shahane SA, Witt KL, Smith-Roe SL, Tice RR, Takeda S, Xia M. (2016) Identification of genotoxic compounds using isogenic DNA repair deficient DT40 cell lines on a quantitative high throughput screening platform. Mutagenesis, 31(1):69-81.

2015


A New Publicly Available Chemical Query Language, CSRML, to support Chemotype Representations for Application to Data-Mining and Modeling

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).

Applying Adverse Outcome Pathways (AOPs) to support Integrated Approaches to Testing and Assessment (IATA workshop report)

Tollefsena, K., S. Scholz, M. Cronin, S. Edwards, J. de Knecht, K. Crofton, N. Garcia-Reyero, T. Hartung, A. Worth, AND C. Patlewicz. Applying Adverse Outcome Pathways (AOPs) to support Integrated Approaches to Testing and Assessment (IATA workshop report). REGULATORY TOXICOLOGY AND PHARMACOLOGY. Elsevier Science Ltd, New York, NY, 70(3):629-640, (2014).

Integrated Model of Chemical Perturbations of a Biological Pathway Using 18 In Vitro High Throughput Screening Assays for the Estrogen Receptor

Judson RS, Magpantay FM, Chickarmane V, Haskell C, Tania N, Taylor J, Xia M, Huang R, Rotroff DM, Filer DM, Houck KA, Martin MT, Sipes N, Richard AM, Mansouri K, Setzer W, Knudsen TB, Crofton KM, Thomas RS. (2015) Integrated Model of Chemical Perturbations of a Biological Pathway Using 18 In Vitro High Throughput Screening Assays for the Estrogen Receptor. Toxicological Sciences, 148:137-154.

Evaluation of CYP3A4 inhibition and hepatotoxicity using DMSO-treated human hepatoma HuH-7 cells

Liu Y, Flynn TJ, Xia M, Wiesenfeld PL, Ferguson MS. (2015) Evaluation of CYP3A4 inhibition and hepatotoxicity using DMSO-treated human hepatoma HuH-7 cells. Cell Biology and Toxicology, 31:221-230.

Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library

Chen S, Hsieh JH, Huang R, Sakamuru S, Hsin LY, Xia M, Shockley KR, Auerbach S, Kanaya N, Lu H, Svoboda D, Witt KL, Merrick BA, Teng CT, Tice RR. (2015) Cell-Based High-Throughput Screening for Aromatase Inhibitors in the Tox21 10K Library. Toxicological Sciences, 147(2):446-57.

Prediction of human population responses to toxic compounds by a collaborative competition

Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O, NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration, Friend S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J. (2015) Prediction of human population responses to toxic compounds by a collaborative competition. Nature Biotechnology, 33(9):933-40.

A Data Analysis Pipeline Accounting for Artifacts in Tox21 Quantitative High-Throughput Screening Assays

Hsieh JH, Sedykh A, Huang R, Xia M, Tice RR. (2015) A Data Analysis Pipeline Accounting for Artifacts in Tox21 Quantitative High-Throughput Screening Assays. Journal of Biomolecular Screening, 20(7):887-97.

Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: focus on the cancer hallmark of tumor angiogenesis

Hu Z, Brooks SA, Dormoy V, Hsu CW, Hsu HY, Lin LT, Massfelder T, Rathmell WK, Xia M, Al-Mulla F, Al-Temaimi R, Amedei A, Brown DG, Prudhomme KR, Colacci A, Hamid RA, Mondello C, Raju J, Ryan EP, Woodrick J, Scovassi AI, Singh N, Vaccari M, Roy R, Forte S, Memeo L, Salem HK, Lowe L, Jensen L, Bisson WH, Kleinstreuer N. (2015) Assessing the carcinogenic potential of low-dose exposures to chemical mixtures in the environment: focus on the cancer hallmark of tumor angiogenesis. Carcinogenesis, 36 Suppl 1:S184-202.

Quantitative high-throughput identification of drugs as modulators of human constitutive androstane receptor

Lynch C, Zhao J, Huang R, Xiao J, Li L, Heyward S, Xia M, Wang H. (2015) Quantitative high-throughput identification of drugs as modulators of human constitutive androstane receptor. Scientific Reports, 5:10405.

Population-based in vitro hazard and concentration-response assessment of chemicals: the 1000 genomes high-throughput screening study

Abdo N, Xia M, Brown CC, Kosyk O, Huang R, Sakamuru S, Zhou YH, Jack JR, Gallins P, Xia K, Li Y, Chiu WA, Motsinger-Reif AA, Austin CP, Tice RR, Rusyn I, Wright FA. (2015) Population-based in vitro hazard and concentration-response assessment of chemicals: the 1000 genomes high-throughput screening study. Environmental Health Perspectives, 123(5):458-66.

Profiling of the Tox21 chemical collection for mitochondrial function to identify compounds that acutely decrease mitochondrial membrane potential

Attene-Ramos MS, Huang R, Michael S, Witt KL, Richard A, Tice RR, Simeonov A, Austin CP, Xia M. (2015) Profiling of the Tox21 chemical collection for mitochondrial function to identify compounds that acutely decrease mitochondrial membrane potential. Environmental Health Perspectives, 123(1):49-56.

Performance of the BG1Luc ER TA method in a qHTS format

Ceger P, Allen D, Huang R, Xia M, Casey W. (2015) Performance of the BG1Luc ER TA method in a qHTS format. Altex, 32(4):287-96.

2014


Profiling of the Tox21 Chemical Collection for Mitochondrial Function: I. Compounds that Decrease Mitochondrial Membrane Potential

Attene-Ramos, M. S., Huang, R., Michael, S., Witt, K. L., Richard, A., Tice, R. R., Simeonov, A., Austin C.P., Xia, M. (2015). Profiling of the Tox21 chemical collection for mitochondrial function to identify compounds that acutely decrease mitochondrial membrane potential. Environmental health perspectives, 123(1), 49–56. doi:10.1289/ehp.1408642

High Throughput Heuristics for Prioritizing Human Exposure to Environmental Chemicals

Wambaugh, J., A. Wang, A. Frame, K. Dionisio, P. Egeghy, R. Judson, AND Woodrow Setzer. High Throughput Heuristics for Prioritizing Human Exposure to Environmental Chemicals. ENVIRONMENTAL SCIENCE & TECHNOLOGY. American Chemical Society, Washington, DC, 48:12760-12767, (2014).

Improving the Human Hazard Characterization of Chemicals: A Tox21 Update

Tice, R. R., Austin, C. P., Kavlock, R. J., & Bucher, J. R. (2013). Improving the human hazard characterization of chemicals: a Tox21 update. Environmental health perspectives, 121(7), 756–765. doi:10.1289/ehp.1205784

Quantitative high-throughput profiling of environmental chemicals and drugs that modulate farnesoid X receptor

Hsu CW, Zhao J, Huang R, Hsieh JH, Hamm J, Chang X, Houck K, Xia M. (2014) Quantitative high-throughput profiling of environmental chemicals and drugs that modulate farnesoid X receptor. Scientific Reports, 4:6437.

Identification of thyroid hormone receptor active compounds using a quantitative high-throughput screening platform

Freitas J, Miller N, Mengeling BJ, Xia M, Huang R, Houck K, Rietjens IM, Furlow JD, Murk AJ. (2014) Identification of thyroid hormone receptor active compounds using a quantitative high-throughput screening platform. Current Chemical Genomics and Translational Medicine, 8:36-46.

Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses

Rotroff DM, Martin MT, Dix DJ, Filer DL, Houck KA, Knudsen TB, Sipes NS, Reif DM, Xia M, Huang R, Judson RS. (2014) Predictive endocrine testing in the 21st century using in vitro assays of estrogen receptor signaling responses. Environmental Science & Technology, 48(15):8706-16.

Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway

Huang R, Sakamuru S, Martin MT, Reif DM, Judson RS, Houck KA, Casey W, Hsieh JH, Shockley KR, Ceger P, Fostel J, Witt KL, Tong W, Rotroff DM, Zhao T, Shinn P, Simeonov A, Dix DJ, Austin CP, Kavlock RJ, Tice RR, Xia M. (2014) Profiling of the Tox21 10K compound library for agonists and antagonists of the estrogen receptor alpha signaling pathway. Scientific Reports, 4:5664.

AroER tri-screen is a biologically relevant assay for endocrine disrupting chemicals modulating the activity of aromatase and/or the estrogen receptor

Chen S, Zhou D, Hsin LY, Kanaya N, Wong C, Yip R, Sakamuru S, Xia M, Yuan YC, Witt K, Teng C. (2014) AroER tri-screen is a biologically relevant assay for endocrine disrupting chemicals modulating the activity of aromatase and/or the estrogen receptor. Toxicol Sci., 139(1): 198–209.

Detection of phospholipidosis induction: a cell-based assay in high-throughput and high-content format

Shahane SA, Huang R, Gerhold D, Baxa U, Austin CP, Xia M. (2014) Detection of phospholipidosis induction: a cell-based assay in high-throughput and high-content format. Journal of Biomolecular Screening, 19(1):66-76.

t4 workshop report: Pathways of Toxicity

Kleensang A, Maertens A, Rosenberg M, Fitzpatrick S, Lamb J, Auerbach S, Brennan R, Crofton KM, Gordon B, Fornace AJ Jr, Gaido K, Gerhold D, Haw R, Henney A, Ma’ayan A, McBride M, Monti S, Ochs MF, Pandey A, Sharan R, Stierum R, Tugendreich S, Willett C, Wittwehr C, Xia J, Pattom GW, Arvidson K, Bouhifd M, Hogberg HT, Luechtefeld T, Smirnova L, Zhao L, Adeleye Y, Kanehisa M, Carmichael P, Andersen ME, Hartung T. (2014) t4 workshop report: Pathways of Toxicity. ALTEX, 31(1):53-61.

2013


Binary Classification of a Large Collection of Environmental Chemicals from Estrogen Receptor Assays by Quantitative Structure-Activity Relationship and Machine Learning Methods

Zang, Q., D. Rotroff, AND R. Judson. Binary Classification of a Large Collection of Environmental Chemicals from Estrogen Receptor Assays by Quantitative Structure-Activity Relationship and Machine Learning Methods. Journal of Chemical Information and Modeling. American Chemical Society, Washington, DC, 53:3244−3261, (2013).

Improving the human hazard characterization of chemicals: a Tox21 update

Tice RR, Austin CP, Kavlock RJ, Bucher JR. (2013) Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Perspect, 121(7):756-65.

Identification of novel activators of constitutive androstane receptor from FDA-approved drugs by integrated computational and biological approaches

Lynch C, Pan Y, Li L, Ferguson SS, Xia M, Swaan PW, Wang H. (2013) Identification of novel activators of constitutive androstane receptor from FDA-approved drugs by integrated computational and biological approaches. Pharmaceutical Research, 30(2):489-501.

Systematic study of mitochondrial toxicity of environmental chemicals using quantitative high throughput screening

Attene-Ramos MS, Huang R, Sakamuru S, Witt KL, Beeson GC, Shou L, Schnellmann RG, Beeson CC, Tice RR, Austin CP, Xia M. (2013) Systematic study of mitochondrial toxicity of environmental chemicals using quantitative high throughput screening. Chemical Research in Toxicology, 26(9):1323-32.

The Tox21 robotic platform for the assessment of environmental chemicals–from vision to reality

Attene-Ramos MS, Miller N, Huang R, Michael S, Itkin M, Kavlock RJ, Austin CP, Shinn P, Simeonov A, Tice RR, Xia M. (2013) The Tox21 robotic platform for the assessment of environmental chemicals–from vision to reality. Drug Discovery Today, 18(15-16):716-23.

Mechanism-based testing strategy using in vitro approaches for identification of thyroid hormone disrupting chemicals

Murk AJ, Rijntjes E, Blaauboer BJ, Clewell R, Crofton KM, Dingemans MM, Furlow JD, Kavlock R, Kohrle J, Opitz R, Traas T, Visser TJ, Xia M, Gutleb AC. (2013) Mechanism-based testing strategy using in vitro approaches for identification of thyroid hormone disrupting chemicals. Toxicology in Vitro, 27(4):1320-46.

Bisphenol A affects androgen receptor function via multiple mechanisms

Teng C, Goodwin B, Shockley K, Xia M, Huang R, Norris J, Merrick A, Jetten AM, Austin CP, Tice RR. (2013) Bisphenol A affects androgen receptor function via multiple mechanisms. Chemico-Biological Interactions, 203(3):556-64.

Using in vitro high throughput screening assays to identify potential endocrine-disrupting chemicals

Rotroff DM, Dix DJ, Houck KA, Knudsen TB, Martin MT, McLaurin KW, Reif DM, Crofton KM, Singh AV, Xia M, Huang R, Judson RS. (2013) Using in vitro high throughput screening assays to identify potential endocrine-disrupting chemicals. Environmental Health Perspectives, 121(1):7-14.

Perspectives on validation of high-throughput assays supporting 21st century toxicity testing

Judson R, Kavlock R, Martin M, Reif D, Houck K, Knudsen T, Richard A, Tice RR, Whelan M, Xia M, Huang R, Austin C, Daston G, Hartung T, Fowle JR 3rd, Wooge W, Tong W, Dix D. (2013) Perspectives on validation of high-throughput assays supporting 21st century toxicity testing. Altex, 30(1):51-6.

2012


Paradigm shift in toxicity testing and modeling

Sun H, Xia M, Austin CP, Huang R. (2012) Paradigm shift in toxicity testing and modeling. AAPS J, 14(3):473-80.

High-throughput genotoxicity assay identifies antioxidants as inducers of DNA damage response and cell death

Fox JT, Sakamuru S, Huang R, Teneva N, Simmons SO, Xia M, Tice RR, Austin CP, Myung K. (2012) High-throughput genotoxicity assay identifies antioxidants as inducers of DNA damage response and cell death. Proc Natl Acad Sci U S A, 109(14):5423-8.

Prediction of Cytochrome P450 Profiles of Environmental Chemicals with QSAR Models Built from Drug-like Molecules

Sun H, Veith H, Xia M, Austin CP, Tice RR, Huang R. (2012) Prediction of Cytochrome P450 Profiles of Environmental Chemicals with QSAR Models Built from Drug-like Molecules. Mol Inform, 31(11-12):783-792.

Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model

Lock EF, Abdo N, Huang R, Xia M, Kosyk O, O’Shea SH, Zhou YH, Sedykh A, Tropsha A, Austin CP, Tice RR, Wright FA, Rusyn I. (2012) Quantitative high-throughput screening for chemical toxicity in a population-based in vitro model. Toxicol Sci, 126(2):578-88.

Application of a homogenous membrane potential assay to assess mitochondrial function

Sakamuru S, Li X, Attene-Ramos MS, Huang R, Lu J, Shou L, Shen M, Tice RR, Austin CP, Xia M. (2012) Application of a homogenous membrane potential assay to assess mitochondrial function. Physiol Genomics, 44(9):495-503.

Profiling environmental chemicals for activity in the antioxidant response element signaling pathway using a high throughput screening approach

Shukla SJ, Huang R, Simmons SO, Tice RR, Witt KL, Vanleer D, Ramabhadran R, Austin CP, Xia M. (2012) Profiling environmental chemicals for activity in the antioxidant response element signaling pathway using a high throughput screening approach. Environ Health Perspect, 120(8):1150-6.

2011


Chemical Genomics Profiling of Environmental Chemical Modulation of Human Nuclear Receptors

HUANG, R., M. XIA, M. CHO, S. SAKAMURU, P. SHINN, K. A. HOUCK, D. J. DIX, R. JUDSON, K. L. WITT, R. J. KAVLOCK, R. R. TICE, AND C. P. AUSTIN. Chemical Genomics Profiling of Environmental Chemical Modulation of Human Nuclear Receptors. ENVIRONMENTAL HEALTH PERSPECTIVES. National Institute of Environmental Health Sciences (NIEHS), Research Triangle Park, NC, 119(8):1142-1148, (2011).

Genetic toxicology in the 21st century: Reflections and future directions

MAHADEVAN, B., R. D. SNYDER, M. D. WATERS, R. D. BENZ, R. A. KEMPER, R. R. TICE, AND A. M. RICHARD. Genetic toxicology in the 21st century: Reflections and future directions. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS. Wiley Liss, New York, NY, 52(5):339 – 354, (2011).

Evaluation of 309 environmental chemicals using a mouse embryonic stem cell adherent cell differentiation and cytotoxicity assay

CHANDLER, K. J., M. BARRIER, S. C. JEFFAY, H. P. NICHOLS, N. KLEINSTREUER, A. Singh, D. REIF, N. SIPES, R. JUDSON, D. J. DIX, R. J. KAVLOCK, E. S. HUNTER, AND T. Knudsen. Evaluation of 309 environmental chemicals using a mouse embryonic stem cell adherent cell differentiation and cytotoxicity assay. PLoS ONE . Public Library of Science, San Francisco, CA, 6(6):e1840, (2011).

Chemical genomics profiling of environmental chemical modulation of human nuclear receptors

Huang R, Xia M, Cho MH, Sakamuru S, Shinn P, Houck KA, Dix DJ, Judson RS, Witt KL, Kavlock RJ, Tice RR, Austin CP. (2011) Chemical genomics profiling of environmental chemical modulation of human nuclear receptors. Environ Health Perspect, 119(8):1142-8.

Characterization of environmental chemicals with potential for DNA damage using isogenic DNA repair-deficient chicken DT40 cell lines

Yamamoto KN, Hirota K, Kono K, Takeda S, Sakamuru S, Xia M, Huang R, Austin CP, Witt KL, Tice RR. (2011) Characterization of environmental chemicals with potential for DNA damage using isogenic DNA repair-deficient chicken DT40 cell lines. Environ Mol Mutagen, 52(7):547-61.

Identification of quaternary ammonium compounds as potent inhibitors of hERG potassium channels

Xia M, Shahane SA, Huang R, Titus SA, Shum E, Zhao Y, Southall N, Zheng W, Witt KL, Tice RR, Austin CP. (2011) Identification of quaternary ammonium compounds as potent inhibitors of hERG potassium channels. Toxicol Appl Pharmacol, 252(3):250-8.

2010


Analysis of eight oil spill dispersants using rapid, in vitro tests for endocrine and other biological activity

Judson RS, Martin MT, Reif DM, Houck KA, Knudsen TB, Rotroff DM, Xia M, Sakamuru S, Huang R, Shinn P, Austin CP, Kavlock RJ, Dix DJ. (2010) Analysis of eight oil spill dispersants using rapid, in vitro tests for endocrine and other biological activity. Environ Sci Technol, 44(15):5979-85.

The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform

Shukla SJ, Huang R, Austin CP, Xia M. (2010) The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform. Drug Discov Today, 15(23-24):997-1007.

2009


Identification of chemical compounds that induce HIF-1alpha activity

Xia M, Huang R, Sun Y, Semenza GL, Aldred SF, Witt KL, Inglese J, Tice RR, Austin CP. (2009) Identification of chemical compounds that induce HIF-1alpha activity. Toxicol Sci, 112(1):153-63.

Weighted feature significance: a simple, interpretable model of compound toxicity based on the statistical enrichment of structural features

Huang R, Southall N, Xia M, Cho MH, Jadhav A, Nguyen DT, Inglese J, Tice RR, Austin CP. (2009) Weighted feature significance: a simple, interpretable model of compound toxicity based on the statistical enrichment of structural features. Toxicol Sci, 112(2):385-93.

2008


Compound cytotoxicity profiling using quantitative high-throughput screening

Xia M, Huang R, Witt KL, Southall N, Fostel J, Cho MH, Jadhav A, Smith CS, Inglese J, Portier CJ, Tice RR, Austin CP. (2008) Compound cytotoxicity profiling using quantitative high-throughput screening. Environ Health Perspect, 116(3):284-91.

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